[Beowulf] shared memory error

Jörg Saßmannshausen j.sassmannshausen at ucl.ac.uk
Mon Apr 4 14:29:11 PDT 2016

Dear all,

I was wondering whether somebody might be able to shed some light on this 
problem I am having with a chemistry code (GAMESS-US):

DDI Process 15: semop return an error performing 1 operation(s) on semid 
semop errno=EINVAL.

This sometimes happens when I need quite a bit of memory for the fortran code 
(1550000000 words). Originally I thought it has to do with the hardware I am 
running it on but meanwhile I found it all over the place, i.e. on some older 
Opterons and on some newer Ivy and Haswell CPUs.

It is not quite reproducible, unfortunately. A run might work ok for a few 
days and then the problem kicks in and the logfile explodes from around 14 MB 
to 17 GB, or it might just work.

Some system informations: I am running Debian Jessie with gcc / gfortran 
version 4.9.2-10. The nodes have 64 GB of RAM and 16 or 20 cores.  As the 
shared memory default settings in Linux are not suitable for GAMESS (there is 
a note in the documentation), I am using these settings on the 64 GB RAM 

kernel.shmmax = 6923000000
kernel.shmall = 25165824
kernel.shmmni = 32768

I got the feeling the problem lies burried in these settings but my knowledge 
here is not sufficient to solve the problem. Could somebody point me in the 
right direction here?

All the best from London


Dr. Jörg Saßmannshausen, MRSC
University College London
Department of Chemistry
20 Gordon Street

email: j.sassmannshausen at ucl.ac.uk
web: http://sassy.formativ.net

Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
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