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April 27, 2010, 07:07 |
openfoam 1.6 on debian etch
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#1 |
Senior Member
Roman Thiele
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Hej,
does anyone have any experience with installing openfoam on a debian etch system with the system provided libraries, namely gcc = 4.1.2 openmpi = 1.1.4 and if not, does anyone know if those library versions are high enough to compile openfoam 1.6
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April 27, 2010, 10:32 |
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#2 |
Retired Super Moderator
Bruno Santos
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Greetings Roman,
I have no experience with building OpenFOAM 1.6(.x) in Debian, but lots in Ubuntu, which derives from Debian As for versions:
As for the rest, the instructions provided by OpenCFD in www.openfoam.com should be enough to build OpenFOAM. Best regards, Bruno
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May 4, 2010, 07:24 |
thank you almost done
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#3 |
Senior Member
Roman Thiele
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Hej,
thank you. I got everything compiled and almost running. I am stuck with the parallel running though. I got myself the source of the MPI libs that the computer is running and compiled it with this changed in the settings.sh file. Unfortunately, I get error messages when I try to run the simulation in parallel. Single thread does not pose a problem. But I don't really want to run anything on the master machine of the cluster. Code:
CMD: mpirun -hostfile /home/roman/hostfile.uybOCy4QV -np 8 compressibleInterFoam -parallel -------------------------------------------------------------------------- Sorry! You were supposed to get help about: argv0-not-found from the file: help-pls-base.txt But I couldn't find any file matching that name. Sorry! -------------------------------------------------------------------------- mpirun noticed that job rank 0 with PID 0 on node "node0014" exited on signal 4. -------------------------------------------------------------------------- Sorry! You were supposed to get help about: argv0-not-found from the file: help-pls-base.txt But I couldn't find any file matching that name. Sorry! --------------------------------------------------------------------------
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May 4, 2010, 19:31 |
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#4 | |
Retired Super Moderator
Bruno Santos
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Hi Roman,
I don't remember seeing an error like that, but by what it says, it seems to me it's looking for a help file, for it to report on the respective error message. It could be that the language files are missing in the MPI's installation. As for testing the connections, try the parallel test utility. To build it, Quote:
The script foamJob should have created a file named log with the same output. It is only configured for using OpenMPI's mpirun, so adapt it to your needs if you're running another MPI application! The host file that foamJob can use by default, is one of these files: Code:
machines hostfile system/machines system/hostfile As for the script foamJob, it has the advantage of requiring a lot less commands to type each time you need to run a parallel job Now, like I said before, and assuming that you defined properly on how the case should be split in 8 sub-domains and you ran decomposePar. There are a few ways of setting the environment variables, whether:
Best regards, Bruno
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May 5, 2010, 12:25 |
thanks for this extensive reply
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#5 |
Senior Member
Roman Thiele
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hej,
ok, i get the output plus something bad. Code:
[node0014:05178] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0014:05177] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0014:05180] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0014:05179] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0014:05177] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0014:05178] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0014:05180] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0014:05179] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0015:04624] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0015:04626] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0015:04623] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0015:04625] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0015:04626] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0015:04624] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0015:04625] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) [node0015:04623] mca: base: component_find: unable to open: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) Code:
Build : 1.6-f802ff2d6c5a Exec : parallelTest -parallel Date : May 05 2010 Time : 18:32:28 Host : node0014 PID : 5177 Case : /home/roman/OpenFOAM/roman-1.6/run/run250cmCondTankCluster nProcs : 8 Slaves : 7 ( node0014.5178 node0014.5179 node0014.5180 node0015.4623 node0015.4624 node0015.4625 node0015.4626 ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time [3] Starting transfers [3] [3] slave sending to master 0 [3] slave receiving from master 0 [1] Starting transfers [1] [1] slave sending to master 0[2] Starting transfers [2] [2] slave sending to master 0 [1] slave receiving from master 0 [2] slave receiving from master 0 [0] Starting transfers [0] [0] master receiving from slave 1 [0] (0 1 2) [0] master receiving from slave 2 [0] (0 1 2) [0] master receiving from slave 3 [0] (0 1 2) [0] master receiving from slave 4 [0] (0 1 2) [0] master receiving from slave 5 [0] (0 1 2) [0] master receiving from slave 6 [0] (0 1 2) [0] master receiving from slave 7 [0] (0 1 2) [0] master sending to slave 1 [0] [1] (0 1 2) master sending to slave 2 [0] [2] (0 1 2) master sending to slave 3 [0] [3] (0 1 2) master sending to slave 4 [0] [4] Starting transfers [4] [4] slave sending to master 0 [4] slave receiving from master 0 [4] (0 1 2) master sending to slave [5] Starting transfers [5] [5] slave sending to master 0 [5] slave receiving from master 0 [5] (0 1 2) 5 [6] Starting transfers [6] [6] slave sending to master 0 [6] slave receiving from master 0 [0] [7] Starting transfers [7] [7] slave sending to master 0 [7] slave receiving from master 0 master sending to slave [6] (06 1 2) [7] (0 1 2) [0] master sending to slave 7 End Finalising parallel run I just found that it might be bug in the MPI version that i compiled, but I am not sure! when this is done, i will def write a install article for debian etch
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May 5, 2010, 12:42 |
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#6 |
Retired Super Moderator
Bruno Santos
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Hello again Roman,
Great! Communications work and I believe that the environment is properly set in all slaves. Your Debian box is missing the library libibverbs.so, so you could install it. Or you could try to use the precompiled OpenMPI that comes with OpenFOAM's ThirdParty binary package; or even try compiling it, using the script Allwmake at the ThirdParty-1.6 folder. Now, if I'm not mistaken, MCA is part of the communications section of MPI. And libibverbs is an library for InfiniBand networking. You can check the forum for more info on mpirun or OpenMPI, or check your MPI's manual for command options. Just recently there has been a post about mca included in the command for calling mpirun: SimpleFoam run in Parallel post #4 Have you tried running your case with foamJob? That thing about libibverbs is just a warning, so it should work! Best regards, Bruno
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May 5, 2010, 12:54 |
working
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#7 |
Senior Member
Roman Thiele
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It seems that it is working with foamJob, but not with the wrapper supplied by the cluster. Which is good to know.
Thanks for the extensive help.
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May 5, 2010, 13:56 |
wiki article on installation
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#8 |
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Roman Thiele
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here one can find the complete solution to the installation of openfoam 1.6 on debian etch in server mode, as it is used on clusters http://openfoamwiki.net/index.php/In...in_Server_Mode
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May 5, 2010, 18:32 |
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#9 |
Retired Super Moderator
Bruno Santos
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Greetings Roman,
I just saw the post you made on the wiki. I'm astonished that a tweaked script of mine ended up on the wiki, without being me putting it there Ah the marvels of GPL Long live free source But there is something I just want to make sure that it's working or not in your installation, specially since I'm the one responsible for the tweaked script! Did you need to change anything in settings.sh for gcc to be properly recognized? Are you sure you used the actual built gcc? Please open a new terminal window, activate (if not sourced automatically) the OpenFOAM environment and confirm that you have the right gcc version up by running: Code:
gcc -v Code:
gcc version 4.3.3 (OpenFOAM) Code:
GMPROOT=${GMP_DIR}/platforms/$WM_ARCH$WM_COMPILER$WM_COMPILER_ARCH MPFRROOT=${MPFR_DIR}/platforms/$WM_ARCH$WM_COMPILER$WM_COMPILER_ARCH GCCROOT=${GCC_DIR}/platforms/$WM_ARCH$WM_COMPILER$WM_COMPILER_ARCH Code:
GMPROOT=${GMP_DIR}/platforms/$WM_ARCH$WM_COMPILER_ARCH MPFRROOT=${MPFR_DIR}/platforms/$WM_ARCH$WM_COMPILER_ARCH GCCROOT=${GCC_DIR}/platforms/$WM_ARCH$WM_COMPILER_ARCH That particular issue on the first moded version is because I copy-pasted from the version I tweaked for cross-compiling OpenFOAM in Linux for running in Windows... and the two names collided (both paths were named linux), so I added $WM_COMPILER to the path for the build compiler (so it could be linuxGcc and linuxmingw32). By the way, why didn't you build the OpenMPI 1.3.3 that comes in the ThirdParty package? It's more recent than 1.1.4! And the building process is already imbued in the Allwmake script in the ThirdParty-1.6 folder! Or is it incompatible with Debian Etch? Best regards, Bruno
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May 6, 2010, 03:26 |
works
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#10 |
Senior Member
Roman Thiele
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Hej,
yeah, your script worked great, thanks for that. I have gcc-4.3.3 (OpenFOAM) working here. So that is not a problem. I didn't know at that point if the openMPI would work the way I intended it to work, so I basically chose the one that was already installed, but didn't seem to work correctly. But right now, it works like a charm with the 1.1.4, I might try to update over the next couple of days, and see how it turns out. If it works, then I will just give it a try with a higher version of mpi and update the post.
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