AMBER Archive (2002)

Subject: Passing arguments with SP2 LoadLeveler

From: Thomas A. Spraggins (tas_at_virginia.edu)
Date: Mon Jun 24 2002 - 09:41:26 CDT

I can't figure out how to pass arguments to sander using LoadLeveler.
Here's my latest try. Does anybody have an example that works?

Thanks.

Tom Spraggins
tas_at_virginia.edu

---------------------

Script started on Mon Jun 24 10:01:26 2002sp2c: /home/tas/cytosine $ cat
<.cmd
# Submit this file with the command llsubmit mpi.cmd
#
# LoadLeveler commands start with "# @".
# Lines with "#" are comments.
#
# -------------------------------------------------------------------
# EDIT : user_id must be changed to computing id
# EDIT : my_directory must be changed to the directory with your
executable
# EDIT : executable_name must be changed to your executable.
# -------------------------------------------------------------------
#
#
# @ environment = LL_JOB=TRUE ; MP_EUILIB=us ; XLFRTEOPTS="namelist=old"
# @ initialdir = /home/tas/cytosine
# @ error = mpi.$(Cluster).err
# @ output = mpi.$(Cluster).out
#
# POE is the Parallel Operating Environment on the SP.
# The executable "poe" runs the MPI job. The path to the compiled
# program is passed to "poe" using the LoadLeveler keyword "arguments"
#
# @ executable = /usr/bin/poe
# @ arguments = /home/tas/cytosine/sander_script1
#
# Classes for parallel jobs are:
#
# PVM3, and MPI
#
# @ class = MPI
# @ job_type = parallel
#
# @ requirements = (Adapter == "hps_user")
#
# @ min_processors = 4
# @ max_processors = 4
#
# @ notification = always
# @ notify_user = tas_at_virginia.edu
#
# @ queue
sp2c: /home/tas/cytosine $ cat <sander_script1
#! /bin/ksh

/home/tas/cytosine/sander.parallel -O -i in.md -c crd.md.23 -o cytosine.out

sp2c: /home/tas/cytosine $ cat <in.md
 cytosine in chloroform
 &cntrl
  irest = 1, ntx = 7,
  ntb = 2, ntp = 2, taup=0.2,
  ntt = 1, tautp=0.2,
  nstlim = 10,
  dt = 0.002, nrespa=1,
  ntpr = 1, ntave=1000,
  temp0 = 300.,
  scee = 1.2,
  ntf = 2, ntc = 2, tol=0.000005,
  vlimit=15.0,
 &end
sp2c: /home/tas/cytosine $ llsubmit mpi2.cmd
llsubmit: A network statement with values css0, not_shared, US was generated
from the adapter = hps_user statement.
llsubmit: The job "sp2c.sp2.virginia.edu.1705" has been submitted.
sp2c: /home/tas/cytosine $ more *1705*
ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing...
1525-113 The options string contains unexpected or invalid text instead of
an op
tion name. The program will stop.
1525-113 The options string contains unexpected or invalid text instead of
an op
tion name. The program will stop.
1525-113 The options string contains unexpected or invalid text instead of
an op
tion name. The program will stop.
ERROR: 0031-250 task 1: Terminated
sp2c: /home/tas/cytosine $ exit

script done on Mon Jun 24 10:04:00 2002