using ifort to compile siesta-4.1-b1 ,when calculating ,result Segment error (core dump)
using ifort to compile siesta-4.1-b1 ,when calculating ,always resulting that Segment error (core dump) ,this is my arch.make
#
# Copyright (C) 1996-2016 The SIESTA group
# This file is distributed under the terms of the
# GNU General Public License: see COPYING in the top directory
# or http://
# See Docs/Contributo
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90
SIESTA_
FPP=
FPP_OUTPUT=
FC=mpiifort
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
FFLAGS=
FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS=
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
DUMMY_FOX= --enable-dummy
FFLAGS_DEBUG= -g -O2
BLAS_LIBS=
LAPACK_
BLACS_LIBS=
SCALAPACK_
COMP_LIBS=
NETCDF_LIBS=
NETCDF_INTERFACE=
LIBS=$(
#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=
MPI_INCLUDE=
#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
atom.o: atom.F
$(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.c.o:
$(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.F.o:
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
Question information
- Language:
- English Edit question
- Status:
- Solved
- For:
- Siesta Edit question
- Assignee:
- No assignee Edit question
- Solved by:
- chenhao
- Solved:
- Last query:
- Last reply:
Revision history for this message
|
#1 |
First, try and delete the COMP_LIBS line. It isn't required and can possibly mess up your compilation.
Secondly, you are compiling with MPI, but in that case you should add the -DMPI preprocessor flag to the FPPFLAGS line.
Try the above, and if it does not work, please add more information, see here for details:
Revision history for this message
|
#2 |
Thank you very much ,this helped me a lot ,but I still have a problem about compilation .I have tried all the ways including the method in the links .While deleting the COMP_LIBS line and(or) change the FFLAGS to FFLAGS= -O0 -g -check bounds -traceback ,it shows the same problem .while adding the -DMPI preprocessor flag to the FPPFLAGS line,the compilation failed ,but the compilation is successful when there is no -DMPI .Without -DMPI ,I get the serial version ,and I add "-heap-arrays 64" to the FFLAGS , there is no this problem .And now my problem is how to get the parallel version.
this is my arch.make
#
# Copyright (C) 1996-2016 The SIESTA group
# This file is distributed under the terms of the
# GNU General Public License: see COPYING in the top directory
# or http://
# See Docs/Contributo
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90
SIESTA_
FPP=
FPP_OUTPUT=
FC=mpiifort
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
#FFLAGS= -O0 -g -check bounds -traceback
FFLAGS=
FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI
LDFLAGS=
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
DUMMY_FOX= --enable-dummy
FFLAGS_DEBUG= -g -O2
BLAS_LIBS=
LAPACK_
BLACS_LIBS=
SCALAPACK_
#COMP_LIBS=
NETCDF_LIBS=
NETCDF_INTERFACE=
LIBS=$(
#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=
MPI_INCLUDE=
#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
atom.o: atom.F
$(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.c.o:
$(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.F.o:
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
When compiling ,the Error is
libSiestaXC.a libmpi_f90.a \
rdiag_mrrr.
/F/siesta/
/F/siesta/
Makefile:481: recipe for target 'siesta' failed
Revision history for this message
|
#3 |
See the documentation,
you should add:
-DSIESTA__NO_MRRR
to your FPPFLAGS.
Revision history for this message
|
#4 |
Thank you very much ,but it still does not work .Referring to *.make in the /Src/Sys ,I tried impi+intel and openmpi +intel ,they all result the same error as long as I add -DMPI to FPPFLAGS .Using the same arch.make with adding -DMPI to FPPFLAGS to compile other versions (4.0 4.0-b1 2.0.2) are successful .
Revision history for this message
|
#5 |
Did you add -DSIESTA__NO_MRRR to the fppflags?
Revision history for this message
|
#7 |
To help you we need more information.
Please attach complete arch.make and output log of the compilation.
(Please attach and do not copy-paste into the field!)
Revision history for this message
|
#8 |
sorry , I do not know how to attach my file .....
This is my arch.make file
#
# Copyright (C) 1996-2016 The SIESTA group
# This file is distributed under the terms of the
# GNU General Public License: see COPYING in the top directory
# or http://
# See Docs/Contributo
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90
SIESTA_
FPP=
FPP_OUTPUT=
FC=mpiifort
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
#FFLAGS= -O0 -g -check bounds -traceback
FFLAGS=
FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DSIESTA__NO_MRRR
LDFLAGS=
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
DUMMY_FOX= --enable-dummy
FFLAGS_DEBUG= -g -O2
BLAS_LIBS=
LAPACK_
BLACS_LIBS=
SCALAPACK_
#COMP_LIBS=
NETCDF_LIBS=
NETCDF_INTERFACE=
LIBS=$(
#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=
MPI_INCLUDE=
#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
atom.o: atom.F
$(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.c.o:
$(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.F.o:
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
This is the output log
Compilation architecture to be used: x86_64-
If this is not what you want, create the right
arch.make file using the models in Src/Sys
Hit ^C to abort...
==> Incorporating information about present compilation (compiler and flags)
make "FPPFLAGS=
make[1]: Entering directory '/F/siesta/
mpiifort -c -I/home/
make[1]: Leaving directory '/F/siesta/
make[1]: Entering directory '/F/siesta/
mpiifort -c -I/home/
if [ -z "4 8" ] ; then make kind_explorer ; fi
The kind numbers for single and double precision reals follow
sh /F/siesta/
===> Generating module files from templates...
4 8
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
ranlib libmpi_f90.a
make[1]: Leaving directory '/F/siesta/
(cd fdf ; make -j 1 "VPATH=
"FPPFLAGS=
"FFLAGS=
make[1]: Entering directory '/F/siesta/
In fdf, INCFLAGS is: -I/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
ar cru libfdf.a \
ranlib libfdf.a
cp libfdf.a ..
make[1]: Leaving directory '/F/siesta/
(cd xmlparser ; make -j 1 "VPATH=
FFFLAGS=
make[1]: Entering directory '/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
ar cru libxmlparser.a m_debug.o m_buffer.o m_elstack.o m_dictionary.o m_io.o m_reader.o m_converters.o m_charset.o m_entities.o m_xml_error.o m_fsm.o m_xml_parser.o flib_sax.o
ranlib libxmlparser.a
cp libxmlparser.a ..
make[1]: Leaving directory '/F/siesta/
(cd SiestaXC ; make -j 1 \
"FFLAGS=
make[1]: Entering directory '/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
ar cru libSiestaXC.a alloc.o bessph.o cellsubs.o debugmpi.o chkgmx.o fft1d.o interpolation.o minvec.o m_io.o moreParallelSubs.o class_OrbitalDi
ranlib libSiestaXC.a
cp *.mod *.a ..
make[1]: Leaving directory '/F/siesta/
(cd FoX; touch arch.make ; \
AR="ar" RANLIB="ranlib" \
$CONFIGURE VPATH="
checking build system type... x86_64-
checking host system type... x86_64-
checking for linker flag to name executables... -o
checking for Fortran compiler default output file name... conftest
checking whether the Fortran compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU Fortran compiler... no
checking whether mpiifort accepts -g... yes
checking for Fortran flag needed to allow free-form source for .f90 suffix... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for fixed form Fortran preprocessor features... done.
checking whether mpiifort compiles programs with cpp directives... yes
checking whether mpiifort accepts -D... yes
checking whether mpiifort accepts -I... yes
checking whether mpiifort fulfils requested features... yes
checking preprocessing mode we may therefore use... direct
checking for Fortran flag needed to allow free-form preprocessed source for .F90 suffix... none
checking for ranlib... ranlib
configure: Could not determine type of compiler
checking for kind number produced by kind(1.0)... 4
checking for kind number produced by kind(1.0d0)... 8
checking for kind number produced by selected_
checking for kind number produced by selected_
checking how to compile a call to FLUSH... default
checking how to compile a call to ABORT... with argument
checking for EOR character used by mpiifort... LF
checking for ASSOCIATED in restricted expression bug... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for flag to alter module search path... -I
checking for suffix of module files... mod
checking whether module filenames are uppercased... no
configure: creating ./config.status
config.status: creating arch.make
config.status: creating FoX-config
(cd FoX ; echo "AR = ar" >> arch.make ; \
echo "RANLIB = ranlib" >> arch.make )
(cd FoX; make -j 1 )
make[1]: Entering directory '/F/siesta/
mkdir -p objs/lib objs/finclude
(cd fsys; make VPATH=/
make[2]: Entering directory '/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
==> Creating libFoX_fsys.a with fox_m_fsys_
cp -p libFoX_fsys.a /F/siesta/
for i in *.mod; do \
cp -p $i /F/siesta/
make[2]: Leaving directory '/F/siesta/
(cd utils; make VPATH=/
make[2]: Entering directory '/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
==> Creating libFoX_utils.a with FoX_utils.o fox_m_utils_
cp -p libFoX_utils.a /F/siesta/
for i in *.mod; do \
cp -p $i /F/siesta/
make[2]: Leaving directory '/F/siesta/
(cd common; make VPATH=/
make[2]: Entering directory '/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
==> Creating libFoX_common.a with m_common_attrs.o m_common_buffer.o m_common_charset.o m_common_
cp -p libFoX_common.a /F/siesta/
for i in *.mod; do \
cp -p $i /F/siesta/
make[2]: Leaving directory '/F/siesta/
(cd wxml; make VPATH=/
make[2]: Entering directory '/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
==> Creating libFoX_wxml.a with m_wxml_escape.o m_wxml_core.o m_wxml_overloads.o FoX_wxml.o
ar cru libFoX_wxml.a m_wxml_escape.o m_wxml_core.o m_wxml_overloads.o FoX_wxml.o
ranlib libFoX_wxml.a
cp -p libFoX_wxml.a /F/siesta/
for i in *.mod; do \
cp -p $i /F/siesta/
make[2]: Leaving directory '/F/siesta/
(cd wcml; make VPATH=/
make[2]: Entering directory '/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
==> Creating libFoX_wcml.a with FoX_wcml.o m_wcml_coma.o m_wcml_core.o m_wcml_stml.o m_wcml_parameter.o m_wcml_property.o m_wcml_metadata.o m_wcml_lattice.o m_wcml_geometry.o m_wcml_molecule.o m_wcml_lists.o
cp -p libFoX_wcml.a /F/siesta/
for i in *.mod ; do \
cp -p $i /F/siesta/
make[2]: Leaving directory '/F/siesta/
if test -d examples; then (cd examples; make VPATH=/
make[1]: Leaving directory '/F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -I/home/
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mpiifort -c -I/home/
mpiifort -c -I/home/
mpiifort -c -g -O2 `FoX/FoX-config --fcflags` -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DSIESTA__NO_MRRR /F/siesta/
mpiifort -c -I/home/
mpiifort -c -I/home/
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arch.make:66: recipe for target 'rdiag_mrrr.o' failed
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#9 |
1. There must be something not in the error log,
when issuing the make command do it like this:
make 2>&1 > output.log
to also capture the error message. (Then only send the last 50 lines or so)
2. Could you try with the beta 2 release?
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#10 |
Thank you very much ,this arch.make can compile beta 2 very successfully ,and I get the parallel version .Thank you so much.
I am going to give up beta 1........
This is the error log when compiling beta 1
...................
bounds -traceback -heap-arrays 64 -g -O2 `FoX/FoX-config --fcflags` -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DSIESTA__NO_MRRR /F/siesta/
arch.make:66: recipe for target 'rdiag_mrrr.o' failed
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#11 |
I can now see the mistake,
See this bug report:
https:/
However, I think there is no reason for you to use b1.
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#12 |
HA-HA , Now , I know where the problem exist .Thank you very very much .