AMBER Archive (2008)

Subject: Re: AMBER: problem of use MPICHI2 to run RMED on amber10

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 30 2008 - 15:45:58 CDT

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_at_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_at_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_at_ca-014:~$ cd $PBS_O_WORKDIR
> ~~input~~ xwu_at_ca-014:~$ . /etc/profile
> ~~input~~ xwu_at_ca-014:~$ module load amber
> ~~input~~ xwu_at_ca-014:~$ mpdboot -v -f $PBS_NODEFILE
> ~~screen~~ running mpdallexit on ca-014.rcac.purdue.edu
> LAUNCHED mpd on ca-014.rcac.purdue.edu via
> RUNNING: mpd on ca-014.rcac.purdue.edu
> ~~input~~ xwu_at_ca-014:~$ 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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