[gmx-users] shortage of shared memory
chris.neale at utoronto.ca
Sat Jul 14 19:33:48 CEST 2007
>So it seems that there is a problem in the shared memory communication
>layer of openmpi that only shows up sporadically. However, if it is not
>reproducible it could also be physical memory problems, i.e. bad DIMMS,
>espcially sice you have data corruption every once in a while. Some
>tests that you can do, take a big file (much larger than the amount of
>memory you have) and run md5sum on it a few times. Copy the file to a
>"good" machine and run it there as well. It should always give the same
>result. If you can rule out hardware than OpenMPI could be the problem.
>You could try the latest LAM or MPICH 2.x (not 1.x!).
Our sysadmin has run Memtest-86 v3.3 and found no problem in 4 passes.
I will look into MPICH 2.x (we found openmpi to run 10% faster than
LAM so don't really want to go back).
Thanks for the reply,
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