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01-15-2009, 06:57 AM
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#1
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Member
Registered: Dec 2008
Posts: 66
Rep:
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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.
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01-15-2009, 09:44 AM
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#2
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LQ Guru
Registered: Jul 2003
Location: Birmingham, Alabama
Distribution: SuSE, RedHat, Slack,CentOS
Posts: 27,468
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Quote:
Originally Posted by hanamilani
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
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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....
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01-16-2009, 12:52 AM
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#3
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Member
Registered: Dec 2008
Posts: 66
Original Poster
Rep:
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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]
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01-16-2009, 09:13 AM
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#4
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LQ Guru
Registered: Jul 2003
Location: Birmingham, Alabama
Distribution: SuSE, RedHat, Slack,CentOS
Posts: 27,468
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Quote:
Originally Posted by hanamilani
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.
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The job itself is where the problem(s) are...and have you looked to see what signal 15 is????
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01-16-2009, 11:06 AM
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#5
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Member
Registered: Dec 2008
Posts: 66
Original Poster
Rep:
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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.
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01-16-2009, 11:19 AM
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#6
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LQ Guru
Registered: Jul 2003
Location: Birmingham, Alabama
Distribution: SuSE, RedHat, Slack,CentOS
Posts: 27,468
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Quote:
Originally Posted by hanamilani
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.
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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
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01-16-2009, 12:56 PM
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#7
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Member
Registered: Dec 2008
Posts: 66
Original Poster
Rep:
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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.
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01-16-2009, 01:22 PM
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#8
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LQ Guru
Registered: Jul 2003
Location: Birmingham, Alabama
Distribution: SuSE, RedHat, Slack,CentOS
Posts: 27,468
|
Quote:
Originally Posted by hanamilani
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.
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My idea would be for you to contact the openpmi people...this issue is with that software, not Linux.
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