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.
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~~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.
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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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Received on Wed Oct 01 2008 - 05:11:49 PDT
