[wenxu]

Dear foamers,

I am installing OF2.3.0 on supercomputer. But I suffer the same problem as others who had posted like: http://www.cfd-online.com/Forums/ope...entos-5-a.html. But the thing of my case is different , so I decide to post a new thread and wish someone reply me accordingly.

OF can run successfully with mpirun -np 4 interFoam -parallel on main(manage) node, but when I submit job to computing node the following error emerging.

It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_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):

opal_shmem_base_select failed
--> Returned value -1 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
[c12n5-ib:27601] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file runtime/orte_init.c at line 79
[c12n5-ib:27601] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file orterun.c at line 694

The compiler is : gcc 4.7.0
The openmpi is : openmpi 1.6.5
The supercomputer has been installed icc 14.0.0 itself. The bash file in my home is like this:

export LANG=C
export LD_LIBRARY_PATH=$HOME/software/gmp/lib:$HOME/software/mpfr/lib:$HOME/software/mpc/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$HOME/software/gcc/lib64:$LD_LIBRARY_PATH
export PATH=$HOME/software/gcc/bin:$PATH
export PATH=$HOME/software/cmake-2.8.12.2/bin:$PATH

#######openmpi#####
export PATH=$HOME/OpenFOAM/ThirdParty-2.3.0/openmpi-1.6.5/bin:$PATH
export MPI_PATH=$HOME/software/openmpi-1.6.5/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/software/openmpi-1.6.5/lib
source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc

Any reply is highly appreciated!

Best regards,
Wen

[wyldckat]

Quick answer: Without and example of the job schedule script it's a bit hard to diagnose the problem, but my guess is that you're missing the source command to OpenFOAM's "bashrc" file for activating OpenFOAM's shell environment.
In essence:

source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc
mpirun -np 4 interFoam -parallel

For more details: http://openfoamwiki.net/index.php/In...with_the_Shell

[wenxu]

Thank you for your quick answer, Bruno. Yes, I have sourced the bash of OF and the mpirun works fine on the main node. But when I submit the job to the computing node, the error in my last thread appears (The supercomputer is a distributed memory system.). Furthermore, I run foamInstallation command, the checking is OK.

Best regards,
Wen

[wyldckat]

Quick answer: OK, then what are the exact detailed steps you use for running the job?
One of the points of failure is somewhere in how you launch the job, but if you don't describe all of the steps you take, it's really hard to diagnose.
The other possibility is that the installation is not available in the supercomputer, because the installation folder might not be visible for all other nodes.