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> >
> > with regards,
> >
> > Xiaoyu
> >
> >
> > Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
> >
> >> have you tested your MPI installation?
> >> you might try normal MD first and see if that works- it's not clear if
> >> this is a general problem or specific to RMED/RMDE (REMD?)
> >>
> >>
> >> On Tue, Sep 30, 2008 at 4:31 PM, <xwu.purdue.edu> wrote:
> >> > Hi,
> >> > I recently started to use AMBER 10 and need to run some RMDE. The AMBER
> 10
> >> is
> >> > compiled with MPICHI2.
> >> >
> >> > I first start a PBS interactive job to make sure everything should be
> >> good,
> >> > while I some problem. The following is what I am did and got.
> >> >
> >>
> -----------------------------------------------------------------------------
> > -
> >> > ~~input~~ xwu.radon:~$ qsub -I -l nodes=32,walltime=24:00:00
> >> > ~~screen~~ qsub: waiting for job 247667.argon.rcac.purdue.edu to
> start
> >> > qsub: job 247667.argon.rcac.purdue.edu ready
> >> > ~~input~~ xwu.ca-014:~$ cd $PBS_O_WORKDIR
> >> > ~~input~~ xwu.ca-014:~$ . /etc/profile
> >> > ~~input~~ xwu.ca-014:~$ module load amber
> >> > ~~input~~ xwu.ca-014:~$ mpdboot -v -f $PBS_NODEFILE
> >> > ~~screen~~ running mpdallexit on ca-014.rcac.purdue.edu
> >> > LAUNCHED mpd on ca-014.rcac.purdue.edu via
> >> > RUNNING: mpd on ca-014.rcac.purdue.edu
> >> > ~~input~~ xwu.ca-014:~$ mpirun -np 32 $AMBERHOME/exe/sander.MPI -ng
> 16
> >> -
> >> > groupfile equilbrate.groupfile
> >> > ~~screen~~ running mpdallexit on ca-014.rcac.purdue.edu
> >> > LAUNCHED mpd on ca-014.rcac.purdue.edu via
> >> > RUNNING: mpd on ca-014.rcac.purdue.edu
> >> > LAUNCHED mpd on ca-030 via ca-014.rcac.purdue.edu
> >> > ........(omission)
> >> > ........
> >> > RUNNING: mpd on dpm-a012
> >> > RUNNING: mpd on dpm-a013
> >> > RUNNING: mpd on dpm-a014
> >> > RUNNING: mpd on dpm-a015
> >> >
> >>
> -----------------------------------------------------------------------------
> > --
> >> >
> >> > After 15 minutes, I got the following message on the screen, and not
> >> output
> >> > file is find.
> >> >
> >> >
> >>
> -----------------------------------------------------------------------------
> > --
> >> > mpdboot_ca-014.rcac.purdue.edu (handle_mpd_output 406): from
> mpd
> >> on
> >> > ca-042, invalid port info:
> >> > no_port
> >> >
> >> > mpdtrace: cannot connect to local mpd
> >> > (/tmp/mpd2.console_xwu_247667.argon.rcac.purdue.edu); 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.
> >> > mpdringtest: cannot connect to local mpd
> >> > (/tmp/mpd2.console_xwu_247667.argon.rcac.purdue.edu); 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.
> >> > mpiexec_ca-014.rcac.purdue.edu: cannot connect to local mpd
> >> > (/tmp/mpd2.console_xwu_247667.argon.rcac.purdue.edu); 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.
> >> >
> >>
> -----------------------------------------------------------------------------
> > --
> >> >
> >> >
> >> > Xiaoyu
> >> > -----------------------------------------------------------------------
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> >> > to majordomo.scripps.edu
> >> >
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> >> to majordomo.scripps.edu
> >>
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> > to majordomo.scripps.edu
> >
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Received on Wed Oct 01 2008 - 05:12:04 PDT