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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Jul 7, 2011, at 8:08 AM, mish <smncbr.gmail.com> wrote: > Thank a lot. configure_mpich2 worked really well but the problem I have now > is something strange. I can see some reports about it earlier but no > solution or further discussion in the post. Also in my sace sander.MPI works > well when I test it for one thread: > sander.MPI -O -i mdt1.in -o md1.out -p disach4.top -c optim1_5.rst -x > test.trj > > then it works. when i use it with mpiexec fir 5 thread in a pbs it produces > error : > > > mpiexec_deca12-2.cmp.mnx.jp: cannot connect to local mpd > (/tmp/mpd2.console_mish); possible causes: > 1. no mpd is running on this host > 2. an mpd is running but was started without a "console" (-n option) > In case 1, you can start an mpd on this host with: > mpd & > and you will be able to run jobs just on this host. > For more details on starting mpds on a set of hosts, see > the MPICH2 Installation Guide. > > What could be the possible mistake ? > > Sincerely > Mish > > On Wed, Jul 6, 2011 at 9:36 PM, David A Case <case.biomaps.rutgers.edu>wrote: > >> On Wed, Jul 06, 2011, mish wrote: >>> >>> Dies anyone have some idea how to properly compile MPICH so that it can >> work >>> here or how to modify ./configure to make in working in this condition. >> >> Please see the "configure_openmpi" or "configure_mpich2" scripts in >> $AMBERHOME/AmberTools/src. These configure and install MPI versions that >> should work with Amber, and will not interfere with other MPI installations >> you may have. >> >> ...dac >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jul 07 2011 - 07:30:11 PDT