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Subject: Re: [OMPI users] signal 15 (terminated)
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2009-02-03 10:06:14


Not to be pedantic, but you haven't answered the questions that I
asked from the last time I tried to help you. :-(

http://www.open-mpi.org/community/lists/users/2009/01/7710.php
http://www.open-mpi.org/community/lists/users/2009/01/7717.php

On Feb 3, 2009, at 6:52 AM, Hana Milani wrote:

> I have posted this problem before, but still I am trying to solve it
> so I put it again so that maybe you can help me. I run my simulating
> code in a system with Intel Core 2 Quad, 4x2.4 GHz cpu, with 7.9 GiB
> memopry. My linux is opensuse 11.0 with gfortran compiler.
>
> I have installed openmpi together with blacs and scalapack from http://www.netlib.org/scalapack/scalapack_installer.tgz
> . They both have been installed smoothly with no problem.
>
> I have also compiled and installed my code "SIESTA" in parallel with
> no problem. But when I execute the following command:
>
> mpirun -np 4 ../../Src/siesta <input> output
>
> I receive the following message and the process is killed:
>
> mpirun noticed that job rank 0 with PID 13234 on node linux-4pel
> exited on signal 15 (Terminated).
>
> After I run the input with debugger I receive the follwing messages:
>
> mpirun --debug-daemons -np 4 ../../Src/siesta <input> output
>
> Daemon [0,0,1] checking in as pid 13286 on host linux-4pel
> [linux-4pel:13286] [0,0,1] orted: received launch callback
> [linux-4pel:13286] [0,0,1] orted_recv_pls: received message from
> [0,0,0]
> [linux-4pel:13286] [0,0,1] orted_recv_pls: received kill_local_procs
> mpirun noticed that job rank 0 with PID 13287 on node linux-4pel
> exited on signal 15 (Terminated).
> [linux-4pel:13286] [0,0,1] orted_recv_pls: received message from
> [0,0,0]
> [linux-4pel:13286] [0,0,1] orted_recv_pls: received exit
> [linux-4pel:13286] [0,0,1] ORTE_ERROR_LOG: Not found in
> file .../../../../../orte/mca/odls/default/odls_default_module.c at
> line 540
> [linux-4pel:13286] [0,0,1] ORTE_ERROR_LOG: Not found in
> file .../../../../../orte/mca/odls/default/odls_default_module.c at
> line 540
>
> I have enclosed a copy of the "arch.make" of the code in which I
> have to make changes to compile the code in parallel. Please let me
> know how to solve the said problem.
>
> Regards,
> Hana
>
> #
> # 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=/home/sara/mpich2-1.0.8/bin/mpif90
> RANLIB=ranlib
>
> SYS=nag
>
> SP_KIND=4
> DP_KIND=8
> KINDS=$(SP_KIND) $(DP_KIND)
>
> FFLAGS=-g -O2
> FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
> LDFLAGS=
>
> ARFLAGS_EXTRA=
>
> FCFLAGS_fixed_f=
> FCFLAGS_free_f90=
> FPPFLAGS_fixed_F=
> FPPFLAGS_free_F90=
>
> BLAS_LIBS=/home/sara/scalapack_installer_0.94/lib/librefblas.a
> LAPACK_LIBS=/home/sara/scalapack_installer_0.94/lib/libreflapack.a
> BLACS_LIBS=/home/sara/scalapack_installer_0.94/lib/blacs.a /home/
> sara/scalapack_installer_0.94/lib/blacsC.a
> SCALAPACK_LIBS=/home/sara/scalapack_installer_0.94/lib/libscalapack.a
>
> COMP_LIBS=dc_lapack.a liblapack.a libblas.a
>
> NETCDF_LIBS=
> NETCDF_INTERFACE=
>
> LIBS=$(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_HOME=$/home/sara/mpich2-1.0.8
> MPI_INCLUDE=$/home/sara/mpich2-1.0.8/src/include
> MPI_LIB=$/home/sara/mpich2-1.0.8/lib
> DEFS_MPI=-DMPI
>
>
> #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) $<
>
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-- 
Jeff Squyres
Cisco Systems