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
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:
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.