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[OpenFOAM.org] mpirun not working in paralleö with OpenMPI |
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February 14, 2012, 06:48 |
mpirun not working in paralleö with OpenMPI
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#1 |
Member
Pekka Pasanen
Join Date: Feb 2012
Location: Finland
Posts: 87
Rep Power: 14 |
I'm having a lot of trouble getting mpirun to work in parallel with OpenFOAM 2.1.0. I compiled it from Thirdparty-2.1.0 with Allwmake and it compiled without errors. I then managed to run decomposePar on my case nicely but when i try to invoke mpirun according to user guide it gives me the following error:
$mpirun -np 2 buoyantBoussinesqSimpleFoam -parallel --> FOAM FATAL ERROR: Trying to use the dummy Pstream library. This dummy library cannot be used in parallel mode From function UPstream::init(int& argc, char**& argv) in file UPstream.C at line 37. FOAM exiting --> FOAM FATAL ERROR: Trying to use the dummy Pstream library. This dummy library cannot be used in parallel mode From function UPstream::init(int& argc, char**& argv) in file UPstream.C at line 37. FOAM exiting -------------------------------------------------------------------------- mpirun noticed that the job aborted, but has no info as to the process that caused that situation. -------------------------------------------------------------------------- It also gives the same error message with Test-parallel. mpirun seems to be working otherwise, just not with the -parallel option. For example i can run following without any problems: $mpirun -np 2 Test-parallel I'm totally stuck with this problem, which seems to be somehow related to Pstream library. I haven't made modifications to files in Thirdparty-2.1.0 or in OpenFOAM installation. There seems to be others with the same errors, but no solutions that i could find. Any help is very much appreciated, as my case could really use more than one core. |
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February 14, 2012, 14:25 |
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#2 |
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Pekka Pasanen
Join Date: Feb 2012
Location: Finland
Posts: 87
Rep Power: 14 |
Okay i'm going to reply to this myself because i think i solved this. I'm not exactly sure what helped but i'm posting what i think did the trick.
1) Make sure that you have correctly set MPI in $WM_PROJECT_DIR/etc/bashrc export WM_MPLIB=OPENMPI 2) Run Allwmake again in Thirdparty dir (possibly best to run Allclean first and if you do, don't forget to compile paraView again ThirdParty-2.1.0$ ./Allwmake 3) Move dummy libs away from default location cd $FOAM_LIBBIN mv dummy/ dummy__ 4) Go to OpenFOAM sources and recompile Pstream and dummyThirdparty cd $FOAM_SRC cd Pstream ./Allwmake cd $FOAM_SRC cd dummyThirdParty ./Allwmake I did some other fidling too, but i belive those should do the trick Feel free to ask if you have been fighting with this too and still can't get mpirun to run in parallel. Mine now runs happily when Pstream was recompiled mpirun -np 2 buoyantBoussinesqSimpleFoam -parallel > log2 & There is now 2 processes running and both cores are working |
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February 16, 2012, 15:11 |
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#3 |
Member
Pierre
Join Date: Sep 2010
Posts: 57
Rep Power: 16 |
You could also use the foamJob script.
I also had problems running mpirun. But hte foamJob script gets the libraries,etc. automatically. foamJob -s -p >solver< |
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August 29, 2013, 03:38 |
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#4 |
New Member
Luca Franceschini
Join Date: Aug 2012
Posts: 29
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Thank you,
this worked also for me. However, I didn't do point 1 and 2. In point 1 i have left export WM_MPLIB=SYSTEMOPENMPI And I didnt recompile the thirdParty library. regards. |
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September 29, 2013, 23:11 |
Thanks!! This helped me too!!
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#5 |
Member
einat
Join Date: Jul 2012
Posts: 31
Rep Power: 14 |
Downloaded ThirdParty-2.2.1, compiled it, moved dummy, etc. Now it's working!! |
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September 9, 2014, 12:37 |
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#6 |
New Member
Anjishnu Choudhury
Join Date: Jul 2014
Posts: 4
Rep Power: 12 |
Only remaking (./Allwmake) dummy files did the work for me !! Thanks!
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February 2, 2015, 21:35 |
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#7 |
Senior Member
Alex
Join Date: Oct 2013
Posts: 337
Rep Power: 22 |
Only recompiling Pstream made it work for me!
Thanks, Alex
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March 4, 2015, 04:41 |
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#8 |
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Stephanie
Join Date: Feb 2015
Location: Magdeburg, Germany
Posts: 71
Rep Power: 11 |
Hello,
today I tried your way to solve the problem. Unfortunatly I got a new message from the program: Code:
[stephanie:04480] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ess_singleton_module.c at line 231 [stephanie:04480] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ess_singleton_module.c at line 140 [stephanie:04480] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file runtime/orte_init.c at line 128 [stephanie:04481] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ess_singleton_module.c at line 231 [stephanie:04481] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ess_singleton_module.c at line 140 [stephanie:04481] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file runtime/orte_init.c at line 128 -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_set_name failed --> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_set_name failed --> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): ompi_mpi_init: orte_init failed --> Returned "A system-required executable either could not be found or was not executable by this user" (-127) instead of "Success" (0) -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): ompi_mpi_init: orte_init failed --> Returned "A system-required executable either could not be found or was not executable by this user" (-127) instead of "Success" (0) -------------------------------------------------------------------------- [stephanie:4480] *** An error occurred in MPI_Init [stephanie:4480] *** on a NULL communicator [stephanie:4480] *** Unknown error [stephanie:4480] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort [stephanie:4481] *** An error occurred in MPI_Init [stephanie:4481] *** on a NULL communicator [stephanie:4481] *** Unknown error [stephanie:4481] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort -------------------------------------------------------------------------- An MPI process is aborting at a time when it cannot guarantee that all of its peer processes in the job will be killed properly. You should double check that everything has shut down cleanly. Reason: Before MPI_INIT completed Local host: stephanie PID: 4480 -------------------------------------------------------------------------- -------------------------------------------------------------------------- An MPI process is aborting at a time when it cannot guarantee that all of its peer processes in the job will be killed properly. You should double check that everything has shut down cleanly. Reason: Before MPI_INIT completed Local host: stephanie PID: 4481 -------------------------------------------------------------------------- =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 1 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== Than I went in ThridPartx and run ./Allwmake. Next I did step 3) und 4) as written. Did I forget something? I would be really grateful if someone could help me. Thank you. Last edited by wyldckat; March 7, 2015 at 20:14. Reason: Added [CODE][/CODE] |
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March 14, 2015, 07:34 |
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#9 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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Greetings Stephanie,
I've finally managed to take a better look into your question and I think I've understood what the problem is. As far as I can figure out, you followed these instructions: http://openfoamwiki.net/index.php/In...u#Ubuntu_14.04 Therefore, I suggest you try the following steps:
Bruno |
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March 18, 2015, 10:43 |
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#10 |
Member
Stephanie
Join Date: Feb 2015
Location: Magdeburg, Germany
Posts: 71
Rep Power: 11 |
Hello Bruno,
the installation of OpenFOAM on Ubuntu 14.4 did a friend of me. Therefore he used a video from YouTube. I'm deeply grateful for your help. I tried the code, you have posted and it worked [Moderator note: text missing here has been copied to a new thread: http://www.cfd-online.com/Forums/ope...out-range.html] Thank you for your help, best regards, Stephie Last edited by wyldckat; March 21, 2015 at 16:47. Reason: see "Moderator note:" |
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July 17, 2017, 10:44 |
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#11 | |
Member
Ali Noaman Ibrahim
Join Date: Sep 2015
Location: US_Chicago
Posts: 97
Rep Power: 11 |
Quote:
I have followed all the steps you described above but unfortunately still have problem with running my code in parallel ( e.g. : -bash: decomposePar: command not found) and I have found the following error message at the end of log.make file :- /usr/bin/ld: cannot find -lfluidThermophysicalModels collect2: ld returned 1 exit status make[2]: *** [/export/home/aibrah8/OpenFOAM/OpenFOAM-2.4.0/platforms/linux64GccDPOpt/bin/twoPhaseEulerFoam] Error 1 make[1]: *** [twoPhaseEulerFoam] Error 2 make[1]: Target `application' not remade because of errors. make: *** [multiphase] Error 2 make: Target `application' not remade because of errors. Any suggestions ? Thanks |
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August 27, 2017, 11:29 |
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#12 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,982
Blog Entries: 45
Rep Power: 128 |
Quick question @alinuman15: Have you solved the problem you were having here?
If not, I need more details.
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August 29, 2017, 16:28 |
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#13 | |
Member
Ali Noaman Ibrahim
Join Date: Sep 2015
Location: US_Chicago
Posts: 97
Rep Power: 11 |
Quote:
I am trying to install Cent OS/OpenFoam4.1 from the website (https://openfoamwiki.net/index.php/I...CentOS_SL_RHEL) on my login node into university HPC cluster without the need to install the third party stuff. Yet, I had succeeded in sourcing it on the terminal, however, when trying to compile it by typing:-./Allwmake -j 4 > log.make 2>&1following step 15 ( on the mentioned page), I got the error shown in the log.make inserted file. As it is clear, that the error is related to the missed GMP_LIBRARIES and as a result, I tried to install the third party components ( beginning from step 8), but again I run into the error shown in (in the inserted image when I reached the command:- ./makeGcc -no-multilib gcc-4.8.5/ Sorry for long text. Any clue? Thanks again! |
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September 2, 2017, 11:35 |
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#14 | |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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Greetings Ali,
OpenFOAM 4.1 cannot be built with GCC 4.4.7 anyway, therefore you will need a more recent GCC version. Following the instructions at https://openfoamwiki.net/index.php/I...HEL#CentOS_6.8 - should have worked as intended, although it didn't in your case. The error message that is in the image you attached states: Code:
configure: error: cannot compute suffix of object files: cannot compile Searching online for the error message lead me to this FAQ entry: https://gcc.gnu.org/wiki/FAQ#Configu...the_problem.3F There it states that it could very likely be because the necessary libraries... and quoting from that entry: Quote:
Therefore, if you activate the shell environment with a command similar to the following: Code:
source $HOME/OpenFOAM/OpenFOAM-4.1/etc/bashrc WM_COMPILER_TYPE=ThirdParty Code:
cd $WM_THIRD_PARTY_DIR ./makeGcc -no-multilib > log.makeGcc 2>&1 Best regards, Bruno |
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September 8, 2017, 14:32 |
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#15 | |
Member
Ali Noaman Ibrahim
Join Date: Sep 2015
Location: US_Chicago
Posts: 97
Rep Power: 11 |
Quote:
I will give it a try. my best. |
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October 5, 2017, 22:45 |
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#16 |
Senior Member
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Dear friends:
I solved this problem by copy the parallel version Pstream into the foam library directory. I use the MPICH for compiling the openFOAM. libPstrea.so is locatin in /OpenFOAM-v1706/platforms/linux64GccDPInt32Opt/lib/mpich-3.2/ copy it to /OpenFOAM-v1706/platforms/linux64GccDPInt32Opt/lib/ and it works hope this help you. |
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