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Environment errors with .deb install and ubuntu 13.04 64 bit |
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September 13, 2013, 12:02 |
Environment errors with .deb install and ubuntu 13.04 64 bit
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#1 |
New Member
Jonathan byrne
Join Date: Sep 2013
Posts: 17
Rep Power: 13 |
Hi,
I apt-get installed openfoam 2.2.1 and it seemed to successfully install. I added the "source /opt/openfoam221/etc/bashrc" to my .bashrc and it picked it up. Unfortunately it still doesn't seem to working. Here are some of the errors I am getting: IcoFoam isn't picked up. When I run wallmake I get: wmakeCheckPwd: not found (I think this has to do with missing third party stuff) If I copy wmakecheckpwd to my bin folder I get: FOAM_EXT_LIBBIN not set My environment variables are correct except there is no third party folder in /opt, should that have been installed? Also the install didn't create my $USER folder, should it have done that or do I create it myself? WM_ARCH_OPTION=64 WM_COMPILE_OPTION=Opt WM_COMPILER=Gcc WM_MPLIB=SYSTEMOPENMPI WM_OSTYPE=POSIX WM_PRECISION_OPTION=DP WM_PROJECT_DIR=/opt/openfoam221 WM_PROJECT_INST_DIR=/opt WM_PROJECT=OpenFOAM WM_PROJECT_USER_DIR=/home/jonathan/OpenFOAM/jonathan-2.2.1 WM_PROJECT_VERSION=2.2.1 WM_THIRD_PARTY_DIR=/opt/ThirdParty-2.2.1 On the plus side paraview seems to be working. Have I done something wrong during the install or should I install an earlier version? |
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September 14, 2013, 13:25 |
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#2 |
Retired Super Moderator
Bruno Santos
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Greetings Jonathan and welcome to the forum!
Well, if you did successfully install OpenFOAM 2.2.1 from the Deb packages, as explained here: http://www.openfoam.org/download/ubuntu.php - then you do not need to run Allwmake. A few questions:
Bruno
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September 15, 2013, 11:51 |
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#3 |
New Member
Jonathan byrne
Join Date: Sep 2013
Posts: 17
Rep Power: 13 |
Thanks for getting back to me, I really appreciate the help. I have opened a new terminal I am still the getting the same issues. I can see that it has sourced the correct bashrc file so I don't think that is the problem.
It is a clean install so there shouldn't be any conflicts. I can see all the executables in the platforms folder but it doesn't seem to have properly linked to them. I was running wallmake out of desperation. The $WM_PROJECT_DIR variable points to /opt/openfoam221 which is correct and this is what is in that folder: -rwxr-xr-x 1 root root 923 Jun 18 11:23 Allwmake -rw-r--r-- 1 root root 123833 Jun 18 14:21 Allwmake.log drwxr-xr-x 5 root root 4096 Sep 13 15:43 applications drwxr-xr-x 3 root root 4096 Sep 13 15:43 bin -rw-r--r-- 1 root root 0 Jun 18 15:06 build-stamp -rw-r--r-- 1 root root 35647 Jun 18 11:23 COPYING drwxr-xr-x 6 root root 4096 Sep 13 15:43 doc drwxr-xr-x 6 root root 4096 Sep 13 15:43 etc drwxr-xr-x 3 root root 4096 Sep 13 15:43 platforms -rw-r--r-- 1 root root 6526 Jun 18 11:23 README.html -rw-r--r-- 1 root root 1584 Jun 18 11:23 README.org drwxr-xr-x 35 root root 4096 Sep 13 15:43 src drwxr-xr-x 16 root root 4096 Sep 13 15:43 tutorials drwxr-xr-x 6 root root 4096 Sep 13 15:43 wmake Thanks again for your help! |
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September 15, 2013, 15:08 |
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#4 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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Hi Jonathan,
OK, my guess is that something got broken when you were trying to fix the problem. Try reinstalling OpenFOAM 2.2.1 with the following command: Code:
sudo apt-get install --reinstall openfoam221 Code:
which icoFoam If it didn't reveal this path: Code:
/opt/openfoam221/platforms/linux64GccDPOpt/bin/icoFoam Best regards, Bruno
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September 15, 2013, 17:02 |
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#5 |
New Member
Jonathan byrne
Join Date: Sep 2013
Posts: 17
Rep Power: 13 |
Hi,
I ran the reinstall, opened a new terminal and there is still no icoFoam. Everything seems to be installed and the bashrc is being sourced, but the environment still isnt being set up. I ran the foamInstallationTest and got: FATAL ERROR: OpenFOAM environment not configured. when I checked the foaminstallationtest code it was checking if two folders existed $WM_PROJECT_INST_DIR (/opt) and $WM_THIRD_PARTY_DIR (/opt/ThirdParty-2.2.1) The third party folder doesn't exist. Should that have been created by the deb installer? |
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September 15, 2013, 17:06 |
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#6 |
Retired Super Moderator
Bruno Santos
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Location: Lisbon, Portugal
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Run these commands:
Code:
source /opt/openfoam221/etc/bashrc which icoFoam
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September 15, 2013, 17:14 |
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#7 |
New Member
Jonathan byrne
Join Date: Sep 2013
Posts: 17
Rep Power: 13 |
Hi,
This is what I got: $ source /opt/openfoam221/etc/bashrc /home/jonathan /home/jonathan /home/jonathan /home/jonathan /home/jonathan jonathan@jonathan-ubuntu /home/jonathan $ which icoFoam Exit 1 jonathan@jonathan-ubuntu /home/jonathan $ icoFoam icoFoam: command not found Exit 127 Still no joy, thanks again for your help and prompt reply. |
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September 15, 2013, 18:41 |
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#8 |
Retired Super Moderator
Bruno Santos
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Hi Jonathan,
This is very strange.... OK, try these steps:
Bruno
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September 15, 2013, 19:11 |
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#9 |
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Jonathan byrne
Join Date: Sep 2013
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I made absolutely sure the folders in opt were removed, here is how the install went:
Do you want to ignore this warning and proceed anyway? To continue, enter "Yes"; to abort, enter "No": yes Selecting previously unselected package libcr0. (Reading database ... 422432 files and directories currently installed.) Unpacking libcr0 (from .../libcr0_0.8.5-2_amd64.deb) ... Selecting previously unselected package blcr-util. Unpacking blcr-util (from .../blcr-util_0.8.5-2_amd64.deb) ... Selecting previously unselected package csh. Unpacking csh (from .../csh_20110502-2ubuntu1_amd64.deb) ... Selecting previously unselected package libptscotch-5.1. Unpacking libptscotch-5.1 (from .../libptscotch-5.1_5.1.12b.dfsg-2_amd64.deb) ... Selecting previously unselected package binutils-dev. Unpacking binutils-dev (from .../binutils-dev_2.23.2-2ubuntu1_amd64.deb) ... Selecting previously unselected package openmpi-bin. Unpacking openmpi-bin (from .../openmpi-bin_1.4.5-1ubuntu1_amd64.deb) ... Selecting previously unselected package openfoam221. Unpacking openfoam221 (from .../openfoam221_0-1_amd64.deb) ... Selecting previously unselected package libptscotch-dev. Unpacking libptscotch-dev (from .../libptscotch-dev_5.1.12b.dfsg-2_amd64.deb) ... Selecting previously unselected package openmpi-checkpoint. Unpacking openmpi-checkpoint (from .../openmpi-checkpoint_1.4.5-1ubuntu1_amd64.deb) ... Processing triggers for man-db ... Processing triggers for doc-base ... Processing 1 added doc-base file... Setting up libcr0 (0.8.5-2) ... Setting up blcr-util (0.8.5-2) ... Setting up csh (20110502-2ubuntu1) ... update-alternatives: using /bin/bsd-csh to provide /bin/csh (csh) in auto mode Setting up libptscotch-5.1 (5.1.12b.dfsg-2) ... Setting up binutils-dev (2.23.2-2ubuntu1) ... Setting up openmpi-bin (1.4.5-1ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode Setting up openfoam221 (0-1) ... ** To use OpenFOAM please add ** ** . /opt/openfoam221/etc/bashrc ** ** To your ~/.bashrc Setting up libptscotch-dev (5.1.12b.dfsg-2) ... Setting up openmpi-checkpoint (1.4.5-1ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place jonathan@jonathan-ubuntu /opt $ source /opt/openfoam221/etc/bashrc /opt /opt /opt /opt /opt jonathan@jonathan-ubuntu /opt $ which icoFoam Exit 1 jonathan@jonathan-ubuntu /opt $ icoFoam icoFoam: command not found Could this be a problem with 13.04? I might try the source install tomorrow or maybe set up a virtual machine with 12.04 to see if that is the problem |
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September 15, 2013, 19:21 |
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#10 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
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I think I finally figure it out. You've got a broken ".bashrc" file, which is why things are not working properly.
Run this command and then start a new terminal: Code:
cp /etc/skel/.bashrc ~/ Code:
source /opt/openfoam221/etc/bashrc which icoFoam
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September 15, 2013, 19:27 |
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#11 |
New Member
Jonathan byrne
Join Date: Sep 2013
Posts: 17
Rep Power: 13 |
That sorted it! It must be something conflicting in my original bashrc. I am getting some new errors with icoFoam but at least this is an improvement thanks again for your help!
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September 24, 2013, 17:22 |
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#12 |
New Member
Fernando
Join Date: Sep 2013
Posts: 4
Rep Power: 13 |
Hello, sorry for reviving this thread, but this was the only place I found some info regarding this issue. I'm trying to compile from the git source in arch linux, and I get the same error with FOAM_EXT_LIBBIN not being set. I went trough the bashrc located in OpenFOAM-2.2.x/etc/ and I didn't find any export setting this variable, and neither I found it when I did a text search over the whole directory.
I'm not sure if the git repo is intended in practice to be a source for compiling (the install wiki at least ses it is) but if it is I'm pretty lost in what to set this variable to Also, this page doesn't show the variable listed http://openfoamwiki.net/index.php/Environment_variables Thanks, and any help would be apreciated |
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September 25, 2013, 06:42 |
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#13 |
New Member
Jonathan byrne
Join Date: Sep 2013
Posts: 17
Rep Power: 13 |
Hey,
I did a clean checkout of openFOAM 2.2.x and managed to find it. The $FOAM_EXT_LIBBIN is being set in ./etc/config/settings.sh which should be called by the bashrc script: _foamSource $WM_PROJECT_DIR/etc/config/settings.sh So it looks like bashrc is not being executed correctly. My problem was a pre-existing bashrc alias was breaking the openfoam bashrc. Have you tried it with a clean .bashrc as Bruno described? |
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September 25, 2013, 12:32 |
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#14 |
New Member
Fernando
Join Date: Sep 2013
Posts: 4
Rep Power: 13 |
You're actually right about both, my bashrc was not loading the configs and I assumed that KDE's search in the contents of a file would include text files even if they were marked as executables. My bad.
Also, I'd like to confirm what the git repo is suposed to be used for, It's as the wiki says where I can finde the lastest versoin with bugfixes or it's suposed to be an unstable developmente version? Thanks for the answer and good luck |
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September 26, 2013, 06:22 |
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#15 |
New Member
Jonathan byrne
Join Date: Sep 2013
Posts: 17
Rep Power: 13 |
Glad to hear you got it working. I built the source but I havent tried it out. I'm sticking with the debs
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