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 - 16:29:19 CDT

Yes. I followed the REMD tutorial step by step. The only diffrence is I use
another protein,Trpcage, and then I changed to 16 temperatures.

Thanks.

Xiaoyu

Quoting Carlos Simmerling <carlos.simmerling_at_gmail.com>:

> 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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