Hi,
We tried to run a pH-REMD simulation with 8 replicas on a GPU node (having
8 CPUs and 4 GPUs). The script is pasted as below:
unset CUDA_VISIBLE_DEVICES
export CUDA_VISIBLE_DEVICES=0,1,2,3
mpirun -np 8 $AMBERHOME/bin/pmemd.cuda.MPI -ng 8 -groupfile groupfile -rem
4 -remlog pHremd.log
But the results suggested we'd better to have 12 or 16 replicas. So we
tried to submit 16 replicas in the same node, using:
mpirun -np 16 $AMBERHOME/bin/pmemd.cuda.MPI -ng 16 -groupfile groupfile
-rem 4 -remlog pHremd.log
But it failed with an error of "MPI size is not a multiple of -ng". We
couldn't understand why it works for 8 replicas but not 16. Or is there any
trick to make it work? Thanks.
Regards,
Yong
--
==========================
Yong Wang
PhD Student, Structural Biology and NMR Laboratory (SBiNLab)
Department of Biology, University of Copenhagen, Denmark
Ole Maaloes Vej 5, DK-2200 Copenhagen N
https://www.researchgate.net/profile/Yong_Wang15
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 25 2016 - 03:00:02 PST
