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. 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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