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 - 16:33:12 CDT

but did the original files work, either the tutorial or the test case?
if you have a problem with your files, you want to try files that
someone else has already tested.
if they don't work, it's the mpi or amber. if they do, then it is in
your inputs.

On Tue, Sep 30, 2008 at 5:29 PM, <xwu_at_purdue.edu> wrote:
> 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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