Dear Siesta Community
This is my first post to the mailing list thus I ask for your kind forbearance
if I violate any mailing list etiquette.
I have been trying to compile siesta-3.1 on our cluster using:
intel fortran compiler v.10.1.017
intel MKL v.10.0.1.014
and OpenMPI v.1.2.7
Using the following arch.make (and several minor variations of it) file
compilation finishes with no errors or warnings but the resulting executable
fails nevertheless.
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arch.make begin:
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#
# 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.
#
#
# arch.make for intel64 archtiecture running intel compiler10 and mkl10 through
openmpi.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90
SIESTA_ARCH=em64t-mkl10
FC=mpif90
# openmpi wrapper for intel fortran compiler
CC=mpicc
# openmpi wrapper for intel C compiler
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
FFLAGS=-O3 -xS -mp #
optimization flags and folating point consistency
FFLAGS_DEBUG=-g # debug
flag
FPPFLAGS_MPI=-DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
MPI_INTERFACE=libmpi_f90.a # using
included MPI interface
MPI_INCLUDE=.
MKLPATH=/opt/intel/cmkl/10.0.1.014/lib/em64t # path to architecture
specific intel MKL
LIBS=-L$(MKLPATH) \
#
-lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 \
# lapack, scalapack, and blacs libs
-lmkl_lapack -lmkl_intel_lp64 -lmkl_em64t -lguide $(EXTRA_LIBS) \ #
blacs openmpi specific
-lmkl_core
#
EXTRA_LIBS=-lpthread -lsvml
#
#COMP_LIBS=dc_lapack.a # tried
as alternative
FPPFLAGS= $(FPPFLAGS_MPI) $(FPPFLAGS_CDF)
#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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arch.make end.
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When I run the resulting executable I get a segmentation fault which seems to
be related to '/lib64/libpthread.so' right after 'siesta: Atomic coordinates
(Bohr) and species' as follows:
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error output begin:
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....
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)
siesta: Atomic coordinates (Bohr) and species
siesta: 1.13185 6.74108 0.00000 1 1
siesta: 3.46731 5.39292 0.00000 1 2
siesta: 3.46731 2.69624 0.00000 1 3
siesta: 1.13185 1.34808 0.00000 1 4
[node15:05358] *** Process received signal ***
[node15:05358] Signal: Segmentation fault (11)
[node15:05358] Signal code: Address not mapped (1)
[node15:05358] Failing at address: (nil)
[node15:05357] *** Process received signal ***
[node15:05357] Signal: Segmentation fault (11)
[node15:05357] Signal code: Address not mapped (1)
[node15:05357] Failing at address: (nil)
[node15:05356] *** Process received signal ***
[node15:05356] Signal: Segmentation fault (11)
[node15:05356] Signal code: Address not mapped (1)
[node15:05356] Failing at address: (nil)
[node15:05358] [ 0] /lib64/libpthread.so.0 [0x2b2802ec8fb0]
[node15:05358] *** End of error message ***
[node15:05355] *** Process received signal ***
[node15:05355] Signal: Segmentation fault (11)
[node15:05355] Signal code: Address not mapped (1)
[node15:05355] Failing at address: (nil)
[node15:05357] [ 0] /lib64/libpthread.so.0 [0x2b825e87dfb0]
[node15:05357] *** End of error message ***
[node15:05356] [ 0] /lib64/libpthread.so.0 [0x2b1e6d87efb0]
[node15:05356] *** End of error message ***
[node15:05355] [ 0] /lib64/libpthread.so.0 [0x2b3993868fb0]
[node15:05355] *** End of error message ***
mpirun noticed that job rank 0 with PID 5355 on node node15 exited on signal 11
(Segmentation fault).
3 additional processes aborted (not shown)
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error output end.
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Any suggestions would be highly appreciated.
Best Regards
Tarek
