Dear Johannes,
Thanks a lot for your answer.
Having Scotch installed fixes the config problem.
However, using dorsal, adding 'scotch' to the packages list did not end
up having SCOTCH in the "optional packages found" list, even though it
fixed the config problem (the full dorsal output is attached, as well as
the dorsal input, i.e. the modified "opensuse11.3.platform" file):
---------
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) MPI
-- (**) PETSC
-- (**) PETSC4PY
-- (**) SLEPC
-- (**) TRILINOS
-- (**) UMFPACK
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) SCOTCH
-- (**) PARMETIS
-- (**) CGAL
-- (**) HDF5
--
-- Found Qt4: /usr/bin/qmake (found version "4.6.3")
-- Enabling generation of documentation.
-- Initializing sphinx projects
-- Enabling generation of html-documentation
-- Configuring done
-- Generating done
--------
So I went on to the build process. There, I encounter a "recompile with
-fPIC" problem (see again in attachment for the full output):
-------
[ 96%] Built target dolfin
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
[ 96%] Built target copy_swig_files
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
Linking CXX shared module _mesh.so
/usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation
R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when
making a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [dolfin/swig/modules/mesh/_mesh.so] Error 1
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[1]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
Failure with exit status:
Exit message: There was a problem building dolfin-1.4.0.
--------
I added the "-fPIC" option in several environment variables (see below),
but can't get over this problem.
Could you please help me with this too?
Thanks a lot again,
Serge
-------
My (unsuccessful) trials:
In: FEniCS/packages/dolfin.package
added:
COMPILERFLAGS="'-fPIC'"
In: MyInstall/Downloads/dolfin-1.4.0/CMakeLists.txt :
added:
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fPIC")
set(CMAKE_CXX_FLAGS_DEVELOPER "${CMAKE_CXX_FLAGS_DEVELOPER} -fPIC")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fPIC")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
"${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -fPIC")
set(DOLFIN_CXX_DEVELOPER_FLAGS "${DOLFIN_CXX_DEVELOPER_FLAGS} -fPIC")
--------
On 19/09/2014 12:44, Johannes Ring wrote:
[Please keep fenics-support in Cc]
On Fri, Sep 19, 2014 at 10:08 AM, Serge Van Criekingen
<[email protected]> wrote:
Dear Johannes,
Thank you for your fast answer.
Please find the complete cmake output in attachment.
Thank you. This is what is causing the problem:
-- Checking for package 'SCOTCH-PT'
CMake Error at cmake/modules/FindSCOTCH.cmake:124 (file):
file STRINGS file
"/home/zatopek/Fenics/TRIALS/ManualInstall/fenics-project-dolfin-dc57a0b75a2e/SCOTCH_INCLUDE_DIRS-NOTFOUND/scotch.h"
cannot be read.
Call Stack (most recent call first):
CMakeLists.txt:396 (find_package)
CMake Error at cmake/modules/FindSCOTCH.cmake:125 (string):
string sub-command REGEX, mode MATCH needs at least 5 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:396 (find_package)
CMake Error at cmake/modules/FindSCOTCH.cmake:126 (string):
string sub-command REGEX, mode MATCH needs at least 5 arguments total to
command.
Call Stack (most recent call first):
CMakeLists.txt:396 (find_package)
-- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing:
SCOTCH_LIBRARIES SCOTCH_INCLUDE_DIRS SCOTCH_TEST_RUNS)
This looks like a bug in DOLFIN. The quickest fix for you would be to
either turn off SCOTCH or let Dorsal build SCOTCH by adding 'scotch'
to the PACKAGES list in opensuse11.3.platform.
Johannes
Thanks again,
Serge
On 18/09/2014 11:05, Johannes Ring wrote:
On Wed, Sep 17, 2014 at 3:48 PM, Serge Van Criekingen
<[email protected]> wrote:
Dear Sir,
I have been successfully using fenics for a little while on my laptop
Ubuntu, for which the install process was straightforward.
Now, I want to install it on the Suse Linux Enterprise Server SLES 11 SP3
platform of the computing center I manage.
I tried both dorsal (based on the
"platforms/supported/opensuse11.3.platform" file) and manual install.
In both cases, installing FFC, FIAT, INSTANT and UFL works fine, but the
DOLFIN installation fails.
I had to install several packages (boost_1_56_0, Eigen3,
ScientificPython-2.8.1, ply-3.4, swig-3.0.2, Sphinx, VTK) and adjust
PATH,
PYTHON_PATH and several *_DIR environment variables to overcome the
errors
that came in the way.
However, whatever I do, I get to a point like this one :
--------
[...]
Please include the complete cmake output, also the part above this line.
Johannes
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) SPHINX
-- (OK) VTK
-- (OK) QT
--
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) PETSC4PY
-- (**) SLEPC
-- (**) TRILINOS
-- (**) UMFPACK
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) SCOTCH
-- (**) PARMETIS
-- (**) HDF5
--
--
-- Generating SWIG interface.
-- --------------------------
-- Found Qt4: /usr/bin/qmake (found version "4.6.3")
-- Enabling generation of documentation.
-- Initializing sphinx projects
-- Enabling generation of html-documentation
-- Configuring incomplete, errors occurred!
See also
"/home/zatopek/Fenics/TRIALS/ManualInstall/fenics-project-dolfin-dc57a0b75a2e/build./CMakeFiles/CMakeOutput.log".
See also
"/home/zatopek/Fenics/TRIALS/ManualInstall/fenics-project-dolfin-dc57a0b75a2e/build./CMakeFiles/CMakeError.log".
-------
And at this point, I do not see any error message giving me a hint of how
to
overcome the "Configuring incomplete, errors occurred!" problem. In
CMakeError.log, the error messages concern optional packages (typically
ParMetis), and Qt ("Q_WS_WIN / Q_WS_QWS / Q_WS_MAC not declared in this
scope") which I guess should not be a problem since Q_WS_X11 was found.
So, I don't know where to go from there.
Any hint?
Thank you very much for Fenics anyway.
With best regards,
Serge Van Criekingen
_______________________________________________
fenics-support mailing list
[email protected]
http://fenicsproject.org/mailman/listinfo/fenics-support
# openSUSE 11.3
# This build script assumes that you have the following packages
# already installed via openSUSE's zypper. In order to install them,
# first run the following to add the required repositories:
#
# sudo zypper addrepo
http://download.opensuse.org/repositories/science/openSUSE_11.3/ Science
# sudo zypper addrepo
http://download.opensuse.org/repositories/Education/openSUSE_11.3/ Education
# sudo zypper addrepo
http://download.opensuse.org/repositories/Education:/Salome:/Factory/openSUSE_11.3/
Education_Salome
# sudo zypper addrepo
http://download.opensuse.org/repositories/openSUSE:/Factory:/Contrib/openSUSE_11.3
Factory_Contrib
#
# Then, run the following to install the actual packages:
#
# sudo zypper install -C lsb bzr subversion libxml2-devel gcc gcc-c++ \
# openmpi-devel python-devel python-numpy python-numpy-devel swig \
# wget boost-devel vtk-python liblapack3 libblas3 liblapack3 \
# mpfr-devel suitesparse-common-devel gmp-devel cmake umfpack-devel \
# libumfpack5 CGAL-devel scotch-devel libatlas3-devel flex python-ply
#
# Make sure to run
#
# mpi-selector --set openmpi-1.3.2
#
# and start a new shell before running the Dorsal script for the first
# time. You may even need to logout or restart.
##
# Platform specific variables
#default PETSC_ARCH=linux-gnu-cxx-opt
#default PETSC_DIR=/home/zatopek/Fenics/MyInstall/Downloads/petsc-3.4.2
default SCOTCH_ARCH=pc_linux2
# Define the packages this platform needs
PACKAGES=(
skip:parmetis
# SVC trilinos
# SVC petsc
#SVC slepc
# SVC armadillo
# swiginac
#added by SVC:cgal and scotch
skip:cgal
scotch
skip:scientificpython
skip:fiat
# ferari
skip:ufl
skip:ffc
# syfi
# SVC viper
instant
dolfin
)
[1;32mFound configuration for project FEniCS.[0m
[1;32mSkipping parmetis-4.0.2[0m
[1;32mSkipping CGAL-4.3[0m
[1;32mFetching scotch_6.0.0_esmumps[0m
[1;32mVerifying scotch_6.0.0_esmumps[0m
scotch_6.0.0_esmumps.tar.gz: OK
[1;32mUnpacking scotch_6.0.0_esmumps[0m
[1;32mBuilding scotch_6.0.0_esmumps[0m
(cd libscotch ; make VERSION=6 RELEASE=0 PATCHLEVEL=0 scotch && make
install)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make CC="mpicc" CCD="mpicc" \
scotch.h
\
scotchf.h
\
libscotch.a
\
libscotcherr.a \
libscotcherrexit.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[2]: `scotch.h' is up to date.
make[2]: `scotchf.h' is up to date.
make[2]: `libscotch.a' is up to date.
make[2]: `libscotcherr.a' is up to date.
make[2]: `libscotcherrexit.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
(cd scotch ; make VERSION=6 RELEASE=0 PATCHLEVEL=0 scotch && make
install)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make CC="mpicc" SCOTCHLIB=scotch \
acpl \
amk_ccc \
amk_fft2
\
amk_grf \
amk_hy \
amk_m2 \
amk_p2 \
atst \
gbase \
gcv \
gmap \
gmk_hy \
gmk_m2 \
gmk_m3 \
gmk_msh \
gmk_ub2 \
gmtst \
gord \
gotst \
gout \
gpart \
gscat \
gtst \
mcv \
mmk_m2 \
mmk_m3 \
mord \
mtst
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[2]: `acpl' is up to date.
make[2]: `amk_ccc' is up to date.
make[2]: `amk_fft2' is up to date.
make[2]: `amk_grf' is up to date.
make[2]: `amk_hy' is up to date.
make[2]: `amk_m2' is up to date.
make[2]: `amk_p2' is up to date.
make[2]: `atst' is up to date.
make[2]: `gbase' is up to date.
make[2]: `gcv' is up to date.
make[2]: `gmap' is up to date.
make[2]: `gmk_hy' is up to date.
make[2]: `gmk_m2' is up to date.
make[2]: `gmk_m3' is up to date.
make[2]: `gmk_msh' is up to date.
make[2]: `gmk_ub2' is up to date.
make[2]: `gmtst' is up to date.
make[2]: `gord' is up to date.
make[2]: `gotst' is up to date.
make[2]: `gout' is up to date.
make[2]: `gpart' is up to date.
make[2]: `gscat' is up to date.
make[2]: `gtst' is up to date.
make[2]: `mcv' is up to date.
make[2]: `mmk_m2' is up to date.
make[2]: `mmk_m3' is up to date.
make[2]: `mord' is up to date.
make[2]: `mtst' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make CC="mpicc" SCOTCHLIB=scotch \
acpl \
amk_ccc \
amk_fft2
\
amk_grf \
amk_hy \
amk_m2 \
amk_p2 \
atst \
gbase \
gcv \
gmap \
gmk_hy \
gmk_m2 \
gmk_m3 \
gmk_msh \
gmk_ub2 \
gmtst \
gord \
gotst \
gout \
gpart \
gscat \
gtst \
mcv \
mmk_m2 \
mmk_m3 \
mord \
mtst
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[2]: `acpl' is up to date.
make[2]: `amk_ccc' is up to date.
make[2]: `amk_fft2' is up to date.
make[2]: `amk_grf' is up to date.
make[2]: `amk_hy' is up to date.
make[2]: `amk_m2' is up to date.
make[2]: `amk_p2' is up to date.
make[2]: `atst' is up to date.
make[2]: `gbase' is up to date.
make[2]: `gcv' is up to date.
make[2]: `gmap' is up to date.
make[2]: `gmk_hy' is up to date.
make[2]: `gmk_m2' is up to date.
make[2]: `gmk_m3' is up to date.
make[2]: `gmk_msh' is up to date.
make[2]: `gmk_ub2' is up to date.
make[2]: `gmtst' is up to date.
make[2]: `gord' is up to date.
make[2]: `gotst' is up to date.
make[2]: `gout' is up to date.
make[2]: `gpart' is up to date.
make[2]: `gscat' is up to date.
make[2]: `gtst' is up to date.
make[2]: `mcv' is up to date.
make[2]: `mmk_m2' is up to date.
make[2]: `mmk_m3' is up to date.
make[2]: `mord' is up to date.
make[2]: `mtst' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
cp acpl amk_ccc amk_fft2 amk_grf amk_hy amk_m2 amk_p2 atst gbase gcv gmap
gmk_hy gmk_m2 gmk_m3 gmk_msh gmk_ub2 gmtst gord gotst gout gpart *gtst gscat
mcv mmk_m2 mmk_m3 mord mtst ../../bin
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
(cd libscotchmetis ; make
scotch && make install)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make CC="mpicc" SCOTCHLIB=ptscotch
\
libscotchmetis.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[2]: `libscotchmetis.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make CC="mpicc" SCOTCHLIB=ptscotch
\
libscotchmetis.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[2]: `libscotchmetis.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
cp metis.h ../../include
cp libscotchmetis.a ../../lib
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
(cd libscotch ; make VERSION=6 RELEASE=0 PATCHLEVEL=0 ptscotch && make
ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make CC="mpicc" CCD="mpicc" \
scotch.h
\
scotchf.h
\
libscotch.a
\
libscotcherr.a \
libscotcherrexit.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[2]: `scotch.h' is up to date.
make[2]: `scotchf.h' is up to date.
make[2]: `libscotch.a' is up to date.
make[2]: `libscotcherr.a' is up to date.
make[2]: `libscotcherrexit.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" \
ptscotch.h
\
ptscotchf.h
\
libptscotch.a
\
libptscotcherr.a
\
libptscotcherrexit.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[2]: `ptscotch.h' is up to date.
make[2]: `ptscotchf.h' is up to date.
make[2]: `libptscotch.a' is up to date.
make[2]: `libptscotcherr.a' is up to date.
make[2]: `libptscotcherrexit.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Nothing to be done for `ptinstall'.
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
(cd scotch ; make VERSION=6 RELEASE=0 PATCHLEVEL=0 ptscotch && make
ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make CC="mpicc" SCOTCHLIB=ptscotch \
dggath \
dgmap \
dgord \
dgpart \
dgscat \
dgtst
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[2]: `dggath' is up to date.
make[2]: `dgmap' is up to date.
make[2]: `dgord' is up to date.
make[2]: `dgpart' is up to date.
make[2]: `dgscat' is up to date.
make[2]: `dgtst' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make CC="mpicc" SCOTCHLIB=ptscotch \
dggath \
dgmap \
dgord \
dgpart \
dgscat \
dgtst
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[2]: `dggath' is up to date.
make[2]: `dgmap' is up to date.
make[2]: `dgord' is up to date.
make[2]: `dgpart' is up to date.
make[2]: `dgscat' is up to date.
make[2]: `dgtst' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
cp dggath dgmap dgord dgpart dgscat dgtst ../../bin
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
(cd libscotchmetis ; make
ptscotch && make ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" SCOTCHLIB=ptscotch \
libptscotchparmetis.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[2]: `libptscotchparmetis.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" SCOTCHLIB=ptscotch \
libptscotchparmetis.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[2]: `libptscotchparmetis.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
cp parmetis.h ../../include
cp libptscotchparmetis.a ../../lib
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
(cd libscotch ; make VERSION=6 RELEASE=0 PATCHLEVEL=0 ptscotch && make
ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make CC="mpicc" CCD="mpicc" \
scotch.h
\
scotchf.h
\
libscotch.a
\
libscotcherr.a \
libscotcherrexit.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[2]: `scotch.h' is up to date.
make[2]: `scotchf.h' is up to date.
make[2]: `libscotch.a' is up to date.
make[2]: `libscotcherr.a' is up to date.
make[2]: `libscotcherrexit.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" \
ptscotch.h
\
ptscotchf.h
\
libptscotch.a
\
libptscotcherr.a
\
libptscotcherrexit.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[2]: `ptscotch.h' is up to date.
make[2]: `ptscotchf.h' is up to date.
make[2]: `libptscotch.a' is up to date.
make[2]: `libptscotcherr.a' is up to date.
make[2]: `libptscotcherrexit.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Nothing to be done for `ptinstall'.
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
(cd scotch ; make VERSION=6 RELEASE=0 PATCHLEVEL=0 ptscotch && make
ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make CC="mpicc" SCOTCHLIB=ptscotch \
dggath \
dgmap \
dgord \
dgpart \
dgscat \
dgtst
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[2]: `dggath' is up to date.
make[2]: `dgmap' is up to date.
make[2]: `dgord' is up to date.
make[2]: `dgpart' is up to date.
make[2]: `dgscat' is up to date.
make[2]: `dgtst' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make CC="mpicc" SCOTCHLIB=ptscotch \
dggath \
dgmap \
dgord \
dgpart \
dgscat \
dgtst
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[2]: `dggath' is up to date.
make[2]: `dgmap' is up to date.
make[2]: `dgord' is up to date.
make[2]: `dgpart' is up to date.
make[2]: `dgscat' is up to date.
make[2]: `dgtst' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
cp dggath dgmap dgord dgpart dgscat dgtst ../../bin
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
(cd libscotchmetis ; make
ptscotch && make ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" SCOTCHLIB=ptscotch \
libptscotchparmetis.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[2]: `libptscotchparmetis.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" SCOTCHLIB=ptscotch \
libptscotchparmetis.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[2]: `libptscotchparmetis.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
cp parmetis.h ../../include
cp libptscotchparmetis.a ../../lib
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
(cd esmumps ; make ptscotch && make ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
rm -f *~ common.h *.o lib*.a main_esmumps
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC=mpicc SCOTCHLIB=ptscotch ESMUMPSLIB=ptesmumps \
libesmumps.a
\
main_esmumps
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
cat module.h ../libscotch/common.h > common.h
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c graph_graph.c -o graph_graph.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c order.c -o order.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c order_scotch_graph.c -o
order_scotch_graph.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c dof.c -o dof.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c symbol.c -o symbol.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c symbol_fax_graph.c -o symbol_fax_graph.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c esmumps.c -o esmumps.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c esmumps_f.c -o esmumps_f.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c esmumps_strats.c -o esmumps_strats.o
ar -ruv libptesmumps.a graph_graph.o order.o order_scotch_graph.o dof.o
symbol.o symbol_fax_graph.o esmumps.o esmumps_f.o esmumps_strats.o
ar: creating libptesmumps.a
a - graph_graph.o
a - order.o
a - order_scotch_graph.o
a - dof.o
a - symbol.o
a - symbol_fax_graph.o
a - esmumps.o
a - esmumps_f.o
a - esmumps_strats.o
ranlib libptesmumps.a
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include main_esmumps.c -o main_esmumps -L../../lib
-lz -lm -lrt -L. -lptesmumps -lptscotch -lscotch -lptscotcherrexit -lm
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
cp esmumps.h ../../include
cp libptesmumps.a ../../lib
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
(cd libscotch ; make VERSION=6 RELEASE=0 PATCHLEVEL=0 ptscotch && make
ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make CC="mpicc" CCD="mpicc" \
scotch.h
\
scotchf.h
\
libscotch.a
\
libscotcherr.a \
libscotcherrexit.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[2]: `scotch.h' is up to date.
make[2]: `scotchf.h' is up to date.
make[2]: `libscotch.a' is up to date.
make[2]: `libscotcherr.a' is up to date.
make[2]: `libscotcherrexit.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" \
ptscotch.h
\
ptscotchf.h
\
libptscotch.a
\
libptscotcherr.a
\
libptscotcherrexit.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[2]: `ptscotch.h' is up to date.
make[2]: `ptscotchf.h' is up to date.
make[2]: `libptscotch.a' is up to date.
make[2]: `libptscotcherr.a' is up to date.
make[2]: `libptscotcherrexit.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
make[1]: Nothing to be done for `ptinstall'.
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotch'
(cd scotch ; make VERSION=6 RELEASE=0 PATCHLEVEL=0 ptscotch && make
ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make CC="mpicc" SCOTCHLIB=ptscotch \
dggath \
dgmap \
dgord \
dgpart \
dgscat \
dgtst
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[2]: `dggath' is up to date.
make[2]: `dgmap' is up to date.
make[2]: `dgord' is up to date.
make[2]: `dgpart' is up to date.
make[2]: `dgscat' is up to date.
make[2]: `dgtst' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make CC="mpicc" SCOTCHLIB=ptscotch \
dggath \
dgmap \
dgord \
dgpart \
dgscat \
dgtst
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
make[2]: `dggath' is up to date.
make[2]: `dgmap' is up to date.
make[2]: `dgord' is up to date.
make[2]: `dgpart' is up to date.
make[2]: `dgscat' is up to date.
make[2]: `dgtst' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
cp dggath dgmap dgord dgpart dgscat dgtst ../../bin
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/scotch'
(cd libscotchmetis ; make
ptscotch && make ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" SCOTCHLIB=ptscotch \
libptscotchparmetis.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[2]: `libptscotchparmetis.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC="mpicc" SCOTCHLIB=ptscotch \
libptscotchparmetis.a
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
make[2]: `libptscotchparmetis.a' is up to date.
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
cp parmetis.h ../../include
cp libptscotchparmetis.a ../../lib
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/libscotchmetis'
(cd esmumps ; make ptscotch && make ptinstall)
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
rm -f *~ common.h *.o lib*.a main_esmumps
make CFLAGS="-fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH" CC=mpicc SCOTCHLIB=ptscotch ESMUMPSLIB=ptesmumps \
libesmumps.a
\
main_esmumps
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
cat module.h ../libscotch/common.h > common.h
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c graph_graph.c -o graph_graph.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c order.c -o order.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c order_scotch_graph.c -o
order_scotch_graph.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c dof.c -o dof.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c symbol.c -o symbol.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c symbol_fax_graph.c -o symbol_fax_graph.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c esmumps.c -o esmumps.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c esmumps_f.c -o esmumps_f.o
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include -c esmumps_strats.c -o esmumps_strats.o
ar -ruv libptesmumps.a graph_graph.o order.o order_scotch_graph.o dof.o
symbol.o symbol_fax_graph.o esmumps.o esmumps_f.o esmumps_strats.o
ar: creating libptesmumps.a
a - graph_graph.o
a - order.o
a - order_scotch_graph.o
a - dof.o
a - symbol.o
a - symbol_fax_graph.o
a - esmumps.o
a - esmumps_f.o
a - esmumps_strats.o
ranlib libptesmumps.a
mpicc -fPIC -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
-DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64
-DSCOTCH_PTSCOTCH -I../../include main_esmumps.c -o main_esmumps -L../../lib
-lz -lm -lrt -L. -lptesmumps -lptscotch -lscotch -lptscotcherrexit -lm
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
cp esmumps.h ../../include
cp libptesmumps.a ../../lib
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/scotch_6.0.0_esmumps/src/esmumps'
mkdir /home/zatopek/Fenics/MyInstall/share/man
mkdir: cannot create directory `/home/zatopek/Fenics/MyInstall/share/man': File
exists
make: [/home/zatopek/Fenics/MyInstall/share/man] Error 1 (ignored)
cp -f ../bin/[agm]* /home/zatopek/Fenics/MyInstall/bin
cp -f ../bin/d[agm]* /home/zatopek/Fenics/MyInstall/bin
cp -f ../include/*scotch*.h /home/zatopek/Fenics/MyInstall/include
cp -f ../lib/*scotch*.a /home/zatopek/Fenics/MyInstall/lib
cp -Rf ../man/* /home/zatopek/Fenics/MyInstall/share/man
[1;32mSkipping ScientificPython-2.8[0m
[1;32mSkipping fiat-1.4.0[0m
[1;32mSkipping ufl-1.4.0[0m
[1;32mSkipping ffc-1.4.0[0m
[1;32mFetching instant-1.4.0[0m
[1;32mVerifying instant-1.4.0[0m
instant-1.4.0.tar.gz: OK
[1;32mUnpacking instant-1.4.0[0m
[1;32mBuilding instant-1.4.0[0m
running install
running build
running build_py
running build_scripts
running install_lib
running install_scripts
changing mode of /home/zatopek/Fenics/MyInstall/bin/instant-clean to 755
changing mode of /home/zatopek/Fenics/MyInstall/bin/instant-showcache to 755
running install_data
running install_egg_info
Removing
/home/zatopek/Fenics/MyInstall/lib/python2.7/site-packages/instant-1.3.0_-py2.7.egg-info
Writing
/home/zatopek/Fenics/MyInstall/lib/python2.7/site-packages/instant-1.3.0_-py2.7.egg-info
[1;32mFetching dolfin-1.4.0[0m
[1;32mVerifying dolfin-1.4.0[0m
dolfin-1.4.0.tar.gz: OK
[1;32mUnpacking dolfin-1.4.0[0m
[1;32mBuilding dolfin-1.4.0[0m
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_STD_CPP11
-- Performing Test HAVE_STD_CPP11 - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of size_t
-- Check size of size_t - done
-- Found MPI_Fortran:
/opt/openmpi/lib/libmpi_f90.so;/opt/openmpi/lib/libmpi_f77.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Performing Test OPENMP_UINT_TEST_RUNS
-- Performing Test OPENMP_UINT_TEST_RUNS - Success
-- Boost version: 1.56.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- thread
-- iostreams
-- UFC version: 1.4.0
-- Found Eigen3: /home/zatopek/Eigen3/eigen-eigen-1306d75b4a21 (Required is at
least version "3.0.0")
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6")
-- Found PythonInterp: /usr/local/bin/python (found suitable version "2.7.7",
minimum required is "2")
-- NumPy header version 1.8.1 found
-- Found SWIG: /home/zatopek/swig-3.0.2/MyInstall/bin/swig (found version
"3.0.2")
-- Checking for package 'PETSc'
-- PETSC_DIR is PETSC_DIR-NOTFOUND
-- PETSC_ARCH is empty
-- Unable to find petscconf.h
-- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. (missing:
PETSC_LIBRARIES PETSC_DIR PETSC_INCLUDE_DIRS PETSC_TEST_RUNS PETSC_VERSION
PETSC_VERSION_OK) (Required is at least version "3.3")
-- Checking for package 'AMD'
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Found HDF5:
/usr/lib64/libhdf5.so;/usr/lib64/libpthread.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so
-- HDF5 has been found, but is missing parallel support. It will not be enabled.
-- PASTIX_LIBRARIES
PASTIX_LIBRARY-NOTFOUND;/usr/lib64/librt.so;/usr/lib64/libm.so
-- A library with BLAS API found.
-- PaStiX could not be found. Be sure to set PASTIX_DIR. (missing:
PASTIX_INCLUDE_DIRS PASTIX_TEST_RUNS PASTIX_VERSION PASTIX_VERSION_OK)
-- Checking for Trilinos
-- Unable to find Trilinos (>= 11.0.0)
-- Trilinos could not be found
-- Checking for package 'CGAL'
-- Performing Test CGAL_TEST_RUNS
-- Performing Test CGAL_TEST_RUNS - Failed
-- CGAL could not be found. Be sure to set CGAL_DIR (missing: CGAL_TEST_RUNS)
(Required is at least version "4.1")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
-- checking for module 'cppunit'
-- package 'cppunit' not found
-- CPPUNIT could not be found. Be sure to set CPPUNIT_DIR. (missing:
CPPUNIT_LIBRARIES CPPUNIT_INCLUDE_DIRS)
-- Checking for package 'Sphinx'
-- Found Sphinx: /home/zatopek/Sphinx/MyInstall/bin/sphinx-build (Required is
at least version "1.1.0")
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.6.3")
-- Found VTK: /home/zatopek/VTK/MyInstall/lib/cmake/vtk-6.1 (found version
"6.1")
--
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) SPHINX
-- (OK) VTK
-- (OK) QT
--
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) MPI
-- (**) PETSC
-- (**) PETSC4PY
-- (**) SLEPC
-- (**) TRILINOS
-- (**) UMFPACK
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) SCOTCH
-- (**) PARMETIS
-- (**) CGAL
-- (**) HDF5
--
-- Found Qt4: /usr/bin/qmake (found version "4.6.3")
-- Enabling generation of documentation.
-- Initializing sphinx projects
-- Enabling generation of html-documentation
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CGAL_DISABLE_ROUNDING_MATH_CHECK
-- Build files have been written to:
/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
make: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[1]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
Scanning dependencies of target dolfin
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
[ 0%] Building CXX object dolfin/CMakeFiles/dolfin.dir/graph/SCOTCH.cpp.o
Linking CXX shared library libdolfin.so
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
[ 96%] Built target dolfin
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
[ 96%] Built target copy_swig_files
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Entering directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
Linking CXX shared module _mesh.so
/usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S
against `_Py_NotImplementedStruct' can not be used when making a shared object;
recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [dolfin/swig/modules/mesh/_mesh.so] Error 1
make[2]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[1]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2
make[1]: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
[1;31mFailure with exit status: 2[0m
[1;31mExit message: There was a problem building dolfin-1.4.0.[0m
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