[petsc-users] Compilation error in petsc 3.1-p8 with ParMetis
Mohammad Mirzadeh
mirzadeh at gmail.com
Tue Jul 26 22:43:03 CDT 2011
Hi all,
I am having trouble configuring PETSc 3.1-p8 with ParMetis 3.2 and below (I
have tried all of their versions). What I can understand from the
configure.log (attached below) is that for some reason PETSc cannot find the
libs . I have tried the flag --download-parmetis=/path/to/tar.gz and also
tried compiling ParMetis myself and using
--with-parmetis-dir=/path/to/build_dir and none seem to work. In the latter
case, ParMetis compiles just fine but it does not put the libs and header
files under /build_dir/include or /buid_dir/lib.
Does using --with-parmetis-include and --with-parmetis-lib work with
multiple directory locations? I tried putting all the hear files in one
directory but there are multiple header files with the same name and I do
not know which one I should use. Any help is greatly appreciated.
Thanks,
Mohammad
================================================================================
TEST configureLibrary from
PETSc.packages.ParMetis(/home/mohammad/soft/petsc-3.1-p8-debug/config/BuildSystem/config/package.py:370)
TESTING: configureLibrary from
PETSc.packages.ParMetis(config/BuildSystem/config/package.py:370)
Find an installation and check if it can work with PETSc
==================================================================================
Checking for a functional ParMetis
Found a copy of PARMETIS in ParMetis-3.2.0
Pushing language C
Popping language C
Have to rebuild ParMetis, make.inc !=
/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/conf/ParMetis
===============================================================================
Compiling & installing Parmetis; this may take several
minutes
===============================================================================
sh: cd
/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0; make
clean; make lib; make minstall; make clean
Executing: cd
/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0; make
clean; make lib; make minstall; make clean
sh: (cd METISLib ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/METISLib'
rm -f *.o
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/METISLib'
(cd ParMETISLib ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/ParMETISLib'
rm -f *.o
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/ParMETISLib'
(cd Programs ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/Programs'
rm -f *.o ;\
rm -f ../Graphs/ptest3.2.0
rm -f ../Graphs/mtest3.2.0
rm -f ../Graphs/parmetis3.2.0
rm -f ../Graphs/pometis3.2.0
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/Programs'
(cd METISLib ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/METISLib'
rm -f *.o
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/METISLib'
(cd ParMETISLib ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/ParMETISLib'
rm -f *.o
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/ParMETISLib'
(cd Programs ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/Programs'
rm -f *.o ;\
rm -f ../Graphs/ptest3.2.0
rm -f ../Graphs/mtest3.2.0
rm -f ../Graphs/parmetis3.2.0
rm -f ../Graphs/pometis3.2.0
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/Programs'
********Output of running make on ParMetis follows *******
(cd METISLib ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/METISLib'
rm -f *.o
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/METISLib'
(cd ParMETISLib ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/ParMETISLib'
rm -f *.o
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/ParMETISLib'
(cd Programs ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/Programs'
rm -f *.o ;\
rm -f ../Graphs/ptest3.2.0
rm -f ../Graphs/mtest3.2.0
rm -f ../Graphs/parmetis3.2.0
rm -f ../Graphs/pometis3.2.0
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/Programs'
(cd METISLib ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/METISLib'
rm -f *.o
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/METISLib'
(cd ParMETISLib ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/ParMETISLib'
rm -f *.o
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/ParMETISLib'
(cd Programs ; make clean )
make[1]: Entering directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/Programs'
rm -f *.o ;\
rm -f ../Graphs/ptest3.2.0
rm -f ../Graphs/mtest3.2.0
rm -f ../Graphs/parmetis3.2.0
rm -f ../Graphs/pometis3.2.0
make[1]: Leaving directory
`/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/Programs'
make: *** No rule to make target `lib'. Stop.
make: *** No rule to make target `minstall'. Stop.
********End of Output of running make on ParMetis *******
sh: cp -f
/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/make.inc
/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/conf/ParMetis
Executing: cp -f
/home/mohammad/soft/petsc-3.1-p8-debug/externalpackages/ParMetis-3.2.0/make.inc
/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/conf/ParMetis
sh:
Checking for library in Download PARMETIS:
['/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib/libparmetis.a',
'libmetis.a']
================================================================================
TEST check from
config.libraries(/home/mohammad/soft/petsc-3.1-p8-debug/config/BuildSystem/config/libraries.py:133)
TESTING: check from
config.libraries(config/BuildSystem/config/libraries.py:133)
Checks that the library "libName" contains "funcs", and if it does defines
HAVE_LIB"libName"
- libDir may be a list of directories
- libName may be a list of library names
Checking for functions ['ParMETIS_V3_PartKway'] in library
['/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib/libparmetis.a',
'libmetis.a'] ['libnsl.a', 'librt.a']
Pushing language C
sh: /home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/bin/mpicc -c -o
conftest.o -Wall -Wwrite-strings -Wno-strict-aliasing -g3 conftest.c
Executing:
/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/bin/mpicc -c -o
conftest.o -Wall -Wwrite-strings -Wno-strict-aliasing -g3 conftest.c
sh:
Pushing language C
Popping language C
sh: /home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/bin/mpicc -o
conftest -Wall -Wwrite-strings -Wno-strict-aliasing -g3 conftest.o
-Wl,-rpath,/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib
-L/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib -lparmetis
-lmetis -lnsl -lrt -lmpichcxx -lstdc++
-L/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3
-L/usr/lib/x86_64-linux-gnu -ldl -lmpich -lpthread -lrt -lgcc_s -ldl
Executing:
/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/bin/mpicc -o
conftest -Wall -Wwrite-strings -Wno-strict-aliasing -g3 conftest.o
-Wl,-rpath,/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib
-L/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib -lparmetis
-lmetis -lnsl -lrt -lmpichcxx -lstdc++
-L/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3
-L/usr/lib/x86_64-linux-gnu -ldl -lmpich -lpthread -lrt -lgcc_s -ldl
sh:
Possible ERROR while running linker: /usr/bin/ld: cannot find -lparmetis
collect2: ld returned 1 exit status
output: ret = 256
error message = {/usr/bin/ld: cannot find -lparmetis
collect2: ld returned 1 exit status
}
Pushing language C
Popping language C
in /home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/bin/mpicc -o
conftest -Wall -Wwrite-strings -Wno-strict-aliasing -g3 conftest.o
-Wl,-rpath,/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib
-L/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib -lparmetis
-lmetis -lnsl -lrt -lmpichcxx -lstdc++
-L/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug/lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3
-L/usr/lib/x86_64-linux-gnu -ldl -lmpich -lpthread -lrt -lgcc_s -ldl
Source:
#include "confdefs.h"
#include "conffix.h"
/* Override any gcc2 internal prototype to avoid an error. */
char ParMETIS_V3_PartKway();
int main() {
ParMETIS_V3_PartKway()
;
return 0;
}
Popping language C
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
details):
-------------------------------------------------------------------------------
Downloaded parmetis could not be used. Please check install in
/home/mohammad/soft/petsc-3.1-p8-debug/linux-gnu-c-debug
*******************************************************************************
File "./config/configure.py", line 257, in petsc_configure
framework.configure(out = sys.stdout)
File
"/home/mohammad/soft/petsc-3.1-p8-debug/config/BuildSystem/config/framework.py",
line 944, in configure
child.configure()
File
"/home/mohammad/soft/petsc-3.1-p8-debug/config/BuildSystem/config/package.py",
line 456, in configure
self.executeTest(self.configureLibrary)
File
"/home/mohammad/soft/petsc-3.1-p8-debug/config/BuildSystem/config/base.py",
line 97, in executeTest
ret = apply(test, args,kargs)
File
"/home/mohammad/soft/petsc-3.1-p8-debug/config/BuildSystem/config/package.py",
line 395, in configureLibrary
for location, directory, lib, incl in self.generateGuesses():
File
"/home/mohammad/soft/petsc-3.1-p8-debug/config/BuildSystem/config/package.py",
line 210, in generateGuesses
raise RuntimeError('Downloaded '+self.package+' could not be used.
Please check install in '+d+'\n')
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