On Thu, Aug 14, 2025, YASHIKA . via AMBER wrote:
>
>mpirun -n 64 /home/apps/amber16_intel/bin/pmemd.MPI -O -i equi_50.in -o
>equi_50.out -p with_184.parm7 -c heat_hold.rst7 -r equi_50.rst7 -inf
>equi_50.info -ref heat_hold.rst7 -x equi_50.mdcrd;
Using 64 MPI threads is way too many: pmemd code usually maxes out in
preformance at 16 to 32 threads.
Debug this in pieces: run a short simulation (nstlim=25, ntpr=1) using
pmemd; if that works, try pmemd.MPI with two MPI threads, and gradually
increase the number of threads.
If even serial pmemd fails before the first energy printout, try sander:
sometimes that will give better error messages.
...hope this helps....dac
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Received on Fri Aug 15 2025 - 07:00:03 PDT
