AMBER Archive (2008)

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

From: xwu_at_purdue.edu
Date: Tue Sep 30 2008 - 16:03:08 CDT

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
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> >      to majordomo_at_scripps.edu
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>       to majordomo_at_scripps.edu
> 
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu