On 4/18/2011 4:39 PM, delara aghaie wrote:
Dear Gromacs users
I run DPPC monolayer on Tip4p2005 water layer system with gromacs 3.3
I had no problem before but when I run the system with command
grompp_mpi -c .gro -f .mdp -n .ndx -p .top -o .tpr -np 8
and then qsub .ll
the run starts but it has break down several times, each ime after for
ex 987654 steps or more steps or less.
If you've changed nothing, and it used to work, and now doesn't, then
something about your computer has changed. We can't really help there -
and there must be better people to ask.
Mark
I get in .o.ii file this message:
PBS has allocated the following nodes:
cx1-25-8-4
cx1-25-8-4
cx1-25-8-4
cx1-25-8-4
cx1-25-8-4
cx1-25-8-4
cx1-25-8-4
cx1-25-8-4
---
mpiexec.intel -genv I_MPI_DEVICE ssm -genv I_MPI_DEBUG 0 -genv
I_MPI_PIN yes -genv I_MPI_PIN_MODE lib -genv I_MPI_FALLBACK_DEVICE
disable -genv DAPL_MAX_CM_RETRIES 500 -genv DAPL_MAX_CM_RESPONSE_TIME
300 -genv I_MPI_DAPL_CONNECTION_TIMEOUT 300 -machinefile
/tmp/pbs.5455562.cx1/tmp.VRhkM11825 -n 8 -wdir /tmp/pbs.5455562.cx1
mdrun_mpi -v -s topol.tpr -np 8
Job output begins below
---
mpdallexit: cannot connect to local mpd
(/tmp/pbs.5455562.cx1/mpd2.console_dmohamma_110411.074928); possible
causes:
1. no mpd is running on this host
2. an mpd is running but was started without a console (-n option)
---
what can be the solvation of the possible problem?
Thanks
D. Aghaie
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