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Old 01-15-2009, 06:57 AM   #1
hanamilani
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problem with openmpi


Dear all,

I have to run my code in parallel, therefore, I have installed openmpi-1.2.8 on a core2quad system with suse 11.0 linux and gfortran compiler. I have also downloaded blacs and scalapack from: http://www.netlib.org/scalapack/scalapack_installer.tgz.

Everything has gone smoothly in installing the code and enabling mpi for it, but when I want to run my test I receive the following error:

mpirun noticed that job rank 0 with PID 2407 on node linux-4pel exited on signal 15 (Terminated).

Please let me know how to solve this problem.

Regards,
Hana

Last edited by hanamilani; 01-15-2009 at 07:10 AM.
 
Old 01-15-2009, 09:44 AM   #2
TB0ne
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Quote:
Originally Posted by hanamilani View Post
Dear all,

I have to run my code in parallel, therefore, I have installed openmpi-1.2.8 on a core2quad system with suse 11.0 linux and gfortran compiler. I have also downloaded blacs and scalapack from: http://www.netlib.org/scalapack/scalapack_installer.tgz.

Everything has gone smoothly in installing the code and enabling mpi for it, but when I want to run my test I receive the following error:

mpirun noticed that job rank 0 with PID 2407 on node linux-4pel exited on signal 15 (Terminated).

Please let me know how to solve this problem.

Regards,
Hana
How about what your 'test' is?? You don't post anything about that, only that the job failed. Doesn't give us alot to go on....
 
Old 01-16-2009, 12:52 AM   #3
hanamilani
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problem with openmpi

Hello,

The test I have comes from a simulating code called SIESTA, when I ./configure --enable-mpi for this code it generates an arch.make file in which I mention the addresses of blacs and scalapack for it and then make the code.

My intention to say "test" is the input file I make to simulate and I run it whether sequentially or in parallel.

If you want take a look at the arch.make as enclosed to see whether the problem occurs from that.

Regards,

# This file is part of the SIESTA package.
#
# Copyright (c) Fundacion General Universidad Autonoma de Madrid:
# E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal
# and J.M.Soler, 1996-2006.
#
# Use of this software constitutes agreement with the full conditions
# given in the SIESTA license, as signed by all legitimate users.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90

SIESTA_ARCH=i686-pc-linux-gnu--Gfortran

FPP=
FPP_OUTPUT=
FC=/usr/local/bin/mpif90
RANLIB=ranlib

SYS=nag

SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)

FFLAGS=-g -O2
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS=

ARFLAGS_EXTRA=

FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=

BLAS_LIBS=/home/hana/scalapack_installer_0.94/lib/librefblas.a
LAPACK_LIBS=/home/hana/scalapack_installer_0.94/lib/libreflapack.a
BLACS_LIBS=/home/hana/scalapack_installer_0.94/lib/blacs.a /home/hana/scalapack_installer_0.94/lib/blacsC.a
SCALAPACK_LIBS=/home/hana/scalapack_installer_0.94/lib/libscalapack.a

COMP_LIBS=dc_lapack.a liblapack.a libblas.a

NETCDF_LIBS=
NETCDF_INTERFACE=

LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)

#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=.

#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
[/SIZE]
 
Old 01-16-2009, 09:13 AM   #4
TB0ne
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Quote:
Originally Posted by hanamilani View Post
Hello,

The test I have comes from a simulating code called SIESTA, when I ./configure --enable-mpi for this code it generates an arch.make file in which I mention the addresses of blacs and scalapack for it and then make the code.

My intention to say "test" is the input file I make to simulate and I run it whether sequentially or in parallel.

If you want take a look at the arch.make as enclosed to see whether the problem occurs from that.
The job itself is where the problem(s) are...and have you looked to see what signal 15 is????
 
Old 01-16-2009, 11:06 AM   #5
hanamilani
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Hi,

I am completely at a loss of it.

I have shared this question in Siesta and openmpi mailing lists as well, butthey could not say anything about it too!!!

Please let me know whetever I should check to see what signal 15 is.
 
Old 01-16-2009, 11:19 AM   #6
TB0ne
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Quote:
Originally Posted by hanamilani View Post
Hi,

I am completely at a loss of it.

I have shared this question in Siesta and openmpi mailing lists as well, butthey could not say anything about it too!!!

Please let me know whetever I should check to see what signal 15 is.
There is lots of information regarding signal:15 on the OpenMPI support forum:

http://www.open-mpi.org/community/help/

An openMPI tutorial is here:

http://www.slac.stanford.edu/comp/unix/farm/mpi.html
 
Old 01-16-2009, 12:56 PM   #7
hanamilani
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I have once read the tutorial and I work directly with openmpi for parallel run for another code.

But, this one which deals with blacs and scalapack has made such
difficulty~!!!

From the openmpi mailing list they told me that:

"Have you checked to ensure that the job manager is not killing your
job? As I mentioned yesterday, SIGTERM is usually when some external
agent kills your job."

what's the job manager? should I look for it in Siesta or openmpi? please let me know what your idea is.
 
Old 01-16-2009, 01:22 PM   #8
TB0ne
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Quote:
Originally Posted by hanamilani View Post
I have once read the tutorial and I work directly with openmpi for parallel run for another code.

But, this one which deals with blacs and scalapack has made such
difficulty~!!!

From the openmpi mailing list they told me that:

"Have you checked to ensure that the job manager is not killing your
job? As I mentioned yesterday, SIGTERM is usually when some external
agent kills your job."

what's the job manager? should I look for it in Siesta or openmpi? please let me know what your idea is.
My idea would be for you to contact the openpmi people...this issue is with that software, not Linux.
 
  


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