[Dock-fans] parallel dock

Scott Brozell sbrozell at scripps.edu
Mon Apr 28 11:54:12 PDT 2008


Hi,

On Sat, 26 Apr 2008, inderjit yadav wrote:

> I have installed the parallel version of dock6.2 .all the programs are
> installed but it is not running the dock program all other programs are
> running smoothly
> path of installed directory
>           /export/apps/dock/dock6
> 
> i used  command
> 
>  mpirun -np 4 dock6.mpi -i mpi.in
> 
> it shows
> 
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> p0_5543:  p4_error: semget failed for setnum: 17
> -----------------------------------------------------------------------------
> It seems that [at least] one of the processes that was started with
> mpirun did not invoke MPI_INIT before quitting (it is possible that
> more than one process did not invoke MPI_INIT -- mpirun was only
> notified of the first one, which was on node n0).
> mpirun can *only* be used with MPI programs (i.e., programs that
> invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
> to run non-MPI programs over the lambooted nodes.
> -----------------------------------------------------------------------------
> p0_5541:  p4_error: interrupt SIGx: 15
> p0_5542:  p4_error: interrupt SIGx: 15
> 
> and terminates
> 
> as my executables are not in the system path I used
> 
>  mpirun -np 4 dock6.mpi -i mpi.in
> 
> then again after some times shows the same error

This is not clear.  Did the dock6/install/test/mpi test ever run ?:
cd dock6/install/test/mpi; make clean; make

Probably you need to delete old semaphores with ipcrm;
see the script below and
http://www.hpcc.nectec.or.th/wiki/index.php/MPI_Error_messsage
If it never ran then maybe the system resources are inadequate;
increase shmmax et al.; see
http://netmirror.org/mirror/lam-mpi.org/6.5/install.php

All this assumes that your MPI is installed correctly and tested...

> would anyone please help me in running the dock parallelly i need it in my
> project .

dock6.mpi is convenient but never critical; see the April 22, 2008 manual:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ParallelProcessing

Scott


#!/bin/sh
#set -vx
# report inter-process communication Shared Memory status on xxx and
# remove the user's shared memory segments using their identifiers.

ipcs -m
type=m
ipcs -m |
grep $USER |
cut -c12-20 |
while read id
do
    echo ipcrm -$type $id
    ipcrm -$type $id
done

exit




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