[gmx-users] Thread affinity error when Running Gromacs 4.6.3 on Bluegene/P

arrow50311 linxingcheng50311 at gmail.com
Wed Mar 12 02:11:17 CET 2014


When trying to run normal mdrun_mpi with Gromacs 4.6.3 on Bluegene/P, I met
this error:

Can not set thread affinities on the current platform. On NUMA systems this
can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers.

The running stops immediately. 

This is the script for running it:

#@ job_name = simulation
#@ step_name = step1
#@ comment = "Hello World Job"
#@ error = $(job_name).$(jobid).err
#@ output = $(job_name).$(jobid).out
#@ environment = COPY_ALL
#@ wall_clock_limit = 24:00:00
#@ notification = error
#@ job_type = bluegene
#@ class = compute
#@ bg_size = 128 
#@ queue
export MDRUN=/opt/apps/gromacs/4.6/bin/mdrun_mpi
mkdir -p $ddir 
cd $ddir

/bgsys/drivers/ppcfloor/bin/mpirun -cwd $ddir -mode VN -np 512 -exe "$MDRUN"
-args "-s $dir/run.tpr -cpi $ddir/state.cpt -cpo $ddir/state.cpt -maxh 23.9
-npme 128 -noappend"

I have no idea what can cause that kind of error, could someone offer a

Thank you,

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