Hi everyone,
I am trying to run a parallel compilation of siesta-3.0-rc2 on my laptop. I
have successfully compiled (or so I thought) siesta with openmpi-1.4.2 with
BLAS, lapack-3.2.2, BLACS and scalapack-1.8.0 downloaded from netlib.org and
compiled with gfortran. When I run the siesta executable in the following
fashion:
mpirun -np 2 siesta <input.fdf >output.out
on one hand I noticed that there is only one siesta running on only one node
and I obtain the following error:
[martin-laptop:21102] *** Process received signal ***
[martin-laptop:21102] Signal: Segmentation fault (11)
[martin-laptop:21102] Signal code: Address not mapped (1)
[martin-laptop:21102] Failing at address: 0x18
[martin-laptop:21103] *** Process received signal ***
[martin-laptop:21103] Signal: Segmentation fault (11)
[martin-laptop:21103] Signal code: Address not mapped (1)
[martin-laptop:21103] Failing at address: 0x18
[martin-laptop:21102] [ 0] [0x8b7410]
[martin-laptop:21102] [ 1] siesta-3.0-MPI(blacs_gridinit_+0xd6) [0x8439c76]
[martin-laptop:21102] [ 2] siesta-3.0-MPI(rdiag_+0x5de) [0x81542be]
[martin-laptop:21102] [ 3] siesta-3.0-MPI(diagg_+0xc61) [0x80b4a09]
[martin-laptop:21102] [ 4] siesta-3.0-MPI(diagon_+0x122c) [0x80a2600]
[martin-laptop:21102] [ 5]
siesta-3.0-MPI(__m_compute_dm_MOD_compute_dm+0x2a8) [0x816bd04]
[martin-laptop:21102] [ 6]
siesta-3.0-MPI(__m_siesta_forces_MOD_siesta_forces+0x1a9) [0x8185e89]
[martin-laptop:21102] [ 7] siesta-3.0-MPI(MAIN__+0x4c) [0x8186014]
[martin-laptop:21102] [ 8] siesta-3.0-MPI(main+0x2b) [0x8480dcb]
[martin-laptop:21102] [ 9]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x506bd6]
[martin-laptop:21102] [10] siesta-3.0-MPI() [0x807b041]
[martin-laptop:21102] *** End of error message ***
[martin-laptop:21103] [ 0] [0x5fd410]
[martin-laptop:21103] [ 1] siesta-3.0-MPI(blacs_gridinit_+0xd6) [0x8439c76]
[martin-laptop:21103] [ 2] siesta-3.0-MPI(rdiag_+0x5de) [0x81542be]
[martin-laptop:21103] [ 3] siesta-3.0-MPI(diagg_+0xc61) [0x80b4a09]
[martin-laptop:21103] [ 4] siesta-3.0-MPI(diagon_+0x122c) [0x80a2600]
[martin-laptop:21103] [ 5]
siesta-3.0-MPI(__m_compute_dm_MOD_compute_dm+0x2a8) [0x816bd04]
[martin-laptop:21103] [ 6]
siesta-3.0-MPI(__m_siesta_forces_MOD_siesta_forces+0x1a9) [0x8185e89]
[martin-laptop:21103] [ 7] siesta-3.0-MPI(MAIN__+0x4c) [0x8186014]
[martin-laptop:21103] [ 8] siesta-3.0-MPI(main+0x2b) [0x8480dcb]
[martin-laptop:21103] [ 9]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x4adbd6]
[martin-laptop:21103] [10] siesta-3.0-MPI() [0x807b041]
[martin-laptop:21103] *** End of error message ***
Anyone could shed some light on the problem I am facing? I am running a
32-bit Ubuntu (10.04). I transcript the arch.make file I used for
compilation:
##########################################################################################################################
# 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- .
#
# 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
FPP=
FPP_OUTPUT=
FC=mpif90
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
FFLAGS=-g #-Wunused
FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT $(DEFS_MPI) $(DEFS_TS)
#FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS=
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
BLAS_LIBS=/usr/local/src/BLAS/LIB/blas_LINUX.a
LAPACK_LIBS=/usr/local/src/lapack-3.2.2/LIB/lapack_LINUX.a
BLACS_LIBS=/usr/local/src/BLACS/LIB/blacsCinit_MPI-LINUX-0.a
/usr/local/src/BLACS/LIB/blacsF77init_MPI-LINUX-0.a
/usr/local/src/BLACS/LIB/blacs_MPI-LINUX-0.a
SCALAPACK_LIBS=/usr/local/src/scalapack-1.8.0/LIB/libscalapack.a
THREAD_LIBS=/usr/lib/libpthread_nonshared.a
COMP_LIBS=dc_lapack.a
NETCDF_LIBS=
NETCDF_INTERFACE=
LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
$(NETCDF_LIBS) $(THREAD_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=./
#MPI_INCLUDE= /usr/local/include
#MPI_LIBS= /usr/local/lib/libmpi.a
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) $<
##########################################################################################################################
Thank you in advance for your time!!!
Cheers,
Martin.-
Dr. Martin E. Zoloff Michoff
--
Universidad Nacional de Córdoba
Facultad de Ciencias Químicas
Departamento de Matemática y Física
Edificio Integrador - Subsuelo
Ciudad Universitaria
X5000HUA - Córdoba
Argentina
Tel/Fax. +54 351 434-4972
