[gmx-users] Well known domain decomposition

Alex alexanderwien2k at gmail.com
Sat Apr 21 15:07:16 CEST 2018

Dear all,
The cluster where my gromac job is submitted on has several nodes each with
16 slots.
My calculation works fine when it is submitted on a single node using 8
slots out of 16, but it crashes when the 16 slots in a single node are used
due to the well known domain decomposition issue.
It also crashes with the same error when it is summited over more than one
node, using 32 slots.
I played blindly around with different available options of -ntomp/
-npme/-ntomp_pme/ ... or also export OMP_NUM_THREADS=8 but no success. I
tried the -nt = 8  in single node also but it does not work as the gromacs
had not been compiled without thread-MPI in our machine.
Actually I can not do that much about the compilation or recompile it again
with proper options as it has been compiled by our IT administration to be
used with VOTCA program (in my case),

So, in such cluster, would you please help me to figure out the problem and
run the simulation by higher than 8 number of slots? at least with 16 slots
in a single node or even better with two or 4 nodes.

Thank you.

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