From am15f10.debbarma at nitk.edu.in Wed Jul 20 04:16:36 2016 From: am15f10.debbarma at nitk.edu.in (Surajit Deb barma) Date: Wed, 20 Jul 2016 15:46:36 +0530 Subject: [parflow-users] Installation of pfsimulator problem on Ubuntu 14.04 -64 bit system Message-ID: Hi, I run the command $ ./configure -prefix=${HOME}/parflow/parflow-enable-timing-with-clm-with-silo=${HOME}/parflow/silo-with-hypre=${HOME}/parflow/hypre/src/hypre-with-amps=mpi1 Then $ make install followed by $ gedit config/Makefile.config, which shows the following: ## ## File: $URL: svn+ssh:// tux262.llnl.gov/usr/casc/samrai/repository/PARFLOW/trunk/config/Makefile.config.in $ ## Package: PARFLOW makefile system ## Copyright: (c) 1997-2008 Lawrence Livermore National Security, LLC ## Revision: $LastChangedRevision: 2195 $ ## Modified: $LastChangedDate: 2008-05-14 11:33:30 -0700 (Wed, 14 May 2008) $ ## Description: configuration makefile included by all PARFLOW makefiles ## .SUFFIXES: .SUFFIXES: .o .F .f .c .C .cc .cxx .F90 .F90.o: $(FC) $(FCFLAGS) -c $< -o $@ .F.o: $(F77) $(FFLAGS) -c $< -o $@ .f.o: $(F77) $(FFLAGS) -c $< -o $@ .c.o: $(CC) $(CFLAGS) $(CPPFLAGS) -c $< -o $@ .cxx.o: $(CXX) $(CFLAGS) $(CPPFLAGS) -c $< -o $@ SHELL = /bin/sh INSTALL = sh $(PARFLOW)/config/install-sh PARFLOW_INSTALL_DIR = /home/applied/parflow/parflow-enable-timing-with-clm-with-silo=/home/applied/parflow/silo-with-hypre=/home/applied/parflow/hypre/src/hypre-with-amps=mpi1 AMPS = seq AMPS_DIR = amps/$(AMPS) AMPS_INCLUDE_DIR = $(PARFLOW)/$(AMPS_DIR) AMPS_COMMON_INCLUDE_DIR = $(PARFLOW)/amps/common KINSOL_INCLUDE_DIR = $(PARFLOW)/kinsol # SGS these need to be generated by configure AMPS_FLAGS = -DAMPS_PRINT_HOSTNAME AMPS_LIB = libamps.a AMPS_COMMON_LIB = libamps_common.a PARFLOW_LIB = libparflow.a KINSOL_LIB = libkinsol.a SAMRAI_DIR = # # These are controlled by the ?with-clm flag to configure # CLM_LIB = libclm.a CLM_LIBS = CLM_DIR = CLM_LIB_DEPEND = PARFLOW_INCLUDE_DIR = $(PARFLOW)/parflow_lib PARFLOW_CONFIGURE_INCLUDE_DIR = $(OBJECT)/include PARFLOW_LIB_DIR = $(OBJECT)/lib PARFLOW_BIN_DIR = $(OBJECT)/bin AMPS_LIBS = -lamps_common AMPS_LIB_DEPEND = $(PARFLOW_LIB_DIR)/libamps_common.a PARFLOW_LIBS = -L$(PARFLOW_LIB_DIR) -lparflow $(CLM_LIBS) $(AMPS_LIBS) -lkinsol PARFLOW_LIB_DEPEND = $(PARFLOW_LIB_DIR)/$(PARFLOW_LIB) $(PARFLOW_LIB_DIR)/$(KINSOL_LIB) LIB_SUFFIX=.a M4 = RM = rm -fr CP = cp XARGS = F77 = gfortran FFLAGS = -O2 $(FFLAGS_EXTRA) FC = gfortran FCFLAGS = -Wall -Wunused -fimplicit-none -free -O2 CC = gcc CFLAGS = -Wno-write-strings -Wconversion -Wextra -Wall -O2 $(CFLAGS_EXTRA) $(AMPS_FLAGS) CPPFLAGS = -I. \ -I$(PARFLOW_CONFIGURE_INCLUDE_DIR) -I$(PARFLOW_INCLUDE_DIR) \ -I$(AMPS_COMMON_INCLUDE_DIR) -I$(AMPS_INCLUDE_DIR) \ $(CPPFLAGS_EXTRA) AR = ar LDFLAGS = -L$(PARFLOW_LIB_DIR) -L/usr/lib/gcc/i686-linux-gnu/4.8 -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.8/../../.. $(LDFLAGS_EXTRA) LDLIBS = $(LDLIBS_EXTRA) -lmpi -L/usr/lib/gcc/i686-linux-gnu/4.8/../../.. -L/usr/lib/../lib -L/usr/lib/i386-linux-gnu -L/lib/../lib -L/lib/i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8 -L/usr/lib/gcc/i686-linux-gnu/4.8/../../.. -L/usr/lib/../lib -L/usr/lib/i386-linux-gnu -L/lib/../lib -L/lib/i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../../lib -L/usr/lib/gcc/i686-linux-gnu/4.8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/4.8 -lgfortran -lm -lm -lgfortran -lm -lquadmath PARFLOW_HAVE_CLM = no PARFLOW_HAVE_SILO = no PARFLOW_HAVE_HYPRE = PARFLOW_HAVE_SAMRAI = no PARFLOW_HAVE_OAS3 = no ###################################################################### # Rules used in all directories. ###################################################################### PARFLOW_CLEAN=@$(RM) *.o *.ii *.int.c *.log *.log.* stamp-* core core.* stats -r ti_files ii_files I could install OpenMPI, Silo and Hypre successfully in their respective folders under /parflow main directory, but while configuring pfsimulator following the commands mentioned by you and parflow.blogspot site I get similar outcome as mentioned in my previous posting. I don?t know why it shows $PARFLOW_DIR has no OPENMPI, SILO and HYPRE in Makefile.config. I am wondering whether I am missing anything. I have tried several times, but still get the same outcome. Prior to compiling anything I set executed the command $ gedit ~/.bash_aliases and the following were added: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/applied/parflow/parflow export SILO_DIR=/home/applied/parflow/silo export HYPRE_DIR=/home/applied/parflow/hypre export PATH=$PATH:/home/applied/parflow/visit/bin I run all compilations on Ubuntu 14.04 -64 bit system and latest parflow version. Can anyone figure out if there is anything wrong with my execution? Thanking you. Cheers! Surajit -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Mon Jul 25 11:57:45 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Mon, 25 Jul 2016 13:57:45 -0400 Subject: [parflow-users] Question about Starting a new project using DEM Message-ID: Dear All, I am a PhD student and I am planning on using ParFlow for my research. I have a question, I have read the manual and have attended the Short Course at CSM in May 2016. However, I am not sure how to start my tcl file. I have created the DEM using GRASS GIS following the terrain processing blog post (http://parflow.blogspot.com/2015/08/terrain-processing.html). I have reached step 7, and I am not sure how to proceed to step 8, which is to verify what I created in ParFlow. My questions are: - How can I identify the DEM to be my domain? - How can I identify the X-Slope, Y-Slope, Accumulation, Flow Direction, Segments, Basins and other files I created with GRASS GIS in ParFlow? I need these to be able to run the "Parking Lot Test" to check the files I created. Looking forward to hearing from you. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology ?? Department of Geological Sciences ? Indiana University - Bloomington? -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Tue Jul 26 10:11:52 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Tue, 26 Jul 2016 12:11:52 -0400 Subject: [parflow-users] a question about starting a new project with DEM Message-ID: ??Dear All, I am a PhD student and I am planning on using ParFlow for my research. I have a question, I have read the manual and have attended the Short Course at CSM in May 2016. However, I am not sure how to start my tcl file. I have created the DEM using GRASS GIS following the terrain processing blog post (http://parflow.blogspot.com/2015/08/terrain-processing.html). I have reached step 7, and I am not sure how to proceed to step 8, which is to verify what I created in ParFlow. My questions are: - How to convert the ascii files to .pfb to use the grid files? - How can I identify the DEM to be my domain? - How can I identify the X-Slope, Y-Slope, Accumulation, Flow Direction, Segments, Basins and other files I created with GRASS GIS in ParFlow? I need these to be able to run the "Parking Lot Test" to check the files I created. Looking forward to hearing from you. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From lfoster at mymail.mines.edu Wed Jul 27 09:15:18 2016 From: lfoster at mymail.mines.edu (Lauren Foster) Date: Wed, 27 Jul 2016 09:15:18 -0600 Subject: [parflow-users] a question about starting a new project with DEM In-Reply-To: References: Message-ID: Hi Anas, 1. To convert the files from ascii to pfb use the pfload and pfsave tools. Don't forget to load the parflow tcl package first, I've attached an example script. 2. Once you've got your files in the correct format, look at the Little Washita tcl script example in the manual for the syntax on how to set up your script. ~Lauren On Tue, Jul 26, 2016 at 10:11 AM, Anas Rabie wrote: > ??Dear All, > > I am a PhD student and I am planning on using ParFlow for my research. I > have a question, I have read the manual and have attended the Short Course > at CSM in May 2016. However, I am not sure how to start my tcl file. > > I have created the DEM using GRASS GIS following the terrain processing > blog post (http://parflow.blogspot.com/2015/08/terrain-processing.html). > I have reached step 7, and I am not sure how to proceed to step 8, which is > to verify what I created in ParFlow. > > My questions are: > - How to convert the ascii files to .pfb to use the grid files? > - How can I identify the DEM to be my domain? > - How can I identify the X-Slope, Y-Slope, Accumulation, Flow Direction, > Segments, Basins and other files I created with GRASS GIS in ParFlow? > > I need these to be able to run the "Parking Lot Test" to check the files I > created. > > Looking forward to hearing from you. > > > Best, > Anas B. Rabie > -==-==-==-==-==-==-==- > Ph.D. Student in Hydrogeology > Department of Geological Sciences > > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > -- Lauren Foster PhD Candidate, Colorado School of Mines Hydrologic Sciences and Engineering www.laurenfoster.net Phone: 303.819.1959 Email: lfoster at mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: conversion_ascii.tcl Type: application/x-tcl Size: 782 bytes Desc: not available URL: From abrabie at umail.iu.edu Thu Jul 28 10:18:38 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Thu, 28 Jul 2016 12:18:38 -0400 Subject: [parflow-users] a question about starting a new project with DEM In-Reply-To: References: Message-ID: Greetings, Thank you for your reply. The tcl file worked and it produced a pfb file. However, that pfb file is only 100 bytes (not kilobytes). The original ASCII file is over 46 megabytes. I have tried two types of ASCII grids; the ESRI ASCII Grid, and the default ASCII Grid that GRASS GIS generates. Both yielded the same 100 bytes file. Regardless, I tried to follow the LW example, and after many trials and errors, I used my X_Slope.pfb and Y_Slope.pfb files. ParFlow create the "output" folder and produced a .pfidb file, but for my lack of experience with ParFlow, even after examining the file, I did not understand if the results are good or not. There were no other files produced. I have attached a zip file that includes X_Slope.pfb Y_Slope.pfb, the .pfidb file, as well as the tcl file I used. Please, if you have the time, can you check them for me? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-07-27 11:15 GMT-04:00 Lauren Foster : > Hi Anas, > > 1. To convert the files from ascii to pfb use the pfload and pfsave tools. > Don't forget to load the parflow tcl package first, I've attached an > example script. > 2. Once you've got your files in the correct format, look at the Little > Washita tcl script example in the manual for the syntax on how to set up > your script. > > ~Lauren > > On Tue, Jul 26, 2016 at 10:11 AM, Anas Rabie wrote: > >> ??Dear All, >> >> I am a PhD student and I am planning on using ParFlow for my research. I >> have a question, I have read the manual and have attended the Short Course >> at CSM in May 2016. However, I am not sure how to start my tcl file. >> >> I have created the DEM using GRASS GIS following the terrain processing >> blog post (http://parflow.blogspot.com/2015/08/terrain-processing.html). >> I have reached step 7, and I am not sure how to proceed to step 8, which is >> to verify what I created in ParFlow. >> >> My questions are: >> - How to convert the ascii files to .pfb to use the grid files? >> - How can I identify the DEM to be my domain? >> - How can I identify the X-Slope, Y-Slope, Accumulation, Flow Direction, >> Segments, Basins and other files I created with GRASS GIS in ParFlow? >> >> I need these to be able to run the "Parking Lot Test" to check the files >> I created. >> >> Looking forward to hearing from you. >> >> >> Best, >> Anas B. Rabie >> -==-==-==-==-==-==-==- >> Ph.D. Student in Hydrogeology >> Department of Geological Sciences >> >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> > > > -- > Lauren Foster > PhD Candidate, Colorado School of Mines > Hydrologic Sciences and Engineering > www.laurenfoster.net > Phone: 303.819.1959 > Email: lfoster at mines.edu > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: AnasRabie.zip Type: application/zip Size: 7465 bytes Desc: not available URL: From abrabie at umail.iu.edu Mon Aug 1 12:00:29 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Mon, 1 Aug 2016 14:00:29 -0400 Subject: [parflow-users] Lost in applying ParFlow - I have many questions Message-ID: Greetings, Thank you for thank you for taking the time reading my email. I am a PhD student in Hydrogeology and I am interested in using ParFlow in my research. I just have many questions about main concepts of ParFlow and the creation if input files as well as tcl files. I am not familiar with ParFlow or R or Matlab or Python, so please make the answer as detailed as possible. -- FIRST: I used GRASS GIS to export that DEM files that I have to ESRI ASCII GRID in order to convert them to PFB file to use as ParFlow input. As I understand ParFlow does not read the files in the same format the ASCII Grid files are written, but parflow reads left to right, and bottom to top. The format the file currently is in is this: ncols 2932 nrows 2965 xllcorner 639950.36457043 yllcorner 1906395.57564654 cellsize 30 NODATA_value -9999 -9999 -9999 -9999 -9999 -9999 ....etc. I tried to use the 'gridtrans.py' python script that was suggested in another answer to a question from a ParFlow user, it reads the .asc file succesfully but doesn't write and new pfb file or re-format the original .asc file to how it should look like in parflow, which as I know is this: 1700 1500 1 2.777778e-05 2.777778e-05 2.777778e-05 2.777778e-05 ....etc. The closest I could get to this format was when I asked GRASS GIS to export it as GRIDATB, and it gave me those headers: 2932 2965 30.000000 9999.00 9999.00 9999.00 ......etc. However, in this case the 30 is cell size and not the layers (z) as explained in the previous file format. Furthermore, those 9999.00 are the No_Data from the DEM I am using. I am not familiar with R or Matlab or Python, so If someone can help how what command line to use to re-format the file, the command line I used was: python gridtrans.py -s input.asc -- SECOND: in the Little Washita example, it stated to use X Slope and Y Slope, but I couldn't find a way to make the GIS software calculate that, as ArcMap only have a "Slope" option, while GRASS GIS has options to calculate East-West slopes and North-South slopes. However, using GRASS GIS and then converting the slope files to ascii always resulted in an empty X_Slope file (E-W slope). So, what is the current way to produce that slope files? -- THIRD: say I got the pfb files I want successfully. How should I know what numbers to use in the tcl file in in the Computational Grid section from the X Y Z, DX DY DZ, and NX NY NZ? Also the numbers for the Domain Geometry section for Lower X Y Z and Upper X Y Z? -- FOURTH: in the LW example, as I understood the indicator file is a description of the geology of the area. How would I create such a file? is it using GIS software? or is there another method? -- FIFTH: I would like to first be able to run the model then try to use CLM, as I have no clue where get the information listed in the manual in 3.1.2. I have the NLCD 2011 data, and I have changed the classifications to IGBP as mentioned in the manual in 3.1.2.8 , but I did not know how to make it look like the vegm file in the example? Sorry for the lengthy email, and thank you for taking the time reading it. It is just I've been stuck with ParFlow for a long time, and my department started thinking that I am slacking since I did not produce any output file. Thank you for your understanding. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From lfoster at mymail.mines.edu Mon Aug 1 14:36:52 2016 From: lfoster at mymail.mines.edu (Lauren Foster) Date: Mon, 1 Aug 2016 14:36:52 -0600 Subject: [parflow-users] Lost in applying ParFlow - I have many questions In-Reply-To: References: Message-ID: Hi Anas, We recommend you learn the basics of one of those programs (Python, R, or Matlab) because those are tools that are required to pre-process or post-process data in parflow. Without that basic skill set it will be really difficult to tackle any of these questions. That being said, I didn't know R (or unix or fortran) at all when I started and I spent a few weeks teaching myself through online tutorials. I still take time out to specifically learn skills in these programs, there are a lot of online resources. Mary Michael is about to send you an R tutorial to start with. Manipulating data with one of these programs (something more powerful than excel) is critical. Good luck, and I recommend asking around your lab or program for people familiar with one of those programs, I'm sure there are people who can help or classes you can take. Thanks, Lauren On Mon, Aug 1, 2016 at 12:00 PM, Anas Rabie wrote: > Greetings, > > Thank you for thank you for taking the time reading my email. I am a PhD > student in Hydrogeology and I am interested in using ParFlow in my > research. I just have many questions about main concepts of ParFlow and the > creation if input files as well as tcl files. I am not familiar with > ParFlow or R or Matlab or Python, so please make the answer as detailed as > possible. > > -- FIRST: I used GRASS GIS to export that DEM files that I have to ESRI > ASCII GRID in order to convert them to PFB file to use as ParFlow input. As > I understand ParFlow does not read the files in the same format the ASCII > Grid files are written, but parflow reads left to right, and bottom to top. > The format the file currently is in is this: > ncols 2932 > nrows 2965 > xllcorner 639950.36457043 > yllcorner 1906395.57564654 > cellsize 30 > NODATA_value -9999 > -9999 -9999 -9999 -9999 -9999 ....etc. > > > I tried to use the 'gridtrans.py' python script that was suggested in > another answer to a question from a ParFlow user, it reads the .asc file > succesfully but doesn't write and new pfb file or re-format the original > .asc file to how it should look like in parflow, which as I know is this: > 1700 1500 1 > 2.777778e-05 > 2.777778e-05 > 2.777778e-05 > 2.777778e-05 > ....etc. > > The closest I could get to this format was when I asked GRASS GIS to > export it as GRIDATB, and it gave me those headers: > 2932 2965 30.000000 > 9999.00 9999.00 9999.00 ......etc. > > However, in this case the 30 is cell size and not the layers (z) as > explained in the previous file format. Furthermore, those 9999.00 are the > No_Data from the DEM I am using. > > I am not familiar with R or Matlab or Python, so If someone can help how > what command line to use to re-format the file, the command line I used was: > > python gridtrans.py -s input.asc > > -- SECOND: in the Little Washita example, it stated to use X Slope and Y > Slope, but I couldn't find a way to make the GIS software calculate that, > as ArcMap only have a "Slope" option, while GRASS GIS has options to > calculate East-West slopes and North-South slopes. However, using GRASS GIS > and then converting the slope files to ascii always resulted in an empty > X_Slope file (E-W slope). So, what is the current way to produce that slope > files? > > -- THIRD: say I got the pfb files I want successfully. How should I know > what numbers to use in the tcl file in in the Computational Grid section > from the X Y Z, DX DY DZ, and NX NY NZ? Also the numbers for the Domain > Geometry section for Lower X Y Z and Upper X Y Z? > > -- FOURTH: in the LW example, as I understood the indicator file is a > description of the geology of the area. How would I create such a file? is > it using GIS software? or is there another method? > > -- FIFTH: I would like to first be able to run the model then try to use > CLM, as I have no clue where get the information listed in the manual in > 3.1.2. I have the NLCD 2011 data, and I have changed the classifications to > IGBP as mentioned in the manual in 3.1.2.8 , but I did not know how to make > it look like the vegm file in the example? > > Sorry for the lengthy email, and thank you for taking the time reading it. > It is just I've been stuck with ParFlow for a long time, and my department > started thinking that I am slacking since I did not produce any output file. > > Thank you for your understanding. > > Best, > Anas B. Rabie > -==-==-==-==-==-==-==- > Ph.D. Student in Hydrogeology > Department of Geological Sciences > > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > -- Lauren Foster PhD Candidate, Colorado School of Mines Hydrologic Sciences and Engineering www.laurenfoster.net Phone: 303.819.1959 Email: lfoster at mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From haqatherley at hotmail.com Mon Sep 5 13:39:06 2016 From: haqatherley at hotmail.com (HUGH ATHERLEY) Date: Mon, 5 Sep 2016 15:39:06 -0400 Subject: [parflow-users] How do you distribute met forcing files for clm Message-ID: Hi. I am trying a model based on the little washita example but it fails with the error can't find the nldas.dswr.xxxx.dist file. From previous posts this means that I have to distribute my forcing files. Pfdist only creates the file but I can't add the number time steps. Can anyone help? Hugh Atherley -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Tue Oct 4 09:14:32 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Tue, 4 Oct 2016 11:14:32 -0400 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Message-ID: Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From smith84 at llnl.gov Wed Oct 5 17:40:19 2016 From: smith84 at llnl.gov (Smith, Steve) Date: Wed, 5 Oct 2016 23:40:19 +0000 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: Message-ID: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> Did you ?export? the PARFLOW variable? What does : printenv PARFLOW report? Errors seem to indicate that scripts are not finding the environment variable. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Tuesday, October 04, 2016 8:15 AM To: ParFlow Users Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Thu Oct 6 08:01:53 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Thu, 6 Oct 2016 10:01:53 -0400 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Hi, Thank you for your reply. Yes I did export Parflow. This is the bash file I used as mentioned in the instructions: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I try the "printenv PARFLOW" nothing happens. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-05 19:40 GMT-04:00 Smith, Steve : > Did you ?export? the PARFLOW variable? What does : > > > > printenv PARFLOW > > > > report? > > > > Errors seem to indicate that scripts are not finding the environment > variable. > > > > Steve > > > > > > *From:* parflow-users-bounces at mailman.mines.edu [mailto: > parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie > *Sent:* Tuesday, October 04, 2016 8:15 AM > *To:* ParFlow Users > *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS > > > > Greetings, > > > > I am trying to install ParFlow on Ubuntu, I followed the instructions in > the manual, but I was successful, then I followed what is on the blog > > http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html > > and everything was going well until the very last step, > > > > cd ../pftools > > ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 > > make install > > cd ../test > > sudo ldconfig > > make check > > > > When I do that last "make check" it gives me this error: > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check > > Makefile:9: /config/Makefile.config: No such file or directory > > make: *** No rule to make target '/config/Makefile.config'. Stop. > > > > I tired "sudo make check" as well, but received the same error: > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check > > Makefile:9: /config/Makefile.config: No such file or directory > > make: *** No rule to make target '/config/Makefile.config'. Stop. > > > > I tried to run the Little Washita test to try, but it gave me an error > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh > LW_Test.tcl > no such variable > (read trace on "env(PARFLOW_DIR)") > invoked from within > "lappend auto_path $env(PARFLOW_DIR)/bin" > (file "LW_Test.tcl" line 6) > > However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in > my home directory. so I am not sure what that error means? > > > > Can anybody please help me with this? > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lfoster at mymail.mines.edu Thu Oct 6 10:41:21 2016 From: lfoster at mymail.mines.edu (Lauren Foster) Date: Thu, 6 Oct 2016 10:41:21 -0600 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Did you 'source bash_ profile' On Thursday, October 6, 2016, Anas Rabie wrote: > Hi, > > Thank you for your reply. Yes I did export Parflow. This is the bash file > I used as mentioned in the instructions: > > export CC=gcc > export CXX=g++ > export FC=gfortran > export F77=gfortran > > export > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > export SILO_DIR=/home/abrabie/ParFlow/silo > export HYPRE_DIR=/home/abrabie/ParFlow/hypre > export > PATH=$PATH:/home/abrabie/ParFlow/visit/bin > > However, when I try the "printenv PARFLOW" nothing happens. > > > Best, > Anas B. Rabie > -==-==-==-==-==-==-==- > Ph.D. Student in Hydrogeology > Department of Geological Sciences > > > > 2016-10-05 19:40 GMT-04:00 Smith, Steve >: > >> Did you ?export? the PARFLOW variable? What does : >> >> >> >> printenv PARFLOW >> >> >> >> report? >> >> >> >> Errors seem to indicate that scripts are not finding the environment >> variable. >> >> >> >> Steve >> >> >> >> >> >> *From:* parflow-users-bounces at mailman.mines.edu >> >> [mailto:parflow-users-bounces at mailman.mines.edu >> ] >> *On Behalf Of *Anas Rabie >> *Sent:* Tuesday, October 04, 2016 8:15 AM >> *To:* ParFlow Users >> *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS >> >> >> >> Greetings, >> >> >> >> I am trying to install ParFlow on Ubuntu, I followed the instructions in >> the manual, but I was successful, then I followed what is on the blog >> >> http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html >> >> and everything was going well until the very last step, >> >> >> >> cd ../pftools >> >> ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 >> >> make install >> >> cd ../test >> >> sudo ldconfig >> >> make check >> >> >> >> When I do that last "make check" it gives me this error: >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >> >> Makefile:9: /config/Makefile.config: No such file or directory >> >> make: *** No rule to make target '/config/Makefile.config'. Stop. >> >> >> >> I tired "sudo make check" as well, but received the same error: >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >> >> Makefile:9: /config/Makefile.config: No such file or directory >> >> make: *** No rule to make target '/config/Makefile.config'. Stop. >> >> >> >> I tried to run the Little Washita test to try, but it gave me an error >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >> LW_Test.tcl >> no such variable >> (read trace on "env(PARFLOW_DIR)") >> invoked from within >> "lappend auto_path $env(PARFLOW_DIR)/bin" >> (file "LW_Test.tcl" line 6) >> >> However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in >> my home directory. so I am not sure what that error means? >> >> >> >> Can anybody please help me with this? >> >> >> Best, >> >> Anas B. Rabie >> >> -==-==-==-==-==-==-==- >> >> Ph.D. Student in Hydrogeology >> >> Department of Geological Sciences >> >> >> >> >> > > -- Please excuse Siri's mistakes, she's still learning. ~Lauren -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Thu Oct 6 10:53:40 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Thu, 6 Oct 2016 12:53:40 -0400 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Hello, Thank you so much for your reply. It says no such file or directory. I also tried 'source ~/.bash_profile' but it game me the same error. It seems I need to create a bash_profile file. What should I write in it? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-06 12:41 GMT-04:00 Lauren Foster : > Did you 'source bash_ profile' > > > On Thursday, October 6, 2016, Anas Rabie wrote: > >> Hi, >> >> Thank you for your reply. Yes I did export Parflow. This is the bash file >> I used as mentioned in the instructions: >> >> export CC=gcc >> export CXX=g++ >> export FC=gfortran >> export F77=gfortran >> >> export >> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> export SILO_DIR=/home/abrabie/ParFlow/silo >> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >> export >> PATH=$PATH:/home/abrabie/ParFlow/visit/bin >> >> However, when I try the "printenv PARFLOW" nothing happens. >> >> >> Best, >> Anas B. Rabie >> -==-==-==-==-==-==-==- >> Ph.D. Student in Hydrogeology >> Department of Geological Sciences >> >> >> >> 2016-10-05 19:40 GMT-04:00 Smith, Steve : >> >>> Did you ?export? the PARFLOW variable? What does : >>> >>> >>> >>> printenv PARFLOW >>> >>> >>> >>> report? >>> >>> >>> >>> Errors seem to indicate that scripts are not finding the environment >>> variable. >>> >>> >>> >>> Steve >>> >>> >>> >>> >>> >>> *From:* parflow-users-bounces at mailman.mines.edu [mailto: >>> parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie >>> *Sent:* Tuesday, October 04, 2016 8:15 AM >>> *To:* ParFlow Users >>> *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 >>> LTS >>> >>> >>> >>> Greetings, >>> >>> >>> >>> I am trying to install ParFlow on Ubuntu, I followed the instructions in >>> the manual, but I was successful, then I followed what is on the blog >>> >>> http://parflow.blogspot.com/2010/03/running-parflow-on-windo >>> ws-using.html >>> >>> and everything was going well until the very last step, >>> >>> >>> >>> cd ../pftools >>> >>> ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 >>> >>> make install >>> >>> cd ../test >>> >>> sudo ldconfig >>> >>> make check >>> >>> >>> >>> When I do that last "make check" it gives me this error: >>> >>> >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >>> >>> Makefile:9: /config/Makefile.config: No such file or directory >>> >>> make: *** No rule to make target '/config/Makefile.config'. Stop. >>> >>> >>> >>> I tired "sudo make check" as well, but received the same error: >>> >>> >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >>> >>> Makefile:9: /config/Makefile.config: No such file or directory >>> >>> make: *** No rule to make target '/config/Makefile.config'. Stop. >>> >>> >>> >>> I tried to run the Little Washita test to try, but it gave me an error >>> >>> >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >>> LW_Test.tcl >>> no such variable >>> (read trace on "env(PARFLOW_DIR)") >>> invoked from within >>> "lappend auto_path $env(PARFLOW_DIR)/bin" >>> (file "LW_Test.tcl" line 6) >>> >>> However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in >>> my home directory. so I am not sure what that error means? >>> >>> >>> >>> Can anybody please help me with this? >>> >>> >>> Best, >>> >>> Anas B. Rabie >>> >>> -==-==-==-==-==-==-==- >>> >>> Ph.D. Student in Hydrogeology >>> >>> Department of Geological Sciences >>> >>> >>> >>> >>> >> >> > > -- > Please excuse Siri's mistakes, she's still learning. ~Lauren > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AWunsch at leppertassociates.com Thu Oct 6 10:57:36 2016 From: AWunsch at leppertassociates.com (AWunsch) Date: Thu, 6 Oct 2016 16:57:36 +0000 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: You may want to explore the difference between defining environmental variables for a specific user, versus for all users. Would depend on the usage of your computer. You can start with tips such as in: http://unix.stackexchange.com/questions/117467/how-to-permanently-set-environmental-variables Assaf From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Lauren Foster Sent: Thursday, October 06, 2016 10:41 AM To: ParFlow Users Subject: Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Did you 'source bash_ profile' On Thursday, October 6, 2016, Anas Rabie > wrote: Hi, Thank you for your reply. Yes I did export Parflow. This is the bash file I used as mentioned in the instructions: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I try the "printenv PARFLOW" nothing happens. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-05 19:40 GMT-04:00 Smith, Steve >: Did you ?export? the PARFLOW variable? What does : printenv PARFLOW report? Errors seem to indicate that scripts are not finding the environment variable. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Tuesday, October 04, 2016 8:15 AM To: ParFlow Users Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences -- Please excuse Siri's mistakes, she's still learning. ~Lauren -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmaxwell at mines.edu Thu Oct 6 11:02:53 2016 From: rmaxwell at mines.edu (Reed Maxwell) Date: Thu, 6 Oct 2016 17:02:53 +0000 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: <91B2CB0E-38B7-479F-975E-D200AEA30197@mines.edu> Hi Anas- What is the name of the file you list below (with the exports for ParFlow, C etc)? That is essentially what should go into your .bash_profile to build parflow. BTW, the internets offer lots of great advice on bash_profile issues. Hope this helps Reed Reed M. Maxwell, Ph.D. Rowlinson Professor of Hydrology Department of Geology and Geological Engineering Director, Integrated GroundWater Modeling Center Colorado School of Mines http://inside.mines.edu/~rmaxwell/ On Oct 6, 2016, at 10:53 AM, Anas Rabie > wrote: Hello, Thank you so much for your reply. It says no such file or directory. I also tried 'source ~/.bash_profile' but it game me the same error. It seems I need to create a bash_profile file. What should I write in it? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-06 12:41 GMT-04:00 Lauren Foster >: Did you 'source bash_ profile' On Thursday, October 6, 2016, Anas Rabie > wrote: Hi, Thank you for your reply. Yes I did export Parflow. This is the bash file I used as mentioned in the instructions: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I try the "printenv PARFLOW" nothing happens. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-05 19:40 GMT-04:00 Smith, Steve : Did you ?export? the PARFLOW variable? What does : printenv PARFLOW report? Errors seem to indicate that scripts are not finding the environment variable. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Tuesday, October 04, 2016 8:15 AM To: ParFlow Users Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences -- Please excuse Siri's mistakes, she's still learning. ~Lauren _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From smith84 at llnl.gov Thu Oct 6 20:52:04 2016 From: smith84 at llnl.gov (Smith, Steve) Date: Fri, 7 Oct 2016 02:52:04 +0000 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> Hi, Apologies, I should have asked for the output of : printenv | grep PARFLOW If you copied and pasted exactly what is below there is a bug since the export PARFLOW_DIR=/home/abrabie/ParFlow/parflow is 2 commands because of a newline and it should be one command: export PARFLOW_DIR=/home/abrabie/ParFlow/parflow Steve From: Anas Rabie [mailto:abrabie at umail.iu.edu] Sent: Thursday, October 06, 2016 7:02 AM To: Smith, Steve Cc: ParFlow Users Subject: Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Hi, Thank you for your reply. Yes I did export Parflow. This is the bash file I used as mentioned in the instructions: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I try the "printenv PARFLOW" nothing happens. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-05 19:40 GMT-04:00 Smith, Steve >: Did you ?export? the PARFLOW variable? What does : printenv PARFLOW report? Errors seem to indicate that scripts are not finding the environment variable. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Tuesday, October 04, 2016 8:15 AM To: ParFlow Users Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Tue Oct 18 11:46:59 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Tue, 18 Oct 2016 13:46:59 -0400 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Hello, I still run into some issues. I fixed my .bash_profile file, and now it is as follow: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I type "source ~/.bash_profile" nothing happens. However, I tried to continue with the installation. OpenMPI, SILO, and HYPRE all install successfully without any errors. However, again, in the last step of installing ParFlow, when i type "make check", it gives me this error message: ############################################################################## 0% tests passed, 94 tests failed out of 94 FAILED Tests ############################################################################## I tried to run the little washita example, but this is what happened: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: Syntax error: "(" unexpected while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) However, typing "printenv | grep PARFLOW" shows this: PARFLOW_DIR=/home/abrabie/ParFlow/parflow I think maybe because I am installing it on a local windows machine on Virtual Box and not on a super computer that uses parallel or something. should i change anything in the installation process? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-06 22:52 GMT-04:00 Smith, Steve : > Hi, > > > > Apologies, I should have asked for the output of : > > > > printenv | grep PARFLOW > > > > If you copied and pasted exactly what is below there is a bug since the > > > > export > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > > > is 2 commands because of a newline and it should be one command: > > > > export PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > > > Steve > > > > > > *From:* Anas Rabie [mailto:abrabie at umail.iu.edu] > *Sent:* Thursday, October 06, 2016 7:02 AM > *To:* Smith, Steve > *Cc:* ParFlow Users > *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 > LTS > > > > Hi, > > Thank you for your reply. Yes I did export Parflow. This is the bash file > I used as mentioned in the instructions: > > export CC=gcc > export CXX=g++ > export FC=gfortran > export F77=gfortran > > export > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > export SILO_DIR=/home/abrabie/ParFlow/silo > export HYPRE_DIR=/home/abrabie/ParFlow/hypre > export > PATH=$PATH:/home/abrabie/ParFlow/visit/bin > > However, when I try the "printenv PARFLOW" nothing happens. > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > > > > > > 2016-10-05 19:40 GMT-04:00 Smith, Steve : > > Did you ?export? the PARFLOW variable? What does : > > > > printenv PARFLOW > > > > report? > > > > Errors seem to indicate that scripts are not finding the environment > variable. > > > > Steve > > > > > > *From:* parflow-users-bounces at mailman.mines.edu [mailto: > parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie > *Sent:* Tuesday, October 04, 2016 8:15 AM > *To:* ParFlow Users > *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS > > > > Greetings, > > > > I am trying to install ParFlow on Ubuntu, I followed the instructions in > the manual, but I was successful, then I followed what is on the blog > > http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html > > and everything was going well until the very last step, > > > > cd ../pftools > > ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 > > make install > > cd ../test > > sudo ldconfig > > make check > > > > When I do that last "make check" it gives me this error: > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check > > Makefile:9: /config/Makefile.config: No such file or directory > > make: *** No rule to make target '/config/Makefile.config'. Stop. > > > > I tired "sudo make check" as well, but received the same error: > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check > > Makefile:9: /config/Makefile.config: No such file or directory > > make: *** No rule to make target '/config/Makefile.config'. Stop. > > > > I tried to run the Little Washita test to try, but it gave me an error > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh > LW_Test.tcl > no such variable > (read trace on "env(PARFLOW_DIR)") > invoked from within > "lappend auto_path $env(PARFLOW_DIR)/bin" > (file "LW_Test.tcl" line 6) > > However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in > my home directory. so I am not sure what that error means? > > > > Can anybody please help me with this? > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From miguelaguayo at u.boisestate.edu Tue Oct 18 12:25:23 2016 From: miguelaguayo at u.boisestate.edu (Miguel Aguayo) Date: Tue, 18 Oct 2016 12:25:23 -0600 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Hi Anas, I have Parflow installed in a ubuntu machine and running without any issues for a long time. I remember to follow this link: http://parflow.blogspot.com/search/label/linux to get parflow installed correctly. One thing I may suggest here is to set your environment variables into the bash_aliases file instead bash_profile (As far as I know, Ubuntu doesn't come with any bash_profile unless you create one) Once you do this, then you can source bash_aliases either from bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) Cheers Miguel On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie wrote: > Hello, > > I still run into some issues. I fixed my .bash_profile file, and now it is > as follow: > > export CC=gcc > export CXX=g++ > export FC=gfortran > export F77=gfortran > > export PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > export SILO_DIR=/home/abrabie/ParFlow/silo > export HYPRE_DIR=/home/abrabie/ParFlow/hypre > export PATH=$PATH:/home/abrabie/ParFlow/visit/bin > > However, when I type "source ~/.bash_profile" nothing happens. However, I > tried to continue with the installation. OpenMPI, SILO, and HYPRE all > install successfully without any errors. However, again, in the last step > of installing ParFlow, when i type "make check", it gives me this error > message: > > > ############################################################ > ################## > > 0% tests passed, 94 tests failed out of 94 > > FAILED Tests > > ############################################################ > ################## > > I tried to run the little washita example, but this is what happened: > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh > LW_Test.tcl > Files Copied > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > LW > > > /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: > Syntax error: "(" unexpected > while executing > "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" > ("eval" body line 1) > invoked from within > "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" > (procedure "pfrun" line 77) > invoked from within > "pfrun $runname" > (file "LW_Test.tcl" line 512) > > > > However, typing "printenv | grep PARFLOW" shows this: > > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > > I think maybe because I am installing it on a local windows machine on > Virtual Box and not on a super computer that uses parallel or something. > should i change anything in the installation process? > > > Best, > Anas B. Rabie > -==-==-==-==-==-==-==- > Ph.D. Student in Hydrogeology > Department of Geological Sciences > > > > 2016-10-06 22:52 GMT-04:00 Smith, Steve : > >> Hi, >> >> >> >> Apologies, I should have asked for the output of : >> >> >> >> printenv | grep PARFLOW >> >> >> >> If you copied and pasted exactly what is below there is a bug since the >> >> >> >> export >> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> >> >> is 2 commands because of a newline and it should be one command: >> >> >> >> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> >> >> Steve >> >> >> >> >> >> *From:* Anas Rabie [mailto:abrabie at umail.iu.edu] >> *Sent:* Thursday, October 06, 2016 7:02 AM >> *To:* Smith, Steve >> *Cc:* ParFlow Users >> *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu >> 16.04.1 LTS >> >> >> >> Hi, >> >> Thank you for your reply. Yes I did export Parflow. This is the bash file >> I used as mentioned in the instructions: >> >> export CC=gcc >> export CXX=g++ >> export FC=gfortran >> export F77=gfortran >> >> export >> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> export SILO_DIR=/home/abrabie/ParFlow/silo >> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >> export >> PATH=$PATH:/home/abrabie/ParFlow/visit/bin >> >> However, when I try the "printenv PARFLOW" nothing happens. >> >> >> >> Best, >> >> Anas B. Rabie >> >> -==-==-==-==-==-==-==- >> >> Ph.D. Student in Hydrogeology >> >> Department of Geological Sciences >> >> >> >> >> >> >> >> 2016-10-05 19:40 GMT-04:00 Smith, Steve : >> >> Did you ?export? the PARFLOW variable? What does : >> >> >> >> printenv PARFLOW >> >> >> >> report? >> >> >> >> Errors seem to indicate that scripts are not finding the environment >> variable. >> >> >> >> Steve >> >> >> >> >> >> *From:* parflow-users-bounces at mailman.mines.edu [mailto: >> parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie >> *Sent:* Tuesday, October 04, 2016 8:15 AM >> *To:* ParFlow Users >> *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS >> >> >> >> Greetings, >> >> >> >> I am trying to install ParFlow on Ubuntu, I followed the instructions in >> the manual, but I was successful, then I followed what is on the blog >> >> http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html >> >> and everything was going well until the very last step, >> >> >> >> cd ../pftools >> >> ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 >> >> make install >> >> cd ../test >> >> sudo ldconfig >> >> make check >> >> >> >> When I do that last "make check" it gives me this error: >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >> >> Makefile:9: /config/Makefile.config: No such file or directory >> >> make: *** No rule to make target '/config/Makefile.config'. Stop. >> >> >> >> I tired "sudo make check" as well, but received the same error: >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >> >> Makefile:9: /config/Makefile.config: No such file or directory >> >> make: *** No rule to make target '/config/Makefile.config'. Stop. >> >> >> >> I tried to run the Little Washita test to try, but it gave me an error >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >> LW_Test.tcl >> no such variable >> (read trace on "env(PARFLOW_DIR)") >> invoked from within >> "lappend auto_path $env(PARFLOW_DIR)/bin" >> (file "LW_Test.tcl" line 6) >> >> However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in >> my home directory. so I am not sure what that error means? >> >> >> >> Can anybody please help me with this? >> >> >> Best, >> >> Anas B. Rabie >> >> -==-==-==-==-==-==-==- >> >> Ph.D. Student in Hydrogeology >> >> Department of Geological Sciences >> >> >> >> >> >> >> > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > -- Miguel Aguayo PhD Candidate - Geosciences Department of Geosciences Environmental Research Building, MS #1535 Boise State University 1910 University Drive Boise, Idaho 83725 miguelaguayo at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nick.engdahl at wsu.edu Tue Oct 18 17:03:26 2016 From: nick.engdahl at wsu.edu (Engdahl, Nick) Date: Tue, 18 Oct 2016 23:03:26 +0000 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Hi Anas (and ALL Ubuntu users should read the last part), The error is probably not in your environment variables, especially if the installation doesn?t indicate any errors. Most likely this error originates in the /bin directory in a script called ?run? (if this folder does not exist, is empty, or has old files, that would indicate an installation error) You?ll need to edit that script to fix this issue. Open the ?run" script in a text editor and near the top of the script you?ll find two functions ?function usage? and ?function pflog? The default interpreter on Ubuntu doesn?t recognize ?function? as a command so just delete the word ?function" from both and rebuild parflow and pftools. This problem has turned up before on Ubuntu and that change has fixed it every time so far. As a caution to other Ubuntu users, older versions of ParFlow did not use these functions and that's why your older installations, following the blog post, worked fine. Unless you have gone to a lot of trouble to change your default interpreter, you will encounter this problem when you update to the latest version of ParFlow since the version on GitHub uses the ?function? syntax. I?ll be updating the installation instructions on the blog soon for both macOS and Ubuntu and this fix will be included. Nick ------------------------------------------------- Nick Engdahl Assistant Professor Civil and Environmental Engineering Washington State University ------------------------------------------------- On Oct 18, 2016, at 11:25 AM, Miguel Aguayo > wrote: Hi Anas, I have Parflow installed in a ubuntu machine and running without any issues for a long time. I remember to follow this link: http://parflow.blogspot.com/search/label/linux to get parflow installed correctly. One thing I may suggest here is to set your environment variables into the bash_aliases file instead bash_profile (As far as I know, Ubuntu doesn't come with any bash_profile unless you create one) Once you do this, then you can source bash_aliases either from bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) Cheers Miguel On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie > wrote: Hello, I still run into some issues. I fixed my .bash_profile file, and now it is as follow: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I type "source ~/.bash_profile" nothing happens. However, I tried to continue with the installation. OpenMPI, SILO, and HYPRE all install successfully without any errors. However, again, in the last step of installing ParFlow, when i type "make check", it gives me this error message: ############################################################################## 0% tests passed, 94 tests failed out of 94 FAILED Tests ############################################################################## I tried to run the little washita example, but this is what happened: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: Syntax error: "(" unexpected while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) However, typing "printenv | grep PARFLOW" shows this: PARFLOW_DIR=/home/abrabie/ParFlow/parflow I think maybe because I am installing it on a local windows machine on Virtual Box and not on a super computer that uses parallel or something. should i change anything in the installation process? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-06 22:52 GMT-04:00 Smith, Steve >: Hi, Apologies, I should have asked for the output of : printenv | grep PARFLOW If you copied and pasted exactly what is below there is a bug since the export PARFLOW_DIR=/home/abrabie/ParFlow/parflow is 2 commands because of a newline and it should be one command: export PARFLOW_DIR=/home/abrabie/ParFlow/parflow Steve From: Anas Rabie [mailto:abrabie at umail.iu.edu] Sent: Thursday, October 06, 2016 7:02 AM To: Smith, Steve Cc: ParFlow Users Subject: Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Hi, Thank you for your reply. Yes I did export Parflow. This is the bash file I used as mentioned in the instructions: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I try the "printenv PARFLOW" nothing happens. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-05 19:40 GMT-04:00 Smith, Steve >: Did you ?export? the PARFLOW variable? What does : printenv PARFLOW report? Errors seem to indicate that scripts are not finding the environment variable. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Tuesday, October 04, 2016 8:15 AM To: ParFlow Users Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -- Miguel Aguayo PhD Candidate - Geosciences Department of Geosciences Environmental Research Building, MS #1535 Boise State University 1910 University Drive Boise, Idaho 83725 miguelaguayo at u.boisestate.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4-dJ3Ee_HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbwsh1ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmaxwell at mines.edu Tue Oct 18 17:07:19 2016 From: rmaxwell at mines.edu (Reed Maxwell) Date: Tue, 18 Oct 2016 23:07:19 +0000 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> , Message-ID: <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> Hi Anas and all- Thanks for the great replies. Another thought: are you downloading the most recent version of ParFlow from GitHub? I know Steve has updated the build environment / run script for this version. Reed Please excuse the brevity of this message it was sent from my iPhone On Oct 18, 2016, at 5:03 PM, Engdahl, Nick > wrote: Hi Anas (and ALL Ubuntu users should read the last part), The error is probably not in your environment variables, especially if the installation doesn?t indicate any errors. Most likely this error originates in the /bin directory in a script called ?run? (if this folder does not exist, is empty, or has old files, that would indicate an installation error) You?ll need to edit that script to fix this issue. Open the ?run" script in a text editor and near the top of the script you?ll find two functions ?function usage? and ?function pflog? The default interpreter on Ubuntu doesn?t recognize ?function? as a command so just delete the word ?function" from both and rebuild parflow and pftools. This problem has turned up before on Ubuntu and that change has fixed it every time so far. As a caution to other Ubuntu users, older versions of ParFlow did not use these functions and that's why your older installations, following the blog post, worked fine. Unless you have gone to a lot of trouble to change your default interpreter, you will encounter this problem when you update to the latest version of ParFlow since the version on GitHub uses the ?function? syntax. I?ll be updating the installation instructions on the blog soon for both macOS and Ubuntu and this fix will be included. Nick ------------------------------------------------- Nick Engdahl Assistant Professor Civil and Environmental Engineering Washington State University ------------------------------------------------- On Oct 18, 2016, at 11:25 AM, Miguel Aguayo > wrote: Hi Anas, I have Parflow installed in a ubuntu machine and running without any issues for a long time. I remember to follow this link: http://parflow.blogspot.com/search/label/linux to get parflow installed correctly. One thing I may suggest here is to set your environment variables into the bash_aliases file instead bash_profile (As far as I know, Ubuntu doesn't come with any bash_profile unless you create one) Once you do this, then you can source bash_aliases either from bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) Cheers Miguel On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie > wrote: Hello, I still run into some issues. I fixed my .bash_profile file, and now it is as follow: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I type "source ~/.bash_profile" nothing happens. However, I tried to continue with the installation. OpenMPI, SILO, and HYPRE all install successfully without any errors. However, again, in the last step of installing ParFlow, when i type "make check", it gives me this error message: ############################################################################## 0% tests passed, 94 tests failed out of 94 FAILED Tests ############################################################################## I tried to run the little washita example, but this is what happened: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: Syntax error: "(" unexpected while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) However, typing "printenv | grep PARFLOW" shows this: PARFLOW_DIR=/home/abrabie/ParFlow/parflow I think maybe because I am installing it on a local windows machine on Virtual Box and not on a super computer that uses parallel or something. should i change anything in the installation process? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-06 22:52 GMT-04:00 Smith, Steve >: Hi, Apologies, I should have asked for the output of : printenv | grep PARFLOW If you copied and pasted exactly what is below there is a bug since the export PARFLOW_DIR=/home/abrabie/ParFlow/parflow is 2 commands because of a newline and it should be one command: export PARFLOW_DIR=/home/abrabie/ParFlow/parflow Steve From: Anas Rabie [mailto:abrabie at umail.iu.edu] Sent: Thursday, October 06, 2016 7:02 AM To: Smith, Steve Cc: ParFlow Users Subject: Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Hi, Thank you for your reply. Yes I did export Parflow. This is the bash file I used as mentioned in the instructions: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I try the "printenv PARFLOW" nothing happens. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-05 19:40 GMT-04:00 Smith, Steve >: Did you ?export? the PARFLOW variable? What does : printenv PARFLOW report? Errors seem to indicate that scripts are not finding the environment variable. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Tuesday, October 04, 2016 8:15 AM To: ParFlow Users Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -- Miguel Aguayo PhD Candidate - Geosciences Department of Geosciences Environmental Research Building, MS #1535 Boise State University 1910 University Drive Boise, Idaho 83725 miguelaguayo at u.boisestate.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4-dJ3Ee_HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbwsh1ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From smith84 at llnl.gov Tue Oct 18 18:04:30 2016 From: smith84 at llnl.gov (Smith, Steve) Date: Wed, 19 Oct 2016 00:04:30 +0000 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: <399743D90C221740B6399BDE9E58856D0125D02FEF@PRDEXMBX-02.the-lab.llnl.gov> I have pushed a change to github to remove the ?function? from the run scripts. Sorry about that, I thought we had fixed this. Many Linux distributions use the Bash shell as a drop in replacement for the Borne shell (/bin/sh) and bash syntax can creep in. Ubuntu uses dash for sh which exposes this. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Engdahl, Nick Sent: Tuesday, October 18, 2016 4:03 PM To: ParFlow Users Subject: Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Hi Anas (and ALL Ubuntu users should read the last part), The error is probably not in your environment variables, especially if the installation doesn?t indicate any errors. Most likely this error originates in the /bin directory in a script called ?run? (if this folder does not exist, is empty, or has old files, that would indicate an installation error) You?ll need to edit that script to fix this issue. Open the ?run" script in a text editor and near the top of the script you?ll find two functions ?function usage? and ?function pflog? The default interpreter on Ubuntu doesn?t recognize ?function? as a command so just delete the word ?function" from both and rebuild parflow and pftools. This problem has turned up before on Ubuntu and that change has fixed it every time so far. As a caution to other Ubuntu users, older versions of ParFlow did not use these functions and that's why your older installations, following the blog post, worked fine. Unless you have gone to a lot of trouble to change your default interpreter, you will encounter this problem when you update to the latest version of ParFlow since the version on GitHub uses the ?function? syntax. I?ll be updating the installation instructions on the blog soon for both macOS and Ubuntu and this fix will be included. Nick ------------------------------------------------- Nick Engdahl Assistant Professor Civil and Environmental Engineering Washington State University ------------------------------------------------- On Oct 18, 2016, at 11:25 AM, Miguel Aguayo > wrote: Hi Anas, I have Parflow installed in a ubuntu machine and running without any issues for a long time. I remember to follow this link: http://parflow.blogspot.com/search/label/linux to get parflow installed correctly. One thing I may suggest here is to set your environment variables into the bash_aliases file instead bash_profile (As far as I know, Ubuntu doesn't come with any bash_profile unless you create one) Once you do this, then you can source bash_aliases either from bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) Cheers Miguel On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie > wrote: Hello, I still run into some issues. I fixed my .bash_profile file, and now it is as follow: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I type "source ~/.bash_profile" nothing happens. However, I tried to continue with the installation. OpenMPI, SILO, and HYPRE all install successfully without any errors. However, again, in the last step of installing ParFlow, when i type "make check", it gives me this error message: ############################################################################## 0% tests passed, 94 tests failed out of 94 FAILED Tests ############################################################################## I tried to run the little washita example, but this is what happened: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: Syntax error: "(" unexpected while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) However, typing "printenv | grep PARFLOW" shows this: PARFLOW_DIR=/home/abrabie/ParFlow/parflow I think maybe because I am installing it on a local windows machine on Virtual Box and not on a super computer that uses parallel or something. should i change anything in the installation process? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-06 22:52 GMT-04:00 Smith, Steve >: Hi, Apologies, I should have asked for the output of : printenv | grep PARFLOW If you copied and pasted exactly what is below there is a bug since the export PARFLOW_DIR=/home/abrabie/ParFlow/parflow is 2 commands because of a newline and it should be one command: export PARFLOW_DIR=/home/abrabie/ParFlow/parflow Steve From: Anas Rabie [mailto:abrabie at umail.iu.edu] Sent: Thursday, October 06, 2016 7:02 AM To: Smith, Steve Cc: ParFlow Users Subject: Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Hi, Thank you for your reply. Yes I did export Parflow. This is the bash file I used as mentioned in the instructions: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I try the "printenv PARFLOW" nothing happens. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-05 19:40 GMT-04:00 Smith, Steve >: Did you ?export? the PARFLOW variable? What does : printenv PARFLOW report? Errors seem to indicate that scripts are not finding the environment variable. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Tuesday, October 04, 2016 8:15 AM To: ParFlow Users Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -- Miguel Aguayo PhD Candidate - Geosciences Department of Geosciences Environmental Research Building, MS #1535 Boise State University 1910 University Drive Boise, Idaho 83725 miguelaguayo at u.boisestate.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4-dJ3Ee_HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbwsh1ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Tue Oct 18 17:19:17 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Tue, 18 Oct 2016 19:19:17 -0400 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> Message-ID: Thank you all for your reply. Prof. Maxwell, yes, I downloaded the newest version, its number is ParFlow Version 3.2.0. Prof. Engdahl, I will try that and will let you know if this works. Thank you all again for your time and guidance. I really appreciate it. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-18 19:07 GMT-04:00 Reed Maxwell : > Hi Anas and all- > > Thanks for the great replies. Another thought: are you downloading the > most recent version of ParFlow from GitHub? I know Steve has updated the > build environment / run script for this version. > > Reed > > Please excuse the brevity of this message it was sent from my iPhone > > On Oct 18, 2016, at 5:03 PM, Engdahl, Nick wrote: > > Hi Anas (and ALL Ubuntu users should read the last part), > The error is probably not in your environment variables, especially if the > installation doesn?t indicate any errors. > > Most likely this error originates in the /bin > directory in a script called ?run? (if this folder does not exist, is > empty, or has old files, that would indicate an installation error) > You?ll need to edit that script to fix this issue. Open the ?run" script > in a text editor and near the top of the script you?ll find two functions > ?function usage? and ?function pflog? The default interpreter on Ubuntu > doesn?t recognize ?function? as a command so just delete the word > ?function" from both and rebuild parflow and pftools. This problem has > turned up before on Ubuntu and that change has fixed it every time so far. > > As a caution to other Ubuntu users, older versions of ParFlow did not use > these functions and that's why your older installations, following the blog > post, worked fine. Unless you have gone to a lot of trouble to change your > default interpreter, you will encounter this problem when you update to the > latest version of ParFlow since the version on GitHub uses the ?function? > syntax. I?ll be updating the installation instructions on the blog soon for > both macOS and Ubuntu and this fix will be included. > > Nick > > ------------------------------------------------- > Nick Engdahl > Assistant Professor > Civil and Environmental Engineering > Washington State University > ------------------------------------------------- > > > On Oct 18, 2016, at 11:25 AM, Miguel Aguayo > wrote: > > Hi Anas, > > I have Parflow installed in a ubuntu machine and running without any > issues for a long time. I remember to follow this link: > http://parflow.blogspot.com/search/label/linux > to > get parflow installed correctly. One thing I may suggest here is to set > your environment variables into the bash_aliases file instead bash_profile > (As far as I know, Ubuntu doesn't come with any bash_profile unless you > create one) Once you do this, then you can source bash_aliases either from > bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) > > Cheers > > > Miguel > > > > > On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie wrote: > >> Hello, >> >> I still run into some issues. I fixed my .bash_profile file, and now it >> is as follow: >> >> export CC=gcc >> export CXX=g++ >> export FC=gfortran >> export F77=gfortran >> >> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> export SILO_DIR=/home/abrabie/ParFlow/silo >> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >> export PATH=$PATH:/home/abrabie/ParFlow/visit/bin >> >> However, when I type "source ~/.bash_profile" nothing happens. However, I >> tried to continue with the installation. OpenMPI, SILO, and HYPRE all >> install successfully without any errors. However, again, in the last step >> of installing ParFlow, when i type "make check", it gives me this error >> message: >> >> >> ############################################################ >> ################## >> >> 0% tests passed, 94 tests failed out of 94 >> >> FAILED Tests >> >> ############################################################ >> ################## >> >> I tried to run the little washita example, but this is what happened: >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >> LW_Test.tcl >> Files Copied >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> LW >> >> >> /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: >> Syntax error: "(" unexpected >> while executing >> "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" >> ("eval" body line 1) >> invoked from within >> "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" >> (procedure "pfrun" line 77) >> invoked from within >> "pfrun $runname" >> (file "LW_Test.tcl" line 512) >> >> >> >> However, typing "printenv | grep PARFLOW" shows this: >> >> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> >> I think maybe because I am installing it on a local windows machine on >> Virtual Box and not on a super computer that uses parallel or something. >> should i change anything in the installation process? >> >> >> Best, >> Anas B. Rabie >> -==-==-==-==-==-==-==- >> Ph.D. Student in Hydrogeology >> Department of Geological Sciences >> >> >> >> 2016-10-06 22:52 GMT-04:00 Smith, Steve : >> >>> Hi, >>> >>> >>> >>> Apologies, I should have asked for the output of : >>> >>> >>> >>> printenv | grep PARFLOW >>> >>> >>> >>> If you copied and pasted exactly what is below there is a bug since the >>> >>> >>> >>> export >>> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> >>> >>> is 2 commands because of a newline and it should be one command: >>> >>> >>> >>> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> >>> >>> Steve >>> >>> >>> >>> >>> >>> *From:* Anas Rabie [mailto:abrabie at umail.iu.edu] >>> *Sent:* Thursday, October 06, 2016 7:02 AM >>> *To:* Smith, Steve >>> *Cc:* ParFlow Users >>> *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu >>> 16.04.1 LTS >>> >>> >>> >>> Hi, >>> >>> Thank you for your reply. Yes I did export Parflow. This is the bash >>> file I used as mentioned in the instructions: >>> >>> export CC=gcc >>> export CXX=g++ >>> export FC=gfortran >>> export F77=gfortran >>> >>> export >>> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> export SILO_DIR=/home/abrabie/ParFlow/silo >>> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >>> export >>> PATH=$PATH:/home/abrabie/ParFlow/visit/bin >>> >>> However, when I try the "printenv PARFLOW" nothing happens. >>> >>> >>> >>> Best, >>> >>> Anas B. Rabie >>> >>> -==-==-==-==-==-==-==- >>> >>> Ph.D. Student in Hydrogeology >>> >>> Department of Geological Sciences >>> >>> >>> >>> >>> >>> >>> >>> 2016-10-05 19:40 GMT-04:00 Smith, Steve : >>> >>> Did you ?export? the PARFLOW variable? What does : >>> >>> >>> >>> printenv PARFLOW >>> >>> >>> >>> report? >>> >>> >>> >>> Errors seem to indicate that scripts are not finding the environment >>> variable. >>> >>> >>> >>> Steve >>> >>> >>> >>> >>> >>> *From:* parflow-users-bounces at mailman.mines.edu [mailto: >>> parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie >>> *Sent:* Tuesday, October 04, 2016 8:15 AM >>> *To:* ParFlow Users >>> *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 >>> LTS >>> >>> >>> >>> Greetings, >>> >>> >>> >>> I am trying to install ParFlow on Ubuntu, I followed the instructions in >>> the manual, but I was successful, then I followed what is on the blog >>> >>> http://parflow.blogspot.com/2010/03/running-parflow-on-windo >>> ws-using.html >>> >>> >>> and everything was going well until the very last step, >>> >>> >>> >>> cd ../pftools >>> >>> ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 >>> >>> make install >>> >>> cd ../test >>> >>> sudo ldconfig >>> >>> make check >>> >>> >>> >>> When I do that last "make check" it gives me this error: >>> >>> >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >>> >>> Makefile:9: /config/Makefile.config: No such file or directory >>> >>> make: *** No rule to make target '/config/Makefile.config'. Stop. >>> >>> >>> >>> I tired "sudo make check" as well, but received the same error: >>> >>> >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >>> >>> Makefile:9: /config/Makefile.config: No such file or directory >>> >>> make: *** No rule to make target '/config/Makefile.config'. Stop. >>> >>> >>> >>> I tried to run the Little Washita test to try, but it gave me an error >>> >>> >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >>> LW_Test.tcl >>> no such variable >>> (read trace on "env(PARFLOW_DIR)") >>> invoked from within >>> "lappend auto_path $env(PARFLOW_DIR)/bin" >>> (file "LW_Test.tcl" line 6) >>> >>> However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in >>> my home directory. so I am not sure what that error means? >>> >>> >>> >>> Can anybody please help me with this? >>> >>> >>> Best, >>> >>> Anas B. Rabie >>> >>> -==-==-==-==-==-==-==- >>> >>> Ph.D. Student in Hydrogeology >>> >>> Department of Geological Sciences >>> >>> >>> >>> >>> >>> >>> >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> > > > -- > Miguel Aguayo > PhD Candidate - Geosciences > Department of Geosciences > Environmental Research Building, MS #1535 > Boise State University > 1910 University Drive > Boise, Idaho 83725 > miguelaguayo at u.boisestate.edu > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__ > mailman.mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c=C3yme8gMkxg_ > ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4- > dJ3Ee_HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbwsh1 > ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hooria at ucr.edu Wed Oct 19 16:31:02 2016 From: hooria at ucr.edu (Hoori Ajami) Date: Wed, 19 Oct 2016 15:31:02 -0700 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> Message-ID: Hi All, Thanks Nick for your suggestion. Removing the "function" solved my problem with Ubuntu 14.04 and ParFlow 3.2.0. Thanks, Hoori On 10/18/2016 4:19 PM, Anas Rabie wrote: > Thank you all for your reply. > > Prof. Maxwell, yes, I downloaded the newest version, its number is > ParFlow Version 3.2.0. > > Prof. Engdahl, I will try that and will let you know if this works. > > Thank you all again for your time and guidance. I really appreciate it. > > > Best, > Anas B. Rabie > -==-==-==-==-==-==-==- > Ph.D. Student in Hydrogeology > Department of Geological Sciences > > > > 2016-10-18 19:07 GMT-04:00 Reed Maxwell >: > > Hi Anas and all- > > Thanks for the great replies. Another thought: are you > downloading the most recent version of ParFlow from GitHub? I > know Steve has updated the build environment / run script for this > version. > > Reed > > Please excuse the brevity of this message it was sent from my iPhone > > On Oct 18, 2016, at 5:03 PM, Engdahl, Nick > wrote: > >> Hi Anas (and ALL Ubuntu users should read the last part), >> The error is probably not in your environment variables, >> especially if the installation doesn?t indicate any errors. >> >> Most likely this error originates in the >> /bin directory in a script called ?run? >> (if this folder does not exist, is empty, or has old files, that >> would indicate an installation error) >> You?ll need to edit that script to fix this issue. Open the ?run" >> script in a text editor and near the top of the script you?ll >> find two functions ?function usage? and ?function pflog? The >> default interpreter on Ubuntu doesn?t recognize ?function? as a >> command so just delete the word ?function" from both and rebuild >> parflow and pftools. This problem has turned up before on Ubuntu >> and that change has fixed it every time so far. >> >> As a caution to other Ubuntu users, older versions of ParFlow did >> not use these functions and that's why your older installations, >> following the blog post, worked fine. Unless you have gone to a >> lot of trouble to change your default interpreter, you will >> encounter this problem when you update to the latest version of >> ParFlow since the version on GitHub uses the ?function? syntax. >> I?ll be updating the installation instructions on the blog soon >> for both macOS and Ubuntu and this fix will be included. >> >> Nick >> >> ------------------------------------------------- >> Nick Engdahl >> Assistant Professor >> Civil and Environmental Engineering >> Washington State University >> ------------------------------------------------- >> >> >>> On Oct 18, 2016, at 11:25 AM, Miguel Aguayo >>> >> > wrote: >>> >>> Hi Anas, >>> >>> I have Parflow installed in a ubuntu machine and running without >>> any issues for a long time. I remember to follow this link: >>> http://parflow.blogspot.com/search/label/linux >>> to >>> get parflow installed correctly. One thing I may suggest here is >>> to set your environment variables into the bash_aliases file >>> instead bash_profile (As far as I know, Ubuntu doesn't come with >>> any bash_profile unless you create one) Once you do this, then >>> you can source bash_aliases either from bashrc or bash_aliases >>> (i.e. source ~/.bash_aliases or source ~/.bashrc) >>> >>> Cheers >>> >>> >>> Miguel >>> >>> >>> >>> >>> On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie >>> > wrote: >>> >>> Hello, >>> >>> I still run into some issues. I fixed my .bash_profile file, >>> and now it is as follow: >>> >>> export CC=gcc >>> export CXX=g++ >>> export FC=gfortran >>> export F77=gfortran >>> >>> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> export SILO_DIR=/home/abrabie/ParFlow/silo >>> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >>> export PATH=$PATH:/home/abrabie/ParFlow/visit/bin >>> >>> However, when I type "source ~/.bash_profile" nothing >>> happens. However, I tried to continue with the installation. >>> OpenMPI, SILO, and HYPRE all install successfully without >>> any errors. However, again, in the last step of installing >>> ParFlow, when i type "make check", it gives me this error >>> message: >>> >>> >>> ############################################################################## >>> >>> 0% tests passed, 94 tests failed out of 94 >>> >>> FAILED Tests >>> >>> ############################################################################## >>> >>> I tried to run the little washita example, but this is what >>> happened: >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ >>> tclsh LW_Test.tcl >>> Files Copied >>> Using process grid (1,1,1) >>> Using process grid (1,1,1) >>> Using process grid (1,1,1) >>> Using process grid (1,1,1) >>> LW >>> >>> >>> /home/abrabie/ParFlow/parflow/bin/run: 39: >>> /home/abrabie/ParFlow/parflow/bin/run: Syntax error: "(" >>> unexpected >>> while executing >>> "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" >>> ("eval" body line 1) >>> invoked from within >>> "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname >>> $NumProcs $NumNodes" >>> (procedure "pfrun" line 77) >>> invoked from within >>> "pfrun $runname" >>> (file "LW_Test.tcl" line 512) >>> >>> >>> >>> However, typing "printenv | grep PARFLOW" shows this: >>> >>> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> >>> I think maybe because I am installing it on a local windows >>> machine on Virtual Box and not on a super computer that uses >>> parallel or something. should i change anything in the >>> installation process? >>> >>> >>> Best, >>> Anas B. Rabie >>> -==-==-==-==-==-==-==- >>> Ph.D. Student in Hydrogeology >>> Department of Geological Sciences >>> >>> >>> >>> 2016-10-06 22:52 GMT-04:00 Smith, Steve >> >: >>> >>> Hi, >>> >>> Apologies, I should have asked for the output of : >>> >>> printenv | grep PARFLOW >>> >>> If you copied and pasted exactly what is below there is >>> a bug since the >>> >>> export >>> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> is 2 commands because of a newline and it should be one >>> command: >>> >>> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> Steve >>> >>> *From:*Anas Rabie [mailto:abrabie at umail.iu.edu >>> ] >>> *Sent:* Thursday, October 06, 2016 7:02 AM >>> *To:* Smith, Steve >>> *Cc:* ParFlow Users >>> *Subject:* Re: [parflow-users] Issue installing ParFlow >>> on Ubuntu 16.04.1 LTS >>> >>> Hi, >>> >>> Thank you for your reply. Yes I did export Parflow. This >>> is the bash file I used as mentioned in the instructions: >>> >>> export CC=gcc >>> export CXX=g++ >>> export FC=gfortran >>> export F77=gfortran >>> >>> export >>> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> export SILO_DIR=/home/abrabie/ParFlow/silo >>> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >>> export >>> PATH=$PATH:/home/abrabie/ParFlow/visit/bin >>> >>> However, when I try the "printenv PARFLOW" nothing happens. >>> >>> >>> >>> Best, >>> >>> Anas B. Rabie >>> >>> -==-==-==-==-==-==-==- >>> >>> Ph.D. Student in Hydrogeology >>> >>> Department of Geological Sciences >>> >>> 2016-10-05 19:40 GMT-04:00 Smith, Steve >>> >: >>> >>> Did you ?export? the PARFLOW variable? What does : >>> >>> printenv PARFLOW >>> >>> report? >>> >>> Errors seem to indicate that scripts are not finding >>> the environment variable. >>> >>> Steve >>> >>> *From:*parflow-users-bounces at mailman.mines.edu >>> >>> [mailto:parflow-users-bounces at mailman.mines.edu >>> ] >>> *On Behalf Of *Anas Rabie >>> *Sent:* Tuesday, October 04, 2016 8:15 AM >>> *To:* ParFlow Users >>> *Subject:* [parflow-users] Issue installing ParFlow >>> on Ubuntu 16.04.1 LTS >>> >>> Greetings, >>> >>> I am trying to install ParFlow on Ubuntu, I followed >>> the instructions in the manual, but I was >>> successful, then I followed what is on the blog >>> >>> http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html >>> >>> >>> and everything was going well until the very last step, >>> >>> cd ../pftools >>> >>> ./configure --prefix=$PARFLOW_DIR >>> --with-silo=$SILO_DIR --with-amps=mpi1 >>> >>> make install >>> >>> cd ../test >>> >>> sudo ldconfig >>> >>> make check >>> >>> When I do that last "make check" it gives me this error: >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >>> >>> Makefile:9: /config/Makefile.config: No such file or >>> directory >>> >>> make: *** No rule to make target >>> '/config/Makefile.config'. Stop. >>> >>> I tired "sudo make check" as well, but received the >>> same error: >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >>> >>> Makefile:9: /config/Makefile.config: No such file or >>> directory >>> >>> make: *** No rule to make target >>> '/config/Makefile.config'. Stop. >>> >>> I tried to run the Little Washita test to try, but >>> it gave me an error >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ >>> tclsh LW_Test.tcl >>> no such variable >>> (read trace on "env(PARFLOW_DIR)") >>> invoked from within >>> "lappend auto_path $env(PARFLOW_DIR)/bin" >>> (file "LW_Test.tcl" line 6) >>> >>> However, when I try cd $PARFLOW_DIR it takes me to >>> the parflow folder in my home directory. so I am not >>> sure what that error means? >>> >>> Can anybody please help me with this? >>> >>> >>> Best, >>> >>> Anas B. Rabie >>> >>> -==-==-==-==-==-==-==- >>> >>> Ph.D. Student in Hydrogeology >>> >>> Department of Geological Sciences >>> >>> >>> >>> _______________________________________________ >>> parflow-users mailing list >>> parflow-users at mailman.mines.edu >>> >>> https://mailman.mines.edu/mailman/listinfo/parflow-users >>> >>> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >>> >>> >>> >>> >>> >>> -- >>> Miguel Aguayo >>> PhD Candidate - Geosciences >>> Department of Geosciences >>> Environmental Research Building, MS #1535 >>> Boise State University >>> 1910 University Drive >>> Boise, Idaho 83725 >>> miguelaguayo at u.boisestate.edu >>> _______________________________________________ >>> parflow-users mailing list >>> parflow-users at mailman.mines.edu >>> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4-dJ3Ee_HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbwsh1ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= >>> >>> >>> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >>> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > > https://mailman.mines.edu/mailman/listinfo/parflow-users > > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -- Hoori Ajami Assistant Professor of Groundwater Hydrology Department of Environmental Sciences University of California, Riverside Room 2322 Geology Riverside, California 92521 Office: (951) 827-4778 E-mail: hoori.ajami at ucr.edu Web: http://envisci.ucr.edu/faculty/ajami.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Thu Oct 20 09:31:29 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Thu, 20 Oct 2016 11:31:29 -0400 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> Message-ID: Hello All, I have deleted the word 'function' from the bin/run file. However, when I try to rebuild Parflow and pftools, it returns the 'function' word to the run file I believe. So, I tried to just delete 'function' , then hit ':wq' in vim to write and quit then I tried to 'make check' the test folder, all of the tests passed, it said PASSED ALL. However, I then tried to run the little washita example, but it still resulted in an error. abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW child process exited abnormally while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) I am not sure what does it mean with "child process", since the first line says it countered an error with "run LW 1 1" , I tried to use : tclsh LW_Test.tcl 1 1 1 But it did not make a difference. Can any body please guide me in this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-19 18:31 GMT-04:00 Hoori Ajami : > Hi All, > > Thanks Nick for your suggestion. Removing the "function" solved my problem > with Ubuntu 14.04 and ParFlow 3.2.0. > Thanks, > Hoori > > On 10/18/2016 4:19 PM, Anas Rabie wrote: > > Thank you all for your reply. > > Prof. Maxwell, yes, I downloaded the newest version, its number is ParFlow > Version 3.2.0. > > Prof. Engdahl, I will try that and will let you know if this works. > > Thank you all again for your time and guidance. I really appreciate it. > > > Best, > Anas B. Rabie > -==-==-==-==-==-==-==- > Ph.D. Student in Hydrogeology > Department of Geological Sciences > > > > 2016-10-18 19:07 GMT-04:00 Reed Maxwell : > >> Hi Anas and all- >> >> Thanks for the great replies. Another thought: are you downloading the >> most recent version of ParFlow from GitHub? I know Steve has updated the >> build environment / run script for this version. >> >> Reed >> >> Please excuse the brevity of this message it was sent from my iPhone >> >> On Oct 18, 2016, at 5:03 PM, Engdahl, Nick wrote: >> >> Hi Anas (and ALL Ubuntu users should read the last part), >> The error is probably not in your environment variables, especially if >> the installation doesn?t indicate any errors. >> >> Most likely this error originates in the /bin >> directory in a script called ?run? (if this folder does not exist, is >> empty, or has old files, that would indicate an installation error) >> You?ll need to edit that script to fix this issue. Open the ?run" script >> in a text editor and near the top of the script you?ll find two functions >> ?function usage? and ?function pflog? The default interpreter on Ubuntu >> doesn?t recognize ?function? as a command so just delete the word >> ?function" from both and rebuild parflow and pftools. This problem has >> turned up before on Ubuntu and that change has fixed it every time so far. >> >> As a caution to other Ubuntu users, older versions of ParFlow did not use >> these functions and that's why your older installations, following the blog >> post, worked fine. Unless you have gone to a lot of trouble to change your >> default interpreter, you will encounter this problem when you update to the >> latest version of ParFlow since the version on GitHub uses the ?function? >> syntax. I?ll be updating the installation instructions on the blog soon for >> both macOS and Ubuntu and this fix will be included. >> >> Nick >> >> ------------------------------------------------- >> Nick Engdahl >> Assistant Professor >> Civil and Environmental Engineering >> Washington State University >> ------------------------------------------------- >> >> >> On Oct 18, 2016, at 11:25 AM, Miguel Aguayo < >> miguelaguayo at u.boisestate.edu> wrote: >> >> Hi Anas, >> >> I have Parflow installed in a ubuntu machine and running without any >> issues for a long time. I remember to follow this link: >> http://parflow.blogspot.com/search/label/linux >> to >> get parflow installed correctly. One thing I may suggest here is to set >> your environment variables into the bash_aliases file instead bash_profile >> (As far as I know, Ubuntu doesn't come with any bash_profile unless you >> create one) Once you do this, then you can source bash_aliases either from >> bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) >> >> Cheers >> >> >> Miguel >> >> >> >> >> On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie >> wrote: >> >>> Hello, >>> >>> I still run into some issues. I fixed my .bash_profile file, and now it >>> is as follow: >>> >>> export CC=gcc >>> export CXX=g++ >>> export FC=gfortran >>> export F77=gfortran >>> >>> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> export SILO_DIR=/home/abrabie/ParFlow/silo >>> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >>> export PATH=$PATH:/home/abrabie/ParFlow/visit/bin >>> >>> However, when I type "source ~/.bash_profile" nothing happens. However, >>> I tried to continue with the installation. OpenMPI, SILO, and HYPRE all >>> install successfully without any errors. However, again, in the last step >>> of installing ParFlow, when i type "make check", it gives me this error >>> message: >>> >>> >>> ############################################################ >>> ################## >>> >>> 0% tests passed, 94 tests failed out of 94 >>> >>> FAILED Tests >>> >>> ############################################################ >>> ################## >>> >>> I tried to run the little washita example, but this is what happened: >>> >>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >>> LW_Test.tcl >>> Files Copied >>> Using process grid (1,1,1) >>> Using process grid (1,1,1) >>> Using process grid (1,1,1) >>> Using process grid (1,1,1) >>> LW >>> >>> >>> /home/abrabie/ParFlow/parflow/bin/run: 39: >>> /home/abrabie/ParFlow/parflow/bin/run: Syntax error: "(" unexpected >>> while executing >>> "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" >>> ("eval" body line 1) >>> invoked from within >>> "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs >>> $NumNodes" >>> (procedure "pfrun" line 77) >>> invoked from within >>> "pfrun $runname" >>> (file "LW_Test.tcl" line 512) >>> >>> >>> >>> However, typing "printenv | grep PARFLOW" shows this: >>> >>> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>> >>> >>> I think maybe because I am installing it on a local windows machine on >>> Virtual Box and not on a super computer that uses parallel or something. >>> should i change anything in the installation process? >>> >>> >>> Best, >>> Anas B. Rabie >>> -==-==-==-==-==-==-==- >>> Ph.D. Student in Hydrogeology >>> Department of Geological Sciences >>> >>> >>> >>> 2016-10-06 22:52 GMT-04:00 Smith, Steve : >>> >>>> Hi, >>>> >>>> >>>> >>>> Apologies, I should have asked for the output of : >>>> >>>> >>>> >>>> printenv | grep PARFLOW >>>> >>>> >>>> >>>> If you copied and pasted exactly what is below there is a bug since the >>>> >>>> >>>> >>>> export >>>> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>>> >>>> >>>> >>>> is 2 commands because of a newline and it should be one command: >>>> >>>> >>>> >>>> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>>> >>>> >>>> >>>> Steve >>>> >>>> >>>> >>>> >>>> >>>> *From:* Anas Rabie [mailto:abrabie at umail.iu.edu] >>>> *Sent:* Thursday, October 06, 2016 7:02 AM >>>> *To:* Smith, Steve >>>> *Cc:* ParFlow Users >>>> *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu >>>> 16.04.1 LTS >>>> >>>> >>>> >>>> Hi, >>>> >>>> Thank you for your reply. Yes I did export Parflow. This is the bash >>>> file I used as mentioned in the instructions: >>>> >>>> export CC=gcc >>>> export CXX=g++ >>>> export FC=gfortran >>>> export F77=gfortran >>>> >>>> export >>>> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >>>> >>>> export SILO_DIR=/home/abrabie/ParFlow/silo >>>> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >>>> export >>>> PATH=$PATH:/home/abrabie/ParFlow/visit/bin >>>> >>>> However, when I try the "printenv PARFLOW" nothing happens. >>>> >>>> >>>> >>>> Best, >>>> >>>> Anas B. Rabie >>>> >>>> -==-==-==-==-==-==-==- >>>> >>>> Ph.D. Student in Hydrogeology >>>> >>>> Department of Geological Sciences >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 2016-10-05 19:40 GMT-04:00 Smith, Steve : >>>> >>>> Did you ?export? the PARFLOW variable? What does : >>>> >>>> >>>> >>>> printenv PARFLOW >>>> >>>> >>>> >>>> report? >>>> >>>> >>>> >>>> Errors seem to indicate that scripts are not finding the environment >>>> variable. >>>> >>>> >>>> >>>> Steve >>>> >>>> >>>> >>>> >>>> >>>> *From:* parflow-users-bounces at mailman.mines.edu [mailto: >>>> parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie >>>> *Sent:* Tuesday, October 04, 2016 8:15 AM >>>> *To:* ParFlow Users >>>> *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 >>>> LTS >>>> >>>> >>>> >>>> Greetings, >>>> >>>> >>>> >>>> I am trying to install ParFlow on Ubuntu, I followed the instructions >>>> in the manual, but I was successful, then I followed what is on the blog >>>> >>>> http://parflow.blogspot.com/2010/03/running-parflow-on-windo >>>> ws-using.html >>>> >>>> >>>> and everything was going well until the very last step, >>>> >>>> >>>> >>>> cd ../pftools >>>> >>>> ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 >>>> >>>> make install >>>> >>>> cd ../test >>>> >>>> sudo ldconfig >>>> >>>> make check >>>> >>>> >>>> >>>> When I do that last "make check" it gives me this error: >>>> >>>> >>>> >>>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >>>> >>>> Makefile:9: /config/Makefile.config: No such file or directory >>>> >>>> make: *** No rule to make target '/config/Makefile.config'. Stop. >>>> >>>> >>>> >>>> I tired "sudo make check" as well, but received the same error: >>>> >>>> >>>> >>>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >>>> >>>> Makefile:9: /config/Makefile.config: No such file or directory >>>> >>>> make: *** No rule to make target '/config/Makefile.config'. Stop. >>>> >>>> >>>> >>>> I tried to run the Little Washita test to try, but it gave me an error >>>> >>>> >>>> >>>> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >>>> LW_Test.tcl >>>> no such variable >>>> (read trace on "env(PARFLOW_DIR)") >>>> invoked from within >>>> "lappend auto_path $env(PARFLOW_DIR)/bin" >>>> (file "LW_Test.tcl" line 6) >>>> >>>> However, when I try cd $PARFLOW_DIR it takes me to the parflow folder >>>> in my home directory. so I am not sure what that error means? >>>> >>>> >>>> >>>> Can anybody please help me with this? >>>> >>>> >>>> Best, >>>> >>>> Anas B. Rabie >>>> >>>> -==-==-==-==-==-==-==- >>>> >>>> Ph.D. Student in Hydrogeology >>>> >>>> Department of Geological Sciences >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> _______________________________________________ >>> parflow-users mailing list >>> parflow-users at mailman.mines.edu >>> https://mailman.mines.edu/mailman/listinfo/parflow-users >>> >>> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >>> >>> >> >> >> -- >> Miguel Aguayo >> PhD Candidate - Geosciences >> Department of Geosciences >> Environmental Research Building, MS #1535 >> Boise State University >> 1910 University Drive >> Boise, Idaho 83725 >> miguelaguayo at u.boisestate.edu >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman >> .mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c= >> C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4-dJ3Ee_ >> HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbw >> sh1ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> > > > _______________________________________________ > parflow-users mailing listparflow-users at mailman.mines.eduhttps://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > -- > Hoori Ajami > Assistant Professor of Groundwater Hydrology > Department of Environmental Sciences > University of California, Riverside > Room 2322 Geology > Riverside, California 92521 > Office: (951) 827-4778 > E-mail: hoori.ajami at ucr.edu > Web: http://envisci.ucr.edu/faculty/ajami.html > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From smith84 at llnl.gov Thu Oct 20 13:39:39 2016 From: smith84 at llnl.gov (Smith, Steve) Date: Thu, 20 Oct 2016 19:39:39 +0000 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> Message-ID: <399743D90C221740B6399BDE9E58856D0125D0449C@PRDEXMBX-02.the-lab.llnl.gov> The run file is copied from the source directory pfsimulator/amps/mpi1/run to the $PARFLOW_DIR/bin directory when parflow is built. Edit the run script in the source directory should fix the issue with change being removed. Regarding the process failure. Is there an LW.pfidb file present? If so try: $PARFLOW_DIR/bin/parflow LW 1 1 Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Thursday, October 20, 2016 8:31 AM To: ParFlow Users Subject: Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Hello All, I have deleted the word 'function' from the bin/run file. However, when I try to rebuild Parflow and pftools, it returns the 'function' word to the run file I believe. So, I tried to just delete 'function' , then hit ':wq' in vim to write and quit then I tried to 'make check' the test folder, all of the tests passed, it said PASSED ALL. However, I then tried to run the little washita example, but it still resulted in an error. abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW child process exited abnormally while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) I am not sure what does it mean with "child process", since the first line says it countered an error with "run LW 1 1" , I tried to use : tclsh LW_Test.tcl 1 1 1 But it did not make a difference. Can any body please guide me in this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-19 18:31 GMT-04:00 Hoori Ajami >: Hi All, Thanks Nick for your suggestion. Removing the "function" solved my problem with Ubuntu 14.04 and ParFlow 3.2.0. Thanks, Hoori On 10/18/2016 4:19 PM, Anas Rabie wrote: Thank you all for your reply. Prof. Maxwell, yes, I downloaded the newest version, its number is ParFlow Version 3.2.0. Prof. Engdahl, I will try that and will let you know if this works. Thank you all again for your time and guidance. I really appreciate it. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-18 19:07 GMT-04:00 Reed Maxwell >: Hi Anas and all- Thanks for the great replies. Another thought: are you downloading the most recent version of ParFlow from GitHub? I know Steve has updated the build environment / run script for this version. Reed Please excuse the brevity of this message it was sent from my iPhone On Oct 18, 2016, at 5:03 PM, Engdahl, Nick > wrote: Hi Anas (and ALL Ubuntu users should read the last part), The error is probably not in your environment variables, especially if the installation doesn?t indicate any errors. Most likely this error originates in the /bin directory in a script called ?run? (if this folder does not exist, is empty, or has old files, that would indicate an installation error) You?ll need to edit that script to fix this issue. Open the ?run" script in a text editor and near the top of the script you?ll find two functions ?function usage? and ?function pflog? The default interpreter on Ubuntu doesn?t recognize ?function? as a command so just delete the word ?function" from both and rebuild parflow and pftools. This problem has turned up before on Ubuntu and that change has fixed it every time so far. As a caution to other Ubuntu users, older versions of ParFlow did not use these functions and that's why your older installations, following the blog post, worked fine. Unless you have gone to a lot of trouble to change your default interpreter, you will encounter this problem when you update to the latest version of ParFlow since the version on GitHub uses the ?function? syntax. I?ll be updating the installation instructions on the blog soon for both macOS and Ubuntu and this fix will be included. Nick ------------------------------------------------- Nick Engdahl Assistant Professor Civil and Environmental Engineering Washington State University ------------------------------------------------- On Oct 18, 2016, at 11:25 AM, Miguel Aguayo > wrote: Hi Anas, I have Parflow installed in a ubuntu machine and running without any issues for a long time. I remember to follow this link: http://parflow.blogspot.com/search/label/linux to get parflow installed correctly. One thing I may suggest here is to set your environment variables into the bash_aliases file instead bash_profile (As far as I know, Ubuntu doesn't come with any bash_profile unless you create one) Once you do this, then you can source bash_aliases either from bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) Cheers Miguel On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie > wrote: Hello, I still run into some issues. I fixed my .bash_profile file, and now it is as follow: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I type "source ~/.bash_profile" nothing happens. However, I tried to continue with the installation. OpenMPI, SILO, and HYPRE all install successfully without any errors. However, again, in the last step of installing ParFlow, when i type "make check", it gives me this error message: ############################################################################## 0% tests passed, 94 tests failed out of 94 FAILED Tests ############################################################################## I tried to run the little washita example, but this is what happened: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: Syntax error: "(" unexpected while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) However, typing "printenv | grep PARFLOW" shows this: PARFLOW_DIR=/home/abrabie/ParFlow/parflow I think maybe because I am installing it on a local windows machine on Virtual Box and not on a super computer that uses parallel or something. should i change anything in the installation process? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-06 22:52 GMT-04:00 Smith, Steve >: Hi, Apologies, I should have asked for the output of : printenv | grep PARFLOW If you copied and pasted exactly what is below there is a bug since the export PARFLOW_DIR=/home/abrabie/ParFlow/parflow is 2 commands because of a newline and it should be one command: export PARFLOW_DIR=/home/abrabie/ParFlow/parflow Steve From: Anas Rabie [mailto:abrabie at umail.iu.edu] Sent: Thursday, October 06, 2016 7:02 AM To: Smith, Steve Cc: ParFlow Users Subject: Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Hi, Thank you for your reply. Yes I did export Parflow. This is the bash file I used as mentioned in the instructions: export CC=gcc export CXX=g++ export FC=gfortran export F77=gfortran export PARFLOW_DIR=/home/abrabie/ParFlow/parflow export SILO_DIR=/home/abrabie/ParFlow/silo export HYPRE_DIR=/home/abrabie/ParFlow/hypre export PATH=$PATH:/home/abrabie/ParFlow/visit/bin However, when I try the "printenv PARFLOW" nothing happens. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-05 19:40 GMT-04:00 Smith, Steve >: Did you ?export? the PARFLOW variable? What does : printenv PARFLOW report? Errors seem to indicate that scripts are not finding the environment variable. Steve From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of Anas Rabie Sent: Tuesday, October 04, 2016 8:15 AM To: ParFlow Users Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS Greetings, I am trying to install ParFlow on Ubuntu, I followed the instructions in the manual, but I was successful, then I followed what is on the blog http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html and everything was going well until the very last step, cd ../pftools ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 make install cd ../test sudo ldconfig make check When I do that last "make check" it gives me this error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tired "sudo make check" as well, but received the same error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check Makefile:9: /config/Makefile.config: No such file or directory make: *** No rule to make target '/config/Makefile.config'. Stop. I tried to run the Little Washita test to try, but it gave me an error abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl no such variable (read trace on "env(PARFLOW_DIR)") invoked from within "lappend auto_path $env(PARFLOW_DIR)/bin" (file "LW_Test.tcl" line 6) However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in my home directory. so I am not sure what that error means? Can anybody please help me with this? Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -- Miguel Aguayo PhD Candidate - Geosciences Department of Geosciences Environmental Research Building, MS #1535 Boise State University 1910 University Drive Boise, Idaho 83725 miguelaguayo at u.boisestate.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4-dJ3Ee_HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbwsh1ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -- Hoori Ajami Assistant Professor of Groundwater Hydrology Department of Environmental Sciences University of California, Riverside Room 2322 Geology Riverside, California 92521 Office: (951) 827-4778 E-mail: hoori.ajami at ucr.edu Web: http://envisci.ucr.edu/faculty/ajami.html _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From alessandro.comunian at gmail.com Mon Oct 24 08:25:54 2016 From: alessandro.comunian at gmail.com (Alessandro Comunian) Date: Mon, 24 Oct 2016 16:25:54 +0200 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: <399743D90C221740B6399BDE9E58856D0125D0449C@PRDEXMBX-02.the-lab.llnl.gov> References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> <399743D90C221740B6399BDE9E58856D0125D0449C@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Hello, some time ago I installed with success parflow on an Ubuntu 16.04 machine. At the beginning, I also had a similar problem, which I solved (without deleting "function"...) changing the default shell by using something like: dpkg-reconfigure bash to use "bash" instead of the default "dash". Hope this helps, Alessandro On 20/10/2016 21:39, Smith, Steve wrote: > > The run file is copied from the source directory > pfsimulator/amps/mpi1/run to the $PARFLOW_DIR/bin directory when > parflow is built. Edit the run script in the source directory should > fix the issue with change being removed. > > Regarding the process failure. > > Is there an LW.pfidb file present? > > If so try: > > $PARFLOW_DIR/bin/parflow LW 1 1 > > Steve > > *From:*parflow-users-bounces at mailman.mines.edu > [mailto:parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie > *Sent:* Thursday, October 20, 2016 8:31 AM > *To:* ParFlow Users > *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu > 16.04.1 LTS > > Hello All, > > I have deleted the word 'function' from the bin/run file. However, > when I try to rebuild Parflow and pftools, it returns the 'function' > word to the run file I believe. So, I tried to just delete 'function' > , then hit ':wq' in vim to write and quit then I tried to 'make check' > the test folder, all of the tests passed, it said PASSED ALL. > > However, I then tried to run the little washita example, but it still > resulted in an error. > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh > LW_Test.tcl > Files Copied > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > LW > > > child process exited abnormally > while executing > "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" > ("eval" body line 1) > invoked from within > "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" > (procedure "pfrun" line 77) > invoked from within > "pfrun $runname" > (file "LW_Test.tcl" line 512) > > I am not sure what does it mean with "child process", since the first > line says it countered an error with "run LW 1 1" , I tried to use : > > tclsh LW_Test.tcl 1 1 1 > > But it did not make a difference. Can any body please guide me in this? > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > 2016-10-19 18:31 GMT-04:00 Hoori Ajami >: > > Hi All, > > Thanks Nick for your suggestion. Removing the "function" solved my > problem with Ubuntu 14.04 and ParFlow 3.2.0. > > Thanks, > Hoori > > On 10/18/2016 4:19 PM, Anas Rabie wrote: > > Thank you all for your reply. > > Prof. Maxwell, yes, I downloaded the newest version, its > number is ParFlow Version 3.2.0. > > Prof. Engdahl, I will try that and will let you know if this > works. > > Thank you all again for your time and guidance. I really > appreciate it. > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > 2016-10-18 19:07 GMT-04:00 Reed Maxwell >: > > Hi Anas and all- > > Thanks for the great replies. Another thought: are you > downloading the most recent version of ParFlow from > GitHub? I know Steve has updated the build environment / > run script for this version. > > Reed > > Please excuse the brevity of this message it was sent from > my iPhone > > > On Oct 18, 2016, at 5:03 PM, Engdahl, Nick > > wrote: > > Hi Anas (and ALL Ubuntu users should read the last part), > > The error is probably not in your environment > variables, especially if the installation doesn?t > indicate any errors. > > Most likely this error originates in the > /bin directory in a script > called ?run? (if this folder does not exist, is empty, > or has old files, that would indicate an installation > error) > > You?ll need to edit that script to fix this issue. > Open the ?run" script in a text editor and near the > top of the script you?ll find two functions ?function > usage? and ?function pflog? The default interpreter on > Ubuntu doesn?t recognize ?function? as a command so > just delete the word ?function" from both and rebuild > parflow and pftools. This problem has turned up before > on Ubuntu and that change has fixed it every time so far. > > As a caution to other Ubuntu users, older versions of > ParFlow did not use these functions and that's why > your older installations, following the blog post, > worked fine. Unless you have gone to a lot of trouble > to change your default interpreter, you will encounter > this problem when you update to the latest version of > ParFlow since the version on GitHub uses the > ?function? syntax. I?ll be updating the installation > instructions on the blog soon for both macOS and > Ubuntu and this fix will be included. > > Nick > > ------------------------------------------------- > > Nick Engdahl > > Assistant Professor > > Civil and Environmental Engineering > > Washington State University > > ------------------------------------------------- > > On Oct 18, 2016, at 11:25 AM, Miguel Aguayo > > wrote: > > Hi Anas, > > I have Parflow installed in a ubuntu machine and > running without any issues for a long time. I > remember to follow this link: > http://parflow.blogspot.com/search/label/linux > to > get parflow installed correctly. One thing I may > suggest here is to set your environment variables > into the bash_aliases file instead bash_profile > (As far as I know, Ubuntu doesn't come with any > bash_profile unless you create one) Once you do > this, then you can source bash_aliases either from > bashrc or bash_aliases (i.e. source > ~/.bash_aliases or source ~/.bashrc) > > Cheers > > Miguel > > On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie > > wrote: > > Hello, > > I still run into some issues. I fixed my > .bash_profile file, and now it is as follow: > > export CC=gcc > export CXX=g++ > export FC=gfortran > export F77=gfortran > > export PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > export SILO_DIR=/home/abrabie/ParFlow/silo > export HYPRE_DIR=/home/abrabie/ParFlow/hypre > export PATH=$PATH:/home/abrabie/ParFlow/visit/bin > > However, when I type "source ~/.bash_profile" > nothing happens. However, I tried to continue with > the installation. OpenMPI, SILO, and HYPRE all > install successfully without any errors. However, > again, in the last step of installing ParFlow, > when i type "make check", it gives me this error > message: > > > ############################################################################## > > 0% tests passed, 94 tests failed out of 94 > > FAILED Tests > > ############################################################################## > > I tried to run the little washita example, but > this is what happened: > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ > tclsh LW_Test.tcl > Files Copied > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > LW > > > /home/abrabie/ParFlow/parflow/bin/run: 39: > /home/abrabie/ParFlow/parflow/bin/run: Syntax > error: "(" unexpected > while executing > "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" > ("eval" body line 1) > invoked from within > "eval exec sh $Parflow::PARFLOW_DIR/bin/run > $runname $NumProcs $NumNodes" > (procedure "pfrun" line 77) > invoked from within > "pfrun $runname" > (file "LW_Test.tcl" line 512) > > > However, typing "printenv | grep PARFLOW" shows this: > > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > I think maybe because I am installing it on a > local windows machine on Virtual Box and not on a > super computer that uses parallel or something. > should i change anything in the installation process? > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > 2016-10-06 22:52 GMT-04:00 Smith, Steve > >: > > Hi, > > Apologies, I should have asked for the output of : > > printenv | grep PARFLOW > > If you copied and pasted exactly what is below > there is a bug since the > > export > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > is 2 commands because of a newline and it > should be one command: > > export PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > Steve > > *From:*Anas Rabie [mailto:abrabie at umail.iu.edu > ] > *Sent:* Thursday, October 06, 2016 7:02 AM > *To:* Smith, Steve > *Cc:* ParFlow Users > *Subject:* Re: [parflow-users] Issue > installing ParFlow on Ubuntu 16.04.1 LTS > > Hi, > > Thank you for your reply. Yes I did export > Parflow. This is the bash file I used as > mentioned in the instructions: > > export CC=gcc > export CXX=g++ > export FC=gfortran > export F77=gfortran > > export > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > export SILO_DIR=/home/abrabie/ParFlow/silo > export HYPRE_DIR=/home/abrabie/ParFlow/hypre > export > PATH=$PATH:/home/abrabie/ParFlow/visit/bin > > However, when I try the "printenv PARFLOW" > nothing happens. > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > 2016-10-05 19:40 GMT-04:00 Smith, Steve > >: > > Did you ?export? the PARFLOW variable? > What does : > > printenv PARFLOW > > report? > > Errors seem to indicate that scripts are > not finding the environment variable. > > Steve > > *From:*parflow-users-bounces at mailman.mines.edu > > [mailto:parflow-users-bounces at mailman.mines.edu > ] > *On Behalf Of *Anas Rabie > *Sent:* Tuesday, October 04, 2016 8:15 AM > *To:* ParFlow Users > *Subject:* [parflow-users] Issue > installing ParFlow on Ubuntu 16.04.1 LTS > > Greetings, > > I am trying to install ParFlow on Ubuntu, > I followed the instructions in the manual, > but I was successful, then I followed what > is on the blog > > http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html > > > and everything was going well until the > very last step, > > cd ../pftools > > ./configure --prefix=$PARFLOW_DIR > --with-silo=$SILO_DIR --with-amps=mpi1 > > make install > > cd ../test > > sudo ldconfig > > make check > > When I do that last "make check" it gives > me this error: > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ > make check > > Makefile:9: /config/Makefile.config: No > such file or directory > > make: *** No rule to make target > '/config/Makefile.config'. Stop. > > I tired "sudo make check" as well, but > received the same error: > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ > make check > > Makefile:9: /config/Makefile.config: No > such file or directory > > make: *** No rule to make target > '/config/Makefile.config'. Stop. > > I tried to run the Little Washita test to > try, but it gave me an error > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ > tclsh LW_Test.tcl > no such variable > (read trace on "env(PARFLOW_DIR)") > invoked from within > "lappend auto_path $env(PARFLOW_DIR)/bin" > (file "LW_Test.tcl" line 6) > > However, when I try cd $PARFLOW_DIR it > takes me to the parflow folder in my home > directory. so I am not sure what that > error means? > > Can anybody please help me with this? > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > > https://mailman.mines.edu/mailman/listinfo/parflow-users > > Unsubscribe: > parflow-users-unsubscribe at mailman.mines.edu > > > > > -- > > Miguel Aguayo > > PhD Candidate - Geosciences > > Department of Geosciences > Environmental Research Building, MS #1535 > Boise State University > 1910 University Drive > Boise, Idaho 83725 > > miguelaguayo at u.boisestate.edu > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4-dJ3Ee_HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbwsh1ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= > > Unsubscribe: > parflow-users-unsubscribe at mailman.mines.edu > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: > parflow-users-unsubscribe at mailman.mines.edu > > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > _______________________________________________ > > parflow-users mailing list > > parflow-users at mailman.mines.edu > > > https://mailman.mines.edu/mailman/listinfo/parflow-users > > Unsubscribe:parflow-users-unsubscribe at mailman.mines.edu > > > -- > > Hoori Ajami > > Assistant Professor of Groundwater Hydrology > > Department of Environmental Sciences > > University of California, Riverside > > Room 2322 Geology > > Riverside, California 92521 > > Office: (951) 827-4778 > > E-mail: hoori.ajami at ucr.edu > > Web: http://envisci.ucr.edu/faculty/ajami.html > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Mon Oct 24 13:57:20 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Mon, 24 Oct 2016 15:57:20 -0400 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> <399743D90C221740B6399BDE9E58856D0125D0449C@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Hello All, Thank you for all the replies. However, ParFlow still did not work for me. I tried to remove the word 'function' from 'pfsimulator/amps/mpi1/run' and then reinstalled everything following the blog post, all test check passed successfully but still I face the same error when I try to run Little Washita example. abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW child process exited abnormally while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) Since the LW.pfidb exists after the error, I tried '$PARFLOW_DIR/bin/parflow LW 1 1' but I received the following error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts/Outputs$ $PARFLOW_DIR/bin/parflow LW 1 1 Node 0: Using process grid (1,1,1) Node 0: Well Information Node 0: No Wells. Node 0: Error: can't open input file ../../NLDAS//NLDAS.DSWR.000001_to_000024.pfb I tried one of the suggestions as well to change the default dash to bash, this was the message: abrabie at Anas-Ubuntu:~$ sudo dpkg-reconfigure bash [sudo] password for abrabie: update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode I re-built ParFlow, and the same thing happened. I even tried to return the 'function' word to the 'run' file, but that did not change anything. Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-24 10:25 GMT-04:00 Alessandro Comunian < alessandro.comunian at gmail.com>: > Hello, > > some time ago I installed with success parflow on an Ubuntu 16.04 machine. > At the beginning, I also had a similar problem, which I solved (without > deleting "function"...) changing the default shell by using something like: > > dpkg-reconfigure bash > > to use "bash" instead of the default "dash". > > Hope this helps, > > Alessandro > > > > > On 20/10/2016 21:39, Smith, Steve wrote: > > The run file is copied from the source directory pfsimulator/amps/mpi1/run > to the $PARFLOW_DIR/bin directory when parflow is built. Edit the run > script in the source directory should fix the issue with change being > removed. > > > > Regarding the process failure. > > > > Is there an LW.pfidb file present? > > > > If so try: > > > > $PARFLOW_DIR/bin/parflow LW 1 1 > > > > Steve > > > > *From:* parflow-users-bounces at mailman.mines.edu [ > mailto:parflow-users-bounces at mailman.mines.edu > ] *On Behalf Of *Anas Rabie > *Sent:* Thursday, October 20, 2016 8:31 AM > *To:* ParFlow Users > *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 > LTS > > > > Hello All, > > > > I have deleted the word 'function' from the bin/run file. However, when I > try to rebuild Parflow and pftools, it returns the 'function' word to the > run file I believe. So, I tried to just delete 'function' , then hit ':wq' > in vim to write and quit then I tried to 'make check' the test folder, all > of the tests passed, it said PASSED ALL. > > > > However, I then tried to run the little washita example, but it still > resulted in an error. > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh > LW_Test.tcl > Files Copied > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > LW > > > child process exited abnormally > while executing > "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" > ("eval" body line 1) > invoked from within > "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" > (procedure "pfrun" line 77) > invoked from within > "pfrun $runname" > (file "LW_Test.tcl" line 512) > > I am not sure what does it mean with "child process", since the first line > says it countered an error with "run LW 1 1" , I tried to use : > > tclsh LW_Test.tcl 1 1 1 > > But it did not make a difference. Can any body please guide me in this? > > > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > > > > > > 2016-10-19 18:31 GMT-04:00 Hoori Ajami : > > Hi All, > > Thanks Nick for your suggestion. Removing the "function" solved my problem > with Ubuntu 14.04 and ParFlow 3.2.0. > > Thanks, > Hoori > > > > On 10/18/2016 4:19 PM, Anas Rabie wrote: > > Thank you all for your reply. > > > > Prof. Maxwell, yes, I downloaded the newest version, its number is ParFlow > Version 3.2.0. > > > > Prof. Engdahl, I will try that and will let you know if this works. > > > > Thank you all again for your time and guidance. I really appreciate it. > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > > > > > > 2016-10-18 19:07 GMT-04:00 Reed Maxwell : > > Hi Anas and all- > > > > Thanks for the great replies. Another thought: are you downloading the > most recent version of ParFlow from GitHub? I know Steve has updated the > build environment / run script for this version. > > > > Reed > > Please excuse the brevity of this message it was sent from my iPhone > > > On Oct 18, 2016, at 5:03 PM, Engdahl, Nick wrote: > > Hi Anas (and ALL Ubuntu users should read the last part), > > The error is probably not in your environment variables, especially if the > installation doesn?t indicate any errors. > > > > Most likely this error originates in the /bin > directory in a script called ?run? (if this folder does not exist, is > empty, or has old files, that would indicate an installation error) > > You?ll need to edit that script to fix this issue. Open the ?run" script > in a text editor and near the top of the script you?ll find two functions > ?function usage? and ?function pflog? The default interpreter on Ubuntu > doesn?t recognize ?function? as a command so just delete the word > ?function" from both and rebuild parflow and pftools. This problem has > turned up before on Ubuntu and that change has fixed it every time so far. > > > > As a caution to other Ubuntu users, older versions of ParFlow did not use > these functions and that's why your older installations, following the blog > post, worked fine. Unless you have gone to a lot of trouble to change your > default interpreter, you will encounter this problem when you update to the > latest version of ParFlow since the version on GitHub uses the ?function? > syntax. I?ll be updating the installation instructions on the blog soon for > both macOS and Ubuntu and this fix will be included. > > > > Nick > > > > ------------------------------------------------- > > Nick Engdahl > > Assistant Professor > > Civil and Environmental Engineering > > Washington State University > > ------------------------------------------------- > > > > > > On Oct 18, 2016, at 11:25 AM, Miguel Aguayo > wrote: > > > > Hi Anas, > > > > I have Parflow installed in a ubuntu machine and running without any > issues for a long time. I remember to follow this link: > http://parflow.blogspot.com/search/label/linux > to > get parflow installed correctly. One thing I may suggest here is to set > your environment variables into the bash_aliases file instead bash_profile > (As far as I know, Ubuntu doesn't come with any bash_profile unless you > create one) Once you do this, then you can source bash_aliases either from > bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) > > > > Cheers > > > > > > Miguel > > > > > > > > > > On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie wrote: > > Hello, > > I still run into some issues. I fixed my .bash_profile file, and now it is > as follow: > > export CC=gcc > export CXX=g++ > export FC=gfortran > export F77=gfortran > > export PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > export SILO_DIR=/home/abrabie/ParFlow/silo > export HYPRE_DIR=/home/abrabie/ParFlow/hypre > export PATH=$PATH:/home/abrabie/ParFlow/visit/bin > > However, when I type "source ~/.bash_profile" nothing happens. However, I > tried to continue with the installation. OpenMPI, SILO, and HYPRE all > install successfully without any errors. However, again, in the last step > of installing ParFlow, when i type "make check", it gives me this error > message: > > > ############################################################ > ################## > > 0% tests passed, 94 tests failed out of 94 > > FAILED Tests > > ############################################################ > ################## > > I tried to run the little washita example, but this is what happened: > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh > LW_Test.tcl > Files Copied > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > LW > > > /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: > Syntax error: "(" unexpected > while executing > "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" > ("eval" body line 1) > invoked from within > "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" > (procedure "pfrun" line 77) > invoked from within > "pfrun $runname" > (file "LW_Test.tcl" line 512) > > > However, typing "printenv | grep PARFLOW" shows this: > > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > I think maybe because I am installing it on a local windows machine on > Virtual Box and not on a super computer that uses parallel or something. > should i change anything in the installation process? > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > > > > > > 2016-10-06 22:52 GMT-04:00 Smith, Steve : > > Hi, > > > > Apologies, I should have asked for the output of : > > > > printenv | grep PARFLOW > > > > If you copied and pasted exactly what is below there is a bug since the > > > > export > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > > > is 2 commands because of a newline and it should be one command: > > > > export PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > > > Steve > > > > > > *From:* Anas Rabie [mailto:abrabie at umail.iu.edu] > *Sent:* Thursday, October 06, 2016 7:02 AM > *To:* Smith, Steve > *Cc:* ParFlow Users > *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 > LTS > > > > Hi, > > Thank you for your reply. Yes I did export Parflow. This is the bash file > I used as mentioned in the instructions: > > export CC=gcc > export CXX=g++ > export FC=gfortran > export F77=gfortran > > export > PARFLOW_DIR=/home/abrabie/ParFlow/parflow > > export SILO_DIR=/home/abrabie/ParFlow/silo > export HYPRE_DIR=/home/abrabie/ParFlow/hypre > export > PATH=$PATH:/home/abrabie/ParFlow/visit/bin > > However, when I try the "printenv PARFLOW" nothing happens. > > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > > > > > > 2016-10-05 19:40 GMT-04:00 Smith, Steve : > > Did you ?export? the PARFLOW variable? What does : > > > > printenv PARFLOW > > > > report? > > > > Errors seem to indicate that scripts are not finding the environment > variable. > > > > Steve > > > > > > *From:* parflow-users-bounces at mailman.mines.edu [mailto: > parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie > *Sent:* Tuesday, October 04, 2016 8:15 AM > *To:* ParFlow Users > *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS > > > > Greetings, > > > > I am trying to install ParFlow on Ubuntu, I followed the instructions in > the manual, but I was successful, then I followed what is on the blog > > http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html > > > and everything was going well until the very last step, > > > > cd ../pftools > > ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 > > make install > > cd ../test > > sudo ldconfig > > make check > > > > When I do that last "make check" it gives me this error: > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check > > Makefile:9: /config/Makefile.config: No such file or directory > > make: *** No rule to make target '/config/Makefile.config'. Stop. > > > > I tired "sudo make check" as well, but received the same error: > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check > > Makefile:9: /config/Makefile.config: No such file or directory > > make: *** No rule to make target '/config/Makefile.config'. Stop. > > > > I tried to run the Little Washita test to try, but it gave me an error > > > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh > LW_Test.tcl > no such variable > (read trace on "env(PARFLOW_DIR)") > invoked from within > "lappend auto_path $env(PARFLOW_DIR)/bin" > (file "LW_Test.tcl" line 6) > > However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in > my home directory. so I am not sure what that error means? > > > > Can anybody please help me with this? > > > Best, > > Anas B. Rabie > > -==-==-==-==-==-==-==- > > Ph.D. Student in Hydrogeology > > Department of Geological Sciences > > > > > > > > > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > > > > -- > > Miguel Aguayo > > PhD Candidate - Geosciences > > Department of Geosciences > Environmental Research Building, MS #1535 > Boise State University > 1910 University Drive > Boise, Idaho 83725 > > miguelaguayo at u.boisestate.edu > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__ > mailman.mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c=C3yme8gMkxg_ > ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4- > dJ3Ee_HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbwsh1 > ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > > > > _______________________________________________ > > parflow-users mailing list > > parflow-users at mailman.mines.edu > > https://mailman.mines.edu/mailman/listinfo/parflow-users > > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > > -- > > Hoori Ajami > > Assistant Professor of Groundwater Hydrology > > Department of Environmental Sciences > > University of California, Riverside > > Room 2322 Geology > > Riverside, California 92521 > > Office: (951) 827-4778 > > E-mail: hoori.ajami at ucr.edu > > Web: http://envisci.ucr.edu/faculty/ajami.html > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > > > _______________________________________________ > parflow-users mailing listparflow-users at mailman.mines.eduhttps://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > > > _______________________________________________ > parflow-users mailing list > parflow-users at mailman.mines.edu > https://mailman.mines.edu/mailman/listinfo/parflow-users > Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abrabie at umail.iu.edu Tue Nov 1 08:28:36 2016 From: abrabie at umail.iu.edu (Anas Rabie) Date: Tue, 1 Nov 2016 10:28:36 -0400 Subject: [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS In-Reply-To: References: <399743D90C221740B6399BDE9E58856DD4BF2097@PRDEXMBX-02.the-lab.llnl.gov> <399743D90C221740B6399BDE9E58856DD4BF2B25@PRDEXMBX-02.the-lab.llnl.gov> <31455B37-E968-4A90-A75D-8B424BD493C4@mines.edu> <399743D90C221740B6399BDE9E58856D0125D0449C@PRDEXMBX-02.the-lab.llnl.gov> Message-ID: Hello All, I am still stuck at this and I don't know how to fix it. I tried to delete the virtual drive and create a new one and install everything from the beginning with the word 'function' removed. I am still facing the same issue. All test would pass but Little Washita example would lead to the same error. abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh LW_Test.tcl Files Copied Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) Using process grid (1,1,1) LW child process exited abnormally while executing "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" ("eval" body line 1) invoked from within "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" (procedure "pfrun" line 77) invoked from within "pfrun $runname" (file "LW_Test.tcl" line 512) Since the LW.pfidb exists after the error, I tried '$PARFLOW_DIR/bin/parflow LW 1 1' but I received the following error: abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts/Outputs$ $PARFLOW_DIR/bin/parflow LW 1 1 Node 0: Using process grid (1,1,1) Node 0: Well Information Node 0: No Wells. Node 0: Error: can't open input file ../../NLDAS//NLDAS.DSWR. 000001_to_000024.pfb Best, Anas B. Rabie -==-==-==-==-==-==-==- Ph.D. Student in Hydrogeology Department of Geological Sciences 2016-10-24 15:57 GMT-04:00 Anas Rabie : > Hello All, > > Thank you for all the replies. However, ParFlow still did not work for me. > > I tried to remove the word 'function' from 'pfsimulator/amps/mpi1/run' and > then reinstalled everything following the blog post, all test check passed > successfully but still I face the same error when I try to run Little > Washita example. > > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh > LW_Test.tcl > Files Copied > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > Using process grid (1,1,1) > LW > > > child process exited abnormally > while executing > "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" > ("eval" body line 1) > invoked from within > "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" > (procedure "pfrun" line 77) > invoked from within > "pfrun $runname" > (file "LW_Test.tcl" line 512) > > > Since the LW.pfidb exists after the error, I tried > '$PARFLOW_DIR/bin/parflow LW 1 1' but I received the following error: > abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts/Outputs$ > $PARFLOW_DIR/bin/parflow LW 1 1 > Node 0: Using process grid (1,1,1) > Node 0: Well Information > Node 0: No Wells. > Node 0: Error: can't open input file ../../NLDAS//NLDAS.DSWR. > 000001_to_000024.pfb > > I tried one of the suggestions as well to change the default dash to bash, > this was the message: > abrabie at Anas-Ubuntu:~$ sudo dpkg-reconfigure bash > [sudo] password for abrabie: > update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to > provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode > > I re-built ParFlow, and the same thing happened. I even tried to return > the 'function' word to the 'run' file, but that did not change anything. > > > > > Best, > Anas B. Rabie > -==-==-==-==-==-==-==- > Ph.D. Student in Hydrogeology > Department of Geological Sciences > > > > 2016-10-24 10:25 GMT-04:00 Alessandro Comunian < > alessandro.comunian at gmail.com>: > >> Hello, >> >> some time ago I installed with success parflow on an Ubuntu 16.04 >> machine. At the beginning, I also had a similar problem, which I solved >> (without deleting "function"...) changing the default shell by using >> something like: >> >> dpkg-reconfigure bash >> >> to use "bash" instead of the default "dash". >> >> Hope this helps, >> >> Alessandro >> >> >> >> >> On 20/10/2016 21:39, Smith, Steve wrote: >> >> The run file is copied from the source directory >> pfsimulator/amps/mpi1/run to the $PARFLOW_DIR/bin directory when parflow is >> built. Edit the run script in the source directory should fix the issue >> with change being removed. >> >> >> >> Regarding the process failure. >> >> >> >> Is there an LW.pfidb file present? >> >> >> >> If so try: >> >> >> >> $PARFLOW_DIR/bin/parflow LW 1 1 >> >> >> >> Steve >> >> >> >> *From:* parflow-users-bounces at mailman.mines.edu [ >> mailto:parflow-users-bounces at mailman.mines.edu >> ] *On Behalf Of *Anas Rabie >> *Sent:* Thursday, October 20, 2016 8:31 AM >> *To:* ParFlow Users >> *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu >> 16.04.1 LTS >> >> >> >> Hello All, >> >> >> >> I have deleted the word 'function' from the bin/run file. However, when I >> try to rebuild Parflow and pftools, it returns the 'function' word to the >> run file I believe. So, I tried to just delete 'function' , then hit ':wq' >> in vim to write and quit then I tried to 'make check' the test folder, all >> of the tests passed, it said PASSED ALL. >> >> >> >> However, I then tried to run the little washita example, but it still >> resulted in an error. >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >> LW_Test.tcl >> Files Copied >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> LW >> >> >> child process exited abnormally >> while executing >> "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" >> ("eval" body line 1) >> invoked from within >> "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" >> (procedure "pfrun" line 77) >> invoked from within >> "pfrun $runname" >> (file "LW_Test.tcl" line 512) >> >> I am not sure what does it mean with "child process", since the first >> line says it countered an error with "run LW 1 1" , I tried to use : >> >> tclsh LW_Test.tcl 1 1 1 >> >> But it did not make a difference. Can any body please guide me in this? >> >> >> >> >> >> Best, >> >> Anas B. Rabie >> >> -==-==-==-==-==-==-==- >> >> Ph.D. Student in Hydrogeology >> >> Department of Geological Sciences >> >> >> >> >> >> >> >> 2016-10-19 18:31 GMT-04:00 Hoori Ajami : >> >> Hi All, >> >> Thanks Nick for your suggestion. Removing the "function" solved my >> problem with Ubuntu 14.04 and ParFlow 3.2.0. >> >> Thanks, >> Hoori >> >> >> >> On 10/18/2016 4:19 PM, Anas Rabie wrote: >> >> Thank you all for your reply. >> >> >> >> Prof. Maxwell, yes, I downloaded the newest version, its number is >> ParFlow Version 3.2.0. >> >> >> >> Prof. Engdahl, I will try that and will let you know if this works. >> >> >> >> Thank you all again for your time and guidance. I really appreciate it. >> >> >> >> Best, >> >> Anas B. Rabie >> >> -==-==-==-==-==-==-==- >> >> Ph.D. Student in Hydrogeology >> >> Department of Geological Sciences >> >> >> >> >> >> >> >> 2016-10-18 19:07 GMT-04:00 Reed Maxwell : >> >> Hi Anas and all- >> >> >> >> Thanks for the great replies. Another thought: are you downloading the >> most recent version of ParFlow from GitHub? I know Steve has updated the >> build environment / run script for this version. >> >> >> >> Reed >> >> Please excuse the brevity of this message it was sent from my iPhone >> >> >> On Oct 18, 2016, at 5:03 PM, Engdahl, Nick wrote: >> >> Hi Anas (and ALL Ubuntu users should read the last part), >> >> The error is probably not in your environment variables, especially if >> the installation doesn?t indicate any errors. >> >> >> >> Most likely this error originates in the /bin >> directory in a script called ?run? (if this folder does not exist, is >> empty, or has old files, that would indicate an installation error) >> >> You?ll need to edit that script to fix this issue. Open the ?run" script >> in a text editor and near the top of the script you?ll find two functions >> ?function usage? and ?function pflog? The default interpreter on Ubuntu >> doesn?t recognize ?function? as a command so just delete the word >> ?function" from both and rebuild parflow and pftools. This problem has >> turned up before on Ubuntu and that change has fixed it every time so far. >> >> >> >> As a caution to other Ubuntu users, older versions of ParFlow did not use >> these functions and that's why your older installations, following the blog >> post, worked fine. Unless you have gone to a lot of trouble to change your >> default interpreter, you will encounter this problem when you update to the >> latest version of ParFlow since the version on GitHub uses the ?function? >> syntax. I?ll be updating the installation instructions on the blog soon for >> both macOS and Ubuntu and this fix will be included. >> >> >> >> Nick >> >> >> >> ------------------------------------------------- >> >> Nick Engdahl >> >> Assistant Professor >> >> Civil and Environmental Engineering >> >> Washington State University >> >> ------------------------------------------------- >> >> >> >> >> >> On Oct 18, 2016, at 11:25 AM, Miguel Aguayo < >> miguelaguayo at u.boisestate.edu> wrote: >> >> >> >> Hi Anas, >> >> >> >> I have Parflow installed in a ubuntu machine and running without any >> issues for a long time. I remember to follow this link: >> http://parflow.blogspot.com/search/label/linux >> to >> get parflow installed correctly. One thing I may suggest here is to set >> your environment variables into the bash_aliases file instead bash_profile >> (As far as I know, Ubuntu doesn't come with any bash_profile unless you >> create one) Once you do this, then you can source bash_aliases either from >> bashrc or bash_aliases (i.e. source ~/.bash_aliases or source ~/.bashrc) >> >> >> >> Cheers >> >> >> >> >> >> Miguel >> >> >> >> >> >> >> >> >> >> On Tue, Oct 18, 2016 at 11:46 AM, Anas Rabie >> wrote: >> >> Hello, >> >> I still run into some issues. I fixed my .bash_profile file, and now it >> is as follow: >> >> export CC=gcc >> export CXX=g++ >> export FC=gfortran >> export F77=gfortran >> >> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> export SILO_DIR=/home/abrabie/ParFlow/silo >> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >> export PATH=$PATH:/home/abrabie/ParFlow/visit/bin >> >> However, when I type "source ~/.bash_profile" nothing happens. However, I >> tried to continue with the installation. OpenMPI, SILO, and HYPRE all >> install successfully without any errors. However, again, in the last step >> of installing ParFlow, when i type "make check", it gives me this error >> message: >> >> >> ############################################################ >> ################## >> >> 0% tests passed, 94 tests failed out of 94 >> >> FAILED Tests >> >> ############################################################ >> ################## >> >> I tried to run the little washita example, but this is what happened: >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >> LW_Test.tcl >> Files Copied >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> Using process grid (1,1,1) >> LW >> >> >> /home/abrabie/ParFlow/parflow/bin/run: 39: /home/abrabie/ParFlow/parflow/bin/run: >> Syntax error: "(" unexpected >> while executing >> "exec sh /home/abrabie/ParFlow/parflow/bin/run LW 1 1" >> ("eval" body line 1) >> invoked from within >> "eval exec sh $Parflow::PARFLOW_DIR/bin/run $runname $NumProcs $NumNodes" >> (procedure "pfrun" line 77) >> invoked from within >> "pfrun $runname" >> (file "LW_Test.tcl" line 512) >> >> >> However, typing "printenv | grep PARFLOW" shows this: >> >> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> I think maybe because I am installing it on a local windows machine on >> Virtual Box and not on a super computer that uses parallel or something. >> should i change anything in the installation process? >> >> >> >> Best, >> >> Anas B. Rabie >> >> -==-==-==-==-==-==-==- >> >> Ph.D. Student in Hydrogeology >> >> Department of Geological Sciences >> >> >> >> >> >> >> >> 2016-10-06 22:52 GMT-04:00 Smith, Steve : >> >> Hi, >> >> >> >> Apologies, I should have asked for the output of : >> >> >> >> printenv | grep PARFLOW >> >> >> >> If you copied and pasted exactly what is below there is a bug since the >> >> >> >> export >> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> >> >> is 2 commands because of a newline and it should be one command: >> >> >> >> export PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> >> >> Steve >> >> >> >> >> >> *From:* Anas Rabie [mailto:abrabie at umail.iu.edu] >> *Sent:* Thursday, October 06, 2016 7:02 AM >> *To:* Smith, Steve >> *Cc:* ParFlow Users >> *Subject:* Re: [parflow-users] Issue installing ParFlow on Ubuntu >> 16.04.1 LTS >> >> >> >> Hi, >> >> Thank you for your reply. Yes I did export Parflow. This is the bash file >> I used as mentioned in the instructions: >> >> export CC=gcc >> export CXX=g++ >> export FC=gfortran >> export F77=gfortran >> >> export >> PARFLOW_DIR=/home/abrabie/ParFlow/parflow >> >> export SILO_DIR=/home/abrabie/ParFlow/silo >> export HYPRE_DIR=/home/abrabie/ParFlow/hypre >> export >> PATH=$PATH:/home/abrabie/ParFlow/visit/bin >> >> However, when I try the "printenv PARFLOW" nothing happens. >> >> >> >> Best, >> >> Anas B. Rabie >> >> -==-==-==-==-==-==-==- >> >> Ph.D. Student in Hydrogeology >> >> Department of Geological Sciences >> >> >> >> >> >> >> >> 2016-10-05 19:40 GMT-04:00 Smith, Steve : >> >> Did you ?export? the PARFLOW variable? What does : >> >> >> >> printenv PARFLOW >> >> >> >> report? >> >> >> >> Errors seem to indicate that scripts are not finding the environment >> variable. >> >> >> >> Steve >> >> >> >> >> >> *From:* parflow-users-bounces at mailman.mines.edu [mailto: >> parflow-users-bounces at mailman.mines.edu] *On Behalf Of *Anas Rabie >> *Sent:* Tuesday, October 04, 2016 8:15 AM >> *To:* ParFlow Users >> *Subject:* [parflow-users] Issue installing ParFlow on Ubuntu 16.04.1 LTS >> >> >> >> Greetings, >> >> >> >> I am trying to install ParFlow on Ubuntu, I followed the instructions in >> the manual, but I was successful, then I followed what is on the blog >> >> http://parflow.blogspot.com/2010/03/running-parflow-on-windows-using.html >> >> >> and everything was going well until the very last step, >> >> >> >> cd ../pftools >> >> ./configure --prefix=$PARFLOW_DIR --with-silo=$SILO_DIR --with-amps=mpi1 >> >> make install >> >> cd ../test >> >> sudo ldconfig >> >> make check >> >> >> >> When I do that last "make check" it gives me this error: >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >> >> Makefile:9: /config/Makefile.config: No such file or directory >> >> make: *** No rule to make target '/config/Makefile.config'. Stop. >> >> >> >> I tired "sudo make check" as well, but received the same error: >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test$ make check >> >> Makefile:9: /config/Makefile.config: No such file or directory >> >> make: *** No rule to make target '/config/Makefile.config'. Stop. >> >> >> >> I tried to run the Little Washita test to try, but it gave me an error >> >> >> >> abrabie at Anas-Ubuntu:~/ParFlow/parflow/test/washita/tcl_scripts$ tclsh >> LW_Test.tcl >> no such variable >> (read trace on "env(PARFLOW_DIR)") >> invoked from within >> "lappend auto_path $env(PARFLOW_DIR)/bin" >> (file "LW_Test.tcl" line 6) >> >> However, when I try cd $PARFLOW_DIR it takes me to the parflow folder in >> my home directory. so I am not sure what that error means? >> >> >> >> Can anybody please help me with this? >> >> >> Best, >> >> Anas B. Rabie >> >> -==-==-==-==-==-==-==- >> >> Ph.D. Student in Hydrogeology >> >> Department of Geological Sciences >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> >> >> >> -- >> >> Miguel Aguayo >> >> PhD Candidate - Geosciences >> >> Department of Geosciences >> Environmental Research Building, MS #1535 >> Boise State University >> 1910 University Drive >> Boise, Idaho 83725 >> >> miguelaguayo at u.boisestate.edu >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman >> .mines.edu_mailman_listinfo_parflow-2Dusers&d=DQICAg&c= >> C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=eY8TwA47EbLeEsz4-dJ3Ee_ >> HC0FiyPm-lFG-Wwxoo3s&m=ff3of3XfC-JKfy6NM5zkekxVYtWemNnisZRbw >> sh1ASo&s=UMsunZ_swbJv31rKVbLYIgkVZ9CEreUUpPjPjnvEL7g&e= >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> >> >> >> _______________________________________________ >> >> parflow-users mailing list >> >> parflow-users at mailman.mines.edu >> >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> >> -- >> >> Hoori Ajami >> >> Assistant Professor of Groundwater Hydrology >> >> Department of Environmental Sciences >> >> University of California, Riverside >> >> Room 2322 Geology >> >> Riverside, California 92521 >> >> Office: (951) 827-4778 >> >> E-mail: hoori.ajami at ucr.edu >> >> Web: http://envisci.ucr.edu/faculty/ajami.html >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> >> >> _______________________________________________ >> parflow-users mailing listparflow-users at mailman.mines.eduhttps://mailman.mines.edu/mailman/listinfo/parflow-users >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> >> >> _______________________________________________ >> parflow-users mailing list >> parflow-users at mailman.mines.edu >> https://mailman.mines.edu/mailman/listinfo/parflow-users >> Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AWunsch at leppertassociates.com Tue Nov 8 16:40:19 2016 From: AWunsch at leppertassociates.com (AWunsch) Date: Tue, 8 Nov 2016 23:40:19 +0000 Subject: [parflow-users] Failed Parflow tests Message-ID: Hi everyone, I found the recent discussion, started by Anas Rabie, really useful. I followed Nick's advice regarding removal of the "function" text from the "bin/run" file, and as a first pass Parflow 3.2.0 appears to work on an Ubuntu 14.04. When I ran the tests, 18 of the 94 tests did not pass: clm_forc_veg.tcl on 4 1 1 clm_forc_veg.tcl on 1 4 1 clm_forc_veg.tcl on 3 3 1 clm_forc_veg.tcl on 2 2 1 clm_forc_veg.tcl on 2 1 1 clm_forc_veg.tcl on 1 2 1 LW_var_dz_spinup.tcl 4 1 1 LW_var_dz_spinup.tcl 1 4 1 LW_var_dz_spinup.tcl 2 1 1 LW_var_dz_spinup.tcl 1 2 1 LW_var_dz.tcl 4 1 1 LW_var_dz.tcl 1 4 1 LW_var_dz.tcl 2 1 1 LW_var_dz.tcl 1 2 1 clm_forc_veg.tcl 1 1 1 indicator_field.tcl LW_var_dz_spinup.tcl LW_var_dz.tcl Is this something to be worried about? Would these failures indicated a specific symptom? Thanks, Assaf Wunsch Hydrogeologist / Project Manager Leppert Associates 1422 Washington Ave. Golden, CO 80401 P: (303) 216-2428 F: (303) 216-1419 www.leppertassociates.com [LeppertLogo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 2751 bytes Desc: image001.jpg URL: From AWunsch at leppertassociates.com Mon Nov 14 09:47:09 2016 From: AWunsch at leppertassociates.com (AWunsch) Date: Mon, 14 Nov 2016 16:47:09 +0000 Subject: [parflow-users] Failed Parflow tests In-Reply-To: References: Message-ID: I think I managed to zoom in on the cause of the test failures. The symptoms for run failures appear to be related to the sequential-io not running properly. Symptoms are: - Slope and manning files, in PFB format, are completely deleted during run. - Instead, files with extensions *.pfb.00000 appear - Log.txt says "AMPS Error: Can't open the distribution file XSLOPE.pfb.dist for reading". When I installed pftools I did not use the "-with-amps-sequential-io" flag because I was following some older instructions (I did included this flag in the Parflow installation). Then I recalled an old post to this forum from Reed and re-installed pftools with this flag, but to no avail. My questions are therefore: 1. Is there some sort of a clean "uninstall" that I need to apply to pftools prior to re-installation, or does a new installation (following a new configure that includes the sequential-io) simply overwrites the previous? 2. Is there a log file where I can see whether the sequential-io was configured / installed correctly? Thanks! Assaf From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of AWunsch Sent: Tuesday, November 08, 2016 4:40 PM To: parflow-users at mailman.mines.edu Subject: [parflow-users] Failed Parflow tests This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing Feedback Hi everyone, I found the recent discussion, started by Anas Rabie, really useful. I followed Nick's advice regarding removal of the "function" text from the "bin/run" file, and as a first pass Parflow 3.2.0 appears to work on an Ubuntu 14.04. When I ran the tests, 18 of the 94 tests did not pass: clm_forc_veg.tcl on 4 1 1 clm_forc_veg.tcl on 1 4 1 clm_forc_veg.tcl on 3 3 1 clm_forc_veg.tcl on 2 2 1 clm_forc_veg.tcl on 2 1 1 clm_forc_veg.tcl on 1 2 1 LW_var_dz_spinup.tcl 4 1 1 LW_var_dz_spinup.tcl 1 4 1 LW_var_dz_spinup.tcl 2 1 1 LW_var_dz_spinup.tcl 1 2 1 LW_var_dz.tcl 4 1 1 LW_var_dz.tcl 1 4 1 LW_var_dz.tcl 2 1 1 LW_var_dz.tcl 1 2 1 clm_forc_veg.tcl 1 1 1 indicator_field.tcl LW_var_dz_spinup.tcl LW_var_dz.tcl Is this something to be worried about? Would these failures indicated a specific symptom? Thanks, Assaf Wunsch Hydrogeologist / Project Manager Leppert Associates 1422 Washington Ave. Golden, CO 80401 P: (303) 216-2428 F: (303) 216-1419 www.leppertassociates.com [LeppertLogo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 2751 bytes Desc: image001.jpg URL: From AWunsch at leppertassociates.com Tue Nov 15 11:46:33 2016 From: AWunsch at leppertassociates.com (AWunsch) Date: Tue, 15 Nov 2016 18:46:33 +0000 Subject: [parflow-users] Failed Parflow tests In-Reply-To: References: Message-ID: Some updates: I previously had success working with version .693, so I figured I'll give it a shot and see if it runs. From previous posts I understood that several versions of Parflow can exist side-by-side, as long as they are in separate directories and as long as the $PARFLOW_DIR environment variable is set to the directory of the version that is currently active. The only hiccup I encountered during installation of version .693 was that pftools would not configure properly because it could not find TCL installed under /usr or /usr/local. I poked around in the pftools configure file, and discovered that version .693 was only looking for TCL versions 8.4 and 8.5, and assumed that if none are present that no TCL is present. I have the latest TCL version on my machine, which is 8.6. The fix was to modify the pftools configure file - I basically replaced every instance of "8.4" with "8.6". I noticed, also, that version 3.2.0 of Parflow does look for version 8.6 of TCL, which is why this issue has not come up before. I also implemented corrections to the Makefile.config files - these are already included in Nick's blog post from October 18, 2014. The make check of version .693 worked well - default_richards.tcl on 1 1 4 was the only test that did not pass, because of computed-vs-"correct" value discrepancies. Also, it appears that at least one pfb.dist file (associated with LW_var_dz_spinup) was generated, which to my understanding means that the sequential-io option is working correctly. This is compared to 18 tests that failed with version 3.2.0, and no successful generation of pfb.dist files with version 3.2.0. Also, I noticed that the some files on GitHub were modified 4 days ago, but they are not yet incorporated into the release package of version 3.2.0. Are these potential fixes to the sequential-io problem? Or could the problem still be on my side? Cheers, Assaf From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of AWunsch Sent: Monday, November 14, 2016 9:47 AM To: ParFlow Users Subject: Re: [parflow-users] Failed Parflow tests This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing Feedback I think I managed to zoom in on the cause of the test failures. The symptoms for run failures appear to be related to the sequential-io not running properly. Symptoms are: - Slope and manning files, in PFB format, are completely deleted during run. - Instead, files with extensions *.pfb.00000 appear - Log.txt says "AMPS Error: Can't open the distribution file XSLOPE.pfb.dist for reading". When I installed pftools I did not use the "-with-amps-sequential-io" flag because I was following some older instructions (I did included this flag in the Parflow installation). Then I recalled an old post to this forum from Reed and re-installed pftools with this flag, but to no avail. My questions are therefore: 1. Is there some sort of a clean "uninstall" that I need to apply to pftools prior to re-installation, or does a new installation (following a new configure that includes the sequential-io) simply overwrites the previous? 2. Is there a log file where I can see whether the sequential-io was configured / installed correctly? Thanks! Assaf From: parflow-users-bounces at mailman.mines.edu [mailto:parflow-users-bounces at mailman.mines.edu] On Behalf Of AWunsch Sent: Tuesday, November 08, 2016 4:40 PM To: parflow-users at mailman.mines.edu Subject: [parflow-users] Failed Parflow tests This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing Feedback Hi everyone, I found the recent discussion, started by Anas Rabie, really useful. I followed Nick's advice regarding removal of the "function" text from the "bin/run" file, and as a first pass Parflow 3.2.0 appears to work on an Ubuntu 14.04. When I ran the tests, 18 of the 94 tests did not pass: clm_forc_veg.tcl on 4 1 1 clm_forc_veg.tcl on 1 4 1 clm_forc_veg.tcl on 3 3 1 clm_forc_veg.tcl on 2 2 1 clm_forc_veg.tcl on 2 1 1 clm_forc_veg.tcl on 1 2 1 LW_var_dz_spinup.tcl 4 1 1 LW_var_dz_spinup.tcl 1 4 1 LW_var_dz_spinup.tcl 2 1 1 LW_var_dz_spinup.tcl 1 2 1 LW_var_dz.tcl 4 1 1 LW_var_dz.tcl 1 4 1 LW_var_dz.tcl 2 1 1 LW_var_dz.tcl 1 2 1 clm_forc_veg.tcl 1 1 1 indicator_field.tcl LW_var_dz_spinup.tcl LW_var_dz.tcl Is this something to be worried about? Would these failures indicated a specific symptom? Thanks, Assaf Wunsch Hydrogeologist / Project Manager Leppert Associates 1422 Washington Ave. Golden, CO 80401 P: (303) 216-2428 F: (303) 216-1419 www.leppertassociates.com [LeppertLogo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 2751 bytes Desc: image001.jpg URL: From merketcb at tamu.edu Tue Nov 22 14:57:25 2016 From: merketcb at tamu.edu (Courtney Merket) Date: Tue, 22 Nov 2016 15:57:25 -0600 Subject: [parflow-users] Streamflow as Boundary Conditions Message-ID: Does anyone have experience implementing transient stream gage data as a boundary condition? I have streams crossing my model domain, and while ParFlow-CLM can use the CLM forcings to get runoff, I need it to also account for inflow in stream channels. The only way I have thought of to do this is to implement an InternalBC or Pressure-Type Injection Well just inside the domain boundary within the stream channel, and to use time cycles to adjust the pressure head. However, if there is a more efficient/appropriate way to do this I would appreciate advice! Thank you, Courtney Merket Graduate Assistant Researcher Texas A&M University -------------- next part -------------- An HTML attachment was scrubbed... URL: From merketcb at tamu.edu Wed Dec 14 18:15:50 2016 From: merketcb at tamu.edu (Courtney Merket) Date: Wed, 14 Dec 2016 19:15:50 -0600 Subject: [parflow-users] Empty out.mask file for solid domain Message-ID: Hi, I am using a Solid File to set my domain. When I include the key *pfset Solver.PrintMask True* the output mask PFB file is created, but it is all zeros - suggesting an entirely empty domain. However, the model runs as it should: I have pressure and saturation output files with no-data values where cells should be inactive, and realistic values where the domain should be active. Does anyone know what might be going wrong with the mask file? Thank you, Courtney Merket Texas A&M University -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljr806916 at 126.com Thu Dec 22 22:15:31 2016 From: ljr806916 at 126.com (ljr806916) Date: Fri, 23 Dec 2016 13:15:31 +0800 (CST) Subject: [parflow-users] unexpected error Message-ID: <6f09aaaf.54a0.1592a1b05eb.Coremail.ljr806916@126.com> Hi, is anyone here? I'm a new learner for Parflow and my name is Lu. I have installed it successfully and passed all the test. But during my leaning and modifying , when I used the test directory's script like default_overland or many other tests ,it appears problems like tclsh samrai.tcl missing operand at _ at _ in expression "_ at _* *" (parsing expression "* *") invoked from within "expr $P * $Q * $R" invoked from within "set NumProcs [expr $P * $Q * $R]" (file "samrai.tcl" line 24) I don't know why and who can help me? and I searched it is the pointer problem, but I can't understand ,it is a passed test! -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmaxwell at mines.edu Thu Dec 22 22:19:23 2016 From: rmaxwell at mines.edu (Reed Maxwell) Date: Fri, 23 Dec 2016 05:19:23 +0000 Subject: [parflow-users] unexpected error In-Reply-To: <6f09aaaf.54a0.1592a1b05eb.Coremail.ljr806916@126.com> References: <6f09aaaf.54a0.1592a1b05eb.Coremail.ljr806916@126.com> Message-ID: <1E84ED30-793C-4B29-9090-7E205FFAB9E7@mines.edu> Hi Lu- When you run the /test problems you need to pass the processor topology as command line arguments. That is you would run it as tclsh defaul_single.tcl 1 1 1 Where the three ?1?s? are assigned to P, Q and R, the processor splits in x, y and z. This is done for the testing suite, to facilitate testing in parallel. Reed Reed M. Maxwell, Ph.D. Rowlinson Professor of Hydrology Department of Geology and Geological Engineering Director, Integrated GroundWater Modeling Center Colorado School of Mines http://inside.mines.edu/~rmaxwell/ On Dec 22, 2016, at 10:15 PM, ljr806916 > wrote: Hi, is anyone here? I'm a new learner for Parflow and my name is Lu. I have installed it successfully and passed all the test. But during my leaning and modifying , when I used the test directory's script like default_overland or many other tests ,it appears problems like tclsh samrai.tcl missing operand at _ at _ in expression "_ at _* *" (parsing expression "* *") invoked from within "expr $P * $Q * $R" invoked from within "set NumProcs [expr $P * $Q * $R]" (file "samrai.tcl" line 24) I don't know why and who can help me? and I searched it is the pointer problem, but I can't understand ,it is a passed test! _______________________________________________ parflow-users mailing list parflow-users at mailman.mines.edu https://mailman.mines.edu/mailman/listinfo/parflow-users Unsubscribe: parflow-users-unsubscribe at mailman.mines.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljr806916 at 126.com Mon Dec 26 02:03:41 2016 From: ljr806916 at 126.com (ljr806916) Date: Mon, 26 Dec 2016 17:03:41 +0800 (CST) Subject: [parflow-users] how to get water banlance items Message-ID: Hi, all I'm a new learner for parflow and I have many problems for it. Can anyone give me some tips? When I used the water balance script, what I see are all silo files ,but I want to know the total water balance items at every step, like total runoff ,total recharge, base flow or what else. In the script , I saw like below and I saw it calculate the total subsurface storage but I don't know how to look into it. Hope for your help, thank you ! set total_subsurface_storage [pfsum $subsurface_storage] if $verbose { puts [format "Subsurface storage\t\t\t\t : %.16e" $total_subsurface_storage] } set total_water_in_domain [expr $total_water_in_domain + $total_subsurface_storage] if $verbose { puts [format "Total water in domain\t\t\t\t : %.16e" $total_water_in_domain] puts "" } -- Jianrong Lu Graduate for Ph.D.degree Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences 73 East Beijing Road, Nanjing 210008, P.R.China -------------- next part -------------- An HTML attachment was scrubbed... URL: