Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

2013-03-22 Thread Szilárd Páll
Hi, Actually, if you don't want to run across the network, with those Westmere processors you should be fine with running OpenMP across the two sockets, i.e mdrun -ntomp 24 or to run without HyperThreading (which can be sometimes faster) just use mdrun -ntomp 12 -pin on Now, when it comes to GPU

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

2013-03-22 Thread George Patargias
Hello Szilard Many thanks for these very useful comments! We run jobs on a single node of a small Apple cluster (no Infiniband unfortunately). One node has two Intel(R) Xeon(R) X5650 Processors each with 6 cores and 12 threads, so in total 12 cores and 24 threads. I have compiled GROMACS 4.6.1 w

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

2013-03-21 Thread Szilárd Páll
FYI: On your machine running OpenMP across two sockets will probably not be very efficient. Depending on the input and at how high paralleliation are you running, you could be better off with running multiple MPI ranks per GPU. This is a bit of an unexplained feature due to it being complicated to

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

2013-03-12 Thread George Patargias
Hi Carsten Thanks a lot for this tip. It worked! George > Hi, > > On Mar 11, 2013, at 10:50 AM, George Patargias wrote: > >> Hello >> >> Sorry for posting this again. >> >> I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration >> (CUDA 5.0 lib) using the following SGE batch scri

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

2013-03-11 Thread Carsten Kutzner
Hi, On Mar 11, 2013, at 10:50 AM, George Patargias wrote: > Hello > > Sorry for posting this again. > > I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration > (CUDA 5.0 lib) using the following SGE batch script. > > #!/bin/sh > #$ -V > #$ -S /bin/sh > #$ -N test-gpus > #$ -l

[gmx-users] Mismatching number of PP MPI processes and GPUs per node

2013-03-11 Thread George Patargias
Hello Sorry for posting this again. I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration (CUDA 5.0 lib) using the following SGE batch script. #!/bin/sh #$ -V #$ -S /bin/sh #$ -N test-gpus #$ -l h="xgrid-node02" #$ -pe mpi_fill_up 12 #$ -cwd source /opt/NetUsers/pgkeka/gromacs-4