[gmx-users] Problem of Gromacs Run on MPICH cluster.

PeiQuan Chen gromacs at 163.com
Tue Dec 23 06:17:01 CET 2003

Dear gmx-users,

I have compiled successfully the parallel version of gromacs in a Linux Cluster implemented with MPICH and PBS batch queue system.

I can successly run the parallel mdrun when I use the interactive mode of PBS with the
following command:
qsub -l nodes=<number of nodes> -I
and then run the parallel mdrun with the mpirun command:
mpirun -np $NP -machinefile ${PBS_NODEFILE} mdrun -np $NP -s myfile.tpr
This model run successfully.

But when I come to use the PBS script files to submit the job,the PBS system complaint that:
    p4_error: latest msg from perror: Resource temporarily unavailable
p0_11046:  p4_error: net_accept accept: -1
Killed by signal 2.^M
p0_11046: (4.112234) net_send: could not write to fd=3, errno = 32

PBS scritp files:
#PBS -l nodes=2:ppn=2:enet
#PBS -N my_job_name
#PBS -j oe
NP=`wc -l ${PBS_NODEFILE} | awk '{ print $1; }'`
cd My_working_directory
mpirun -np $NP -machinefile ${PBS_NODEFILE} mdrun -np $NP -s myfile.tpr

Could anybody tell me how to resolve this problem? 

Thanks in advance.

Sincerely yours
PeiQuan Chen
PeiQuan Chen 	Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223507510		Mobile Phone: (+86)13920675030
gromacs at 163.com	

More information about the gromacs.org_gmx-users mailing list