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 - 16:09:59 CDT

have you run the scripts for the REMD tutorial, or are these your own?
do the REMD test cases work?

On Tue, Sep 30, 2008 at 5:03 PM, <xwu_at_purdue.edu> wrote:
> Thanks.
> Yes, I have used the MPI to run the normal simlation. It works well. The
> difference is in that the execute command in the pbs file becomes" time
> sander -O -i....... ".
>
> I also tried to use " time sander " to replace " sander.MPI " in the pbs file
> to run a REMD simulation. It does not works. The pbs file is shown in the
> following
> -----------------------------------------------------
> #PBS -q workq -l nodes=32,walltime=24:00:00 -j oe
> cd $PBS_O_WORKDIR
> . /etc/profile
> module load amber
> echo "remd"
> date
> time sander -ng 16 -groupfile equilbrate.groupfile
> ----------------------------------------------------------
>
> And I got the error message:
>
> ------------------------------------------------------------------------------
> mdfil: Error unknown flag: -
> ng
>
> usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
> rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|
> 2] -inf mdinfo -radii radii -y inptraj]
> Consult the manual for additional options.
>
> real 0m1.054s
> user 0m0.004s
> sys 0m0.004s
> remd
> Can't receive reply from startd on ca-042.rcac.purdue.edu <172.18.19.52:40250>
>
> -------------------------------------------------------------------------------
>
> with regards,
>
> Xiaoyu
>
>
> Quoting Carlos Simmerling <carlos.simmerling_at_gmail.com>:
>
>> have you tested your MPI installation?
>> you might try normal MD first and see if that works- it's not clear if
>> this is a general problem or specific to RMED/RMDE (REMD?)
>>
>>
>> On Tue, Sep 30, 2008 at 4:31 PM, <xwu_at_purdue.edu> wrote:
>> > Hi,
>> > I recently started to use AMBER 10 and need to run some RMDE. The AMBER 10
>> is
>> > compiled with MPICHI2.
>> >
>> > I first start a PBS interactive job to make sure everything should be
>> good,
>> > while I some problem. The following is what I am did and got.
>> >
>> -----------------------------------------------------------------------------
> -
>> > ~~input~~ xwu_at_radon:~$ 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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>> >
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