Am 30.03.2013 um 05:21 schrieb Duke Nguyen: > Hi folks, > > I am sorry if this question had been asked before, but after ten days of > searching/working on the system, I surrender :(. We try to use mpirun to run > abinit (abinit.org) which in turns will call an input file to run some > simulation. The command to run is pretty simple > > $ mpirun -np 4 /opt/apps/abinit/bin/abinit < input.files >& output.log > > We ran this command on a server with two quad core x5420 and 16GB of memory. > I called only 4 core, and I guess in theory each of the core should take up > to 2GB each. > > In the output of the log, there is something about memory: > > P This job should need less than 717.175 Mbytes of memory. > Rough estimation (10% accuracy) of disk space for files : > WF disk file : 69.524 Mbytes ; DEN or POT disk file : 14.240 Mbytes. > > So basically it reported that the above job should not take more than 718MB > each core. > > But I still have the Segmentation Fault error:
It might also be a programming error in abinit. You compiled abinit with the compiler version they suggest and Open MPI was compiled with the same version? It's running fine in serial mode? The `make check` of abinit succeeded? -- Reuti > mpirun noticed that process rank 0 with PID 16099 on node biobos exited on > signal 11 (Segmentation fault). > > The system already has limits up to unlimited: > > $ cat /etc/security/limits.conf | grep -v '#' > * soft memlock unlimited > * hard memlock unlimited > > I also tried to run > > $ ulimit -l unlimited > > before the mpirun command above, but it did not help at all. > > If we adjust the parameters of the input.files to give the reported mem per > core is less than 512MB, then the job runs fine. > > Please help, > > Thanks, > > D. > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
