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Collection of easyblocks that implement support for building and installing software with EasyBuild.
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Difficulty to build DOLFIN #166

Open fgeorgatos opened 11 years ago

fgeorgatos commented 11 years ago

Hi,

i just hope this is not an error on my end but, can't be sure (and you hope vice-versa :)

Have you been able to build DOLFIN with earlier EasyBuild releases (e.g. v1.2)?

The answer is no, not really, partly because of the elusive MTL4 dependency; as regards the latter, I just obtained a "proper" copy via another channel. fyi. My default builds are more less the ones at: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-92.html

So, the DOLFIN build insists failing for me, here's my current log (at least the last part of it which is the most interesting).

fyi. I have tried to rebuild SCOTCH, just in case;

N.B. notice the errors around MPI_THREAD_MULTIPLE... what do you see instead?

-- Performing Test PARMETIS_TEST_RUNS
-- Performing Test PARMETIS_TEST_RUNS - Success
-- Found ParMETIS: /home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib/libparmetis.a;/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-g
oolf-1.4.10/lib/libmetis.a
-- Checking for package 'SCOTCH-PT'
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:59 ] location of ptscotch.h: /home/users/fgeorgatos/.local/easybuild/software/SCOTCH
/5.1.12b_esmumps-goolf-1.4.10/include/ptscotch.h
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:61 ] location of libptscotch: /home/users/fgeorgatos/.local/easybuild/software/SCOTC
H/5.1.12b_esmumps-goolf-1.4.10/lib/libptscotch.a
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:63 ] location of libptscotcherr: /home/users/fgeorgatos/.local/easybuild/software/SC
OTCH/5.1.12b_esmumps-goolf-1.4.10/lib/libptscotcherr.a
-- Performing test SCOTCH_TEST_RUNS
-- Performing test SCOTCH_TEST_RUNS - Failed
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:171 ] SCOTCH_TEST_LIB_COMPILED = TRUE
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:173 ] SCOTCH_TEST_LIB_COMPILE_OUTPUT = Change Dir: /tmp/DOLFIN/1.0.0/goolf-1.4.10-Py
thon-2.7.3/dolfin-1.0.0/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build
make[1]: Entering directory `/tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/CMakeFiles/CMakeTmp'
/mnt/nfs/users/homedirs/fgeorgatos/.local/easybuild/software/CMake/2.8.4-goolf-1.4.10/bin/cmake -E cmake_progress_report /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/C
MakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec.dir/scotch_test_lib.cpp.o
/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/bin/mpicxx    -fPIC -O2 -march=native   -I/home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10/include -I/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/include   -o CMakeFiles/cmTryCompileExec.dir/scotch_test_lib.cpp.o -c /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/CMakeFiles/scotch_test_lib.cpp
Linking CXX executable cmTryCompileExec
/mnt/nfs/users/homedirs/fgeorgatos/.local/easybuild/software/CMake/2.8.4-goolf-1.4.10/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1
/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/bin/mpicxx    -fPIC -O2 -march=native    -L/opt/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64 -L/home/users/fgeorgatos/.local/easybuild/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib -L/home/users/fgeorgatos/.local/easybuild/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib -L/home/users/fgeorgatos/.local/easybuild/software/FFTW/3.3.3-gompi-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/Python/2.7.3-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/UFC/2.0.5-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/FFC/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/FIAT/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/Instant/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/Viper/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/UFL/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/Armadillo/2.4.4-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/CGAL/4.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/PETSc/3.3-p2-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/SLEPc/3.3-p1-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/Trilinos/10.12.2-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/Sphinx/1.1.3-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/zlib/1.2.7-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/libxml2/2.8.0-goolf-1.4.10/lib CMakeFiles/cmTryCompileExec.dir/scotch_test_lib.cpp.o  -o cmTryCompileExec -rdynamic /home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10/lib/libptscotch.a /home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10/lib/libptscotcherr.a -lmpi
make[1]: Leaving directory `/tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/CMakeFiles/CMakeTmp'

-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:175 ] SCOTCH_TEST_LIB_EXITCODE = 1
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:177 ] SCOTCH_TEST_LIB_OUTPUT = MPI implementation is not thread-safe:
SCOTCH should be compiled without SCOTCH_PTHREAD
(0): ERROR: SCOTCH_dgraphInit: Scotch compiled with SCOTCH_PTHREAD and program not launched with MPI_THREAD_MULTIPLE

-- Found ZLIB: /home/users/fgeorgatos/.local/easybuild/software/zlib/1.2.7-goolf-1.4.10/include (found version "1.2.7")
-- Performing test SCOTCH_ZLIB_TEST_RUNS
-- Performing test SCOTCH_ZLIB_TEST_RUNS - Failed
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:214 ] SCOTCH_ZLIB_TEST_LIB_COMPILED = TRUE
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:216 ] SCOTCH_ZLIB_TEST_LIB_COMPILE_OUTPUT = Change Dir: /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build
make[1]: Entering directory `/tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/CMakeFiles/CMakeTmp'
/mnt/nfs/users/homedirs/fgeorgatos/.local/easybuild/software/CMake/2.8.4-goolf-1.4.10/bin/cmake -E cmake_progress_report /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec.dir/scotch_test_lib.cpp.o
/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/bin/mpicxx    -fPIC -O2 -march=native   -I/home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10/include -I/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/include -I/home/users/fgeorgatos/.local/easybuild/software/zlib/1.2.7-goolf-1.4.10/include   -o CMakeFiles/cmTryCompileExec.dir/scotch_test_lib.cpp.o -c /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/CMakeFiles/scotch_test_lib.cpp
Linking CXX executable cmTryCompileExec
/mnt/nfs/users/homedirs/fgeorgatos/.local/easybuild/software/CMake/2.8.4-goolf-1.4.10/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1
/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/bin/mpicxx    -fPIC -O2 -march=native    -L/opt/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64 -L/home/users/fgeorgatos/.local/easybuild/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib -L/home/users/fgeorgatos/.local/easybuild/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib -L/home/users/fgeorgatos/.local/easybuild/software/FFTW/3.3.3-gompi-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/Python/2.7.3-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/UFC/2.0.5-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/FFC/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/FIAT/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/Instant/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/Viper/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/UFL/1.0.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/Armadillo/2.4.4-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/CGAL/4.0-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/PETSc/3.3-p2-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/SLEPc/3.3-p1-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/Trilinos/10.12.2-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/Sphinx/1.1.3-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/zlib/1.2.7-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/libxml2/2.8.0-goolf-1.4.10/lib CMakeFiles/cmTryCompileExec.dir/scotch_test_lib.cpp.o  -o cmTryCompileExec -rdynamic /home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10/lib/libptscotch.a /home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10/lib/libptscotcherr.a -lmpi /home/users/fgeorgatos/.local/easybuild/software/zlib/1.2.7-goolf-1.4.10/lib/libz.a
make[1]: Leaving directory `/tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/CMakeFiles/CMakeTmp'

-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:218 ] SCOTCH_TEST_LIB_EXITCODE = 1
-- [ /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/cmake/modules/FindScotchPT.cmake:220 ] SCOTCH_TEST_LIB_OUTPUT = MPI implementation is not thread-safe:
SCOTCH should be compiled without SCOTCH_PTHREAD
(0): ERROR: SCOTCH_dgraphInit: Scotch compiled with SCOTCH_PTHREAD and program not launched with MPI_THREAD_MULTIPLE

-- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing:  SCOTCH_TEST_RUNS)
-- Checking for package 'AMD'
-- Found AMD: /home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/lib/libamd.a
-- Checking for package 'BLAS'
-- Found BLAS: -lopenblas -lgfortran
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'BLAS'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Checking for package 'BLAS'
-- Checking for package 'LAPACK'
-- Found LAPACK: -lopenblas -lgfortran
-- Performing Test CHOLMOD_TEST_RUNS
-- Performing Test CHOLMOD_TEST_RUNS - Success
-- Found CHOLMOD: /home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CHOLMOD/lib/libcholmod.a;/home/users/fgeorgatos/.local/easybuild/sof
tware/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/lib/libamd.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CAMD/lib/libcamd.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/COLAMD/lib/libcolamd.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CCOLAMD/lib/libccolamd.a;-lopenblas -lgfortran;/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib/libparmetis.a;/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib/libmetis.a;-lopenblas -lgfortran
-- Performing Test UMFPACK_TEST_RUNS
-- Performing Test UMFPACK_TEST_RUNS - Success
-- Found UMFPACK: /home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/include;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UFconfig
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Checking for package 'BLAS'
-- Checking for package 'LAPACK'
-- Checking for Trilinos
--   Trilinos version 10.12.2 found. Checking for components
--   All necessary Trilinos components found. Trilinos will be enabled
-- Checking for package 'MTL4'
-- Checking for package 'BLAS'
-- [ /mnt/nfs/users/homedirs/fgeorgatos/.local/easybuild/software/CMake/2.8.4-goolf-1.4.10/share/cmake-2.8/Modules/FindBoost.cmake:454 ] boost 1.49.0 is already in the cache.  To view debugging messages, please clear the cache.
-- Performing Test MTL4_TEST_RUNS
-- Performing Test MTL4_TEST_RUNS - Success
-- Found MTL4: /opt/apps/HPCBIOS.20130301/software/MTL4/4.0.8878/include
-- Checking for package 'PETSc'
-- PETSC_DIR is /home/users/fgeorgatos/.local/easybuild/software/PETSc/3.3-p2-goolf-1.4.10-Python-2.7.3
-- PETSC_ARCH is empty
-- Found petscconf.h
-- PETSC_LIB -L/home/users/fgeorgatos/.local/easybuild/software/PETSc/3.3-p2-goolf-1.4.10-Python-2.7.3/lib -L/home/users/fgeorgatos/.local/easybuild/software/PETSc/3.3-p2-goolf-1.4.10-Python-2.7.3/lib -lpetsc -lpthread -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib -lparmetis -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/METIS/5.0.2-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/METIS/5.0.2-goolf-1.4.10/lib -lmetis -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib -L/home/users/fgeorgatos/.local/easybuild/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib -lscalapack -lopenblas -lgfortran -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/Hypre/2.8.0b-goolf-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/Hypre/2.8.0b-goolf-1.4.10/lib -lHYPRE -Wl,-rpath,/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib -L/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib -Wl,-rpath,/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2 -L/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2 -Wl,-rpath,/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib/gcc -L/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib/gcc -Wl,-rpath,/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64 -L/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64 -Wl,-rpath,/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib -L/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib -lmpi_cxx -lstdc++ -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/FFTW/3.3.3-gompi-1.4.10/lib -L/home/users/fgeorgatos/.local/easybuild/software/FFTW/3.3.3-gompi-1.4.10/lib -lfftw3_mpi -lfftw3 -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/Lib -L/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/Lib -lumfpack -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CHOLMOD/Lib -L/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CHOLMOD/Lib -lcholmod -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/COLAMD/Lib -L/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/COLAMD/Lib -lcolamd -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/AMD/Lib -L/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/AMD/Lib -lamd -Wl,-rpath,/home/users/fgeorgatos/.local/easybuild/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib -L/home/users/fgeorgatos/.local/easybuild/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib -lopenblas -lgfortran -lmpi_f90 -lmpi_f77 -lgfortran -lm -lgfortran -lm -lgfortran -lm -lgfortran -lm -lm -lm -lquadmath -lm -lmpi_cxx -lstdc++ -ldl -lmpi -lrt -lnsl -lpthread -lutil -lgcc_s -ldl
-- Unable to find library openblas
-- Unable to find library gfortran
-- PETSC_LIBRARIES /home/users/fgeorgatos/.local/easybuild/software/PETSc/3.3-p2-goolf-1.4.10-Python-2.7.3/lib/libpetsc.a;/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib/libparmetis.a;/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib/libmetis.a;/home/users/fgeorgatos/.local/easybuild/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib/libscalapack.a;/home/users/fgeorgatos/.local/easybuild/software/Hypre/2.8.0b-goolf-1.4.10/lib/libHYPRE.a;/home/users/fgeorgatos/.local/easybuild/software/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3_mpi.a;/home/users/fgeorgatos/.local/easybuild/software/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/Lib/libumfpack.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CHOLMOD/Lib/libcholmod.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/COLAMD/Lib/libcolamd.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/Lib/libamd.a;/home/users/fgeorgatos/.local/easybuild/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib/libopenblas.so;/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi_f90.so;/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi_f77.so;/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64/libgfortran.so;/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64/libquadmath.so;/usr/lib/libm.so;/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi_cxx.so;/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64/libstdc++.so;/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi.so;/usr/lib/librt.so;/usr/lib/libnsl.so;/usr/lib/libpthread.so;/usr/lib/libutil.so;/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64/libgcc_s.so;/usr/lib/libdl.so
-- Performing Test PETSC_TEST_RUNS
-- Performing Test PETSC_TEST_RUNS - Success
-- PETSc test runs
-- Found PETSc: /home/users/fgeorgatos/.local/easybuild/software/PETSc/3.3-p2-goolf-1.4.10-Python-2.7.3/lib/libpetsc.a;/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib/libparmetis.a;/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10/lib/libmetis.a;/home/users/fgeorgatos/.local/easybuild/software/ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2/lib/libscalapack.a;/home/users/fgeorgatos/.local/easybuild/software/Hypre/2.8.0b-goolf-1.4.10/lib/libHYPRE.a;/home/users/fgeorgatos/.local/easybuild/software/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3_mpi.a;/home/users/fgeorgatos/.local/easybuild/software/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/Lib/libumfpack.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CHOLMOD/Lib/libcholmod.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/COLAMD/Lib/libcolamd.a;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/Lib/libamd.a;/home/users/fgeorgatos/.local/easybuild/software/OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2/lib/libopenblas.so;/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi_f90.so;/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi_f77.so;/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64/libgfortran.so;/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64/libquadmath.so;/usr/lib/libm.so;/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi_cxx.so;/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64/libstdc++.so;/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi.so;/usr/lib/librt.so;/usr/lib/libnsl.so;/usr/lib/libpthread.so;/usr/lib/libutil.so;/mnt/nfs/apps/HPCBIOS.20130301/software/GCC/4.7.2/lib64/libgcc_s.so;/usr/lib/libdl.so
-- Checking for package 'SLEPc'
-- SLEPC_DIR is /home/users/fgeorgatos/.local/easybuild/software/SLEPc/3.3-p1-goolf-1.4.10-Python-2.7.3
-- Performing Test SLEPC_TEST_RUNS
-- Performing Test SLEPC_TEST_RUNS - Success
-- SLEPc test runs
-- Found SLEPc: /home/users/fgeorgatos/.local/easybuild/software/SLEPc/3.3-p1-goolf-1.4.10-Python-2.7.3/lib/libslepc.a
-- Checking for package 'CGAL'
-- Performing Test CGAL_TEST_RUNS
-- Performing Test CGAL_TEST_RUNS - Success
-- Found CGAL: /home/users/fgeorgatos/.local/easybuild/software/CGAL/4.0-goolf-1.4.10-Python-2.7.3/lib/libCGAL.so;/usr/lib/libgmpxx.so;/usr/lib/libmpfr.so;/usr/lib/libgmp.so;/home/users/fgeorgatos/.local/easybuild/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_thread.so
-- Checking for package 'CPPUNIT'
-- CPPUNIT could not be found. Be sure to set CPPUNIT_DIR. (missing:  CPPUNIT_LIBRARIES CPPUNIT_INCLUDE_DIRS)
-- Checking for package 'Sphinx'
-- Found Sphinx: /home/users/fgeorgatos/.local/easybuild/software/Sphinx/1.1.3-goolf-1.4.10-Python-2.7.3/bin/sphinx-build (Required is at least version "1.0.7")
--
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) SLEPC
-- (OK) TRILINOS
-- (OK) MTL4
-- (OK) UMFPACK
-- (OK) CHOLMOD
-- (OK) PARMETIS
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) SPHINX
--
-- The following optional packages could not be found:
-- ---------------------------------------------------
-- (**) SCOTCH
--
-- Enabling generation of documentation.
-- Initializing sphinx projects
-- Enabling generation of html-documentation
-- Configuring done
-- Generating done
CMake Warning: The variable, 'CMAKE_Fortran_COMPILER', specified manually, was not used during the generation.
CMake Warning: The variable, 'CMAKE_Fortran_FLAGS', specified manually, was not used during the generation.
CMake Warning: The variable, 'MPI_CXX_COMPILER', specified manually, was not used during the generation.
CMake Warning: The variable, 'MPI_C_COMPILER', specified manually, was not used during the generation.
CMake Warning: The variable, 'UFCONFIG_DIR', specified manually, was not used during the generation.
-- Build files have been written to: /tmp/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0
== 2013-03-31 19:54:18,264 main.filetools INFO parseLogError msg: Command used:  cmake -DCMAKE_INSTALL_PREFIX=/home/users/fgeorgatos/.local/easybuild/software/DOLFIN/1.0.0-goolf-1.4.10-Python-2.7.3 -DCMAKE_C_FLAGS='-fPIC -O2 -march=native' -DCMAKE_C_COMPILER='mpicc' -DCMAKE_CXX_FLAGS='-fPIC -O2 -march=native' -DCMAKE_CXX_COMPILER='mpicxx' -DCMAKE_Fortran_FLAGS='-fPIC -O2 -march=native' -DCMAKE_Fortran_COMPILER='mpif90'  .  -DCMAKE_C_COMPILER='mpicc'   -DCMAKE_CXX_COMPILER='mpicxx'   -DCMAKE_Fortran_COMPILER='mpif90'   -DCMAKE_C_FLAGS="-fPIC -O2 -march=native"  -DCMAKE_CXX_FLAGS="-fPIC -O2 -march=native"  -DCMAKE_Fortran_FLAGS="-fPIC -O2 -march=native"   -DCMAKE_BUILD_TYPE=Debug   -DMPI_C_COMPILER="$MPICC"   -DMPI_CXX_COMPILER="$MPICXX"   -DMPI_COMPILER="mpicc"   -DMPI_LIBRARY="/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/lib/libmpi.so"   -DMPI_INCLUDE_PATH="/opt/apps/HPCBIOS.20130301/software/OpenMPI/1.6.4-GCC-4.7.2/include"  -DZLIB_INCLUDE_DIR=/home/users/fgeorgatos/.local/easybuild/software/zlib/1.2.7-goolf-1.4.10/include  -DZLIB_LIBRARY=/home/users/fgeorgatos/.local/easybuild/software/zlib/1.2.7-goolf-1.4.10/lib/libz.a   -DOpenMP_CXX_FLAGS="-fopenmp"   -DOpenMP_C_FLAGS="-fopenmp"   -DBOOST_INCLUDEDIR=/home/users/fgeorgatos/.local/easybuild/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/include   -DBoost_DEBUG=ON -DBOOST_ROOT=/home/users/fgeorgatos/.local/easybuild/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3   -DUFC_DIR=/home/users/fgeorgatos/.local/easybuild/software/UFC/2.0.5-goolf-1.4.10-Python-2.7.3  -DARMADILLO_DIR:PATH=/home/users/fgeorgatos/.local/easybuild/software/Armadillo/2.4.4-goolf-1.4.10-Python-2.7.3    -DPYTHON_INCLUDE_PATH=/home/users/fgeorgatos/.local/easybuild/software/Python/2.7.3-goolf-1.4.10/include/python2.7   -DPYTHON_LIBRARY=/home/users/fgeorgatos/.local/easybuild/software/Python/2.7.3-goolf-1.4.10/lib/libpython2.7.so   -DUMFPACK_DIR="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK" -DUMFPACK_INCLUDE_DIRS="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK/include;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UFconfig" -DAMD_DIR="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UMFPACK" -DCHOLMOD_DIR="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CHOLMOD" -DCHOLMOD_INCLUDE_DIRS="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CHOLMOD/include;/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UFconfig" -DUFCONFIG_DIR="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/UFconfig" -DCAMD_LIBRARY:PATH="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CAMD/lib/libcamd.a" -DCCOLAMD_LIBRARY:PATH="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/CCOLAMD/lib/libccolamd.a" -DCOLAMD_LIBRARY:PATH="/home/users/fgeorgatos/.local/easybuild/software/SuiteSparse/3.7.0-goolf-1.4.10-withparmetis/COLAMD/lib/libcolamd.a"  -DPARMETIS_DIR="/home/users/fgeorgatos/.local/easybuild/software/ParMETIS/4.0.2-goolf-1.4.10"  -DSCOTCH_DIR="/home/users/fgeorgatos/.local/easybuild/software/SCOTCH/5.1.12b_esmumps-goolf-1.4.10" -DSCOTCH_DEBUG:BOOL=ON  -DBLAS_LIBRARIES:PATH="-lopenblas -lgfortran"  -DLAPACK_LIBRARIES:PATH="-lopenblas -lgfortran"  -DCGAL_DIR:PATH="/home/users/fgeorgatos/.local/easybuild/software/CGAL/4.0-goolf-1.4.10-Python-2.7.3"  -DPETSC_DIR=/home/users/fgeorgatos/.local/easybuild/software/PETSc/3.3-p2-goolf-1.4.10-Python-2.7.3  -DMTL4_DIR:PATH="/opt/apps/HPCBIOS.20130301/software/MTL4/4.0.8878"
== 2013-03-31 19:54:18,264 main.filetools INFO parseLogError (some may be harmless) regExp (?<![(,]|\w)(?:error|segmentation fault|failed)(?![(,]|\.?\w) found:
-- Performing test SCOTCH_TEST_RUNS - Failed
(0): ERROR: SCOTCH_dgraphInit: Scotch compiled with SCOTCH_PTHREAD and program not launched with MPI_THREAD_MULTIPLE
-- Performing test SCOTCH_ZLIB_TEST_RUNS - Failed
(0): ERROR: SCOTCH_dgraphInit: Scotch compiled with SCOTCH_PTHREAD and program not launched with MPI_THREAD_MULTIPLE
== 2013-03-31 19:54:18,264 main.filetools WARNING Found 4 errors in command output (output: -- Performing test SCOTCH_TEST_RUNS - Failed, (0): ERROR: SCOTCH_dgraphInit: Scotch compiled with SCOTCH_PTHREAD and program not launched with MPI_THREAD_MULTIPLE, -- Performing test SCOTCH_ZLIB_TEST_RUNS - Failed, (0): ERROR: SCOTCH_dgraphInit: Scotch compiled with SCOTCH_PTHREAD and program not launched with MPI_THREAD_MULTIPLE)
== 2013-03-31 19:54:18,265 main.EB_DOLFIN ERROR EasyBuild crashed with an error (at easybuild/easyblocks/d/dolfin.py:172 in configure_step): Optional packages could not be found, this should not happen...
== 2013-03-31 19:54:18,266 main ERROR EasyBuild crashed with an error (at easybuild/tools/build_log.py:96 in exception): EasyBuild encountered an exception (at easybuild/main.py:810 in build_and_install_software): autoBuild Failed (last 300 chars): EasyBuild crashed with an error (at easybuild/easyblocks/d/dolfin.py:172 in configure_step): Optional packages could not be found, this should not happen...
Traceback (most recent call last):
  File "/home/users/fgeorgatos/.local/lib/python2.6/site-packages/easybuild_framework-1.3.0rc2-py2.6.egg/easybuild/main.py", line 806, in build_and_install_software
    regtest_online=options.regtest_online)
  File "/home/users/fgeorgatos/.local/lib/python2.6/site-packages/easybuild_framework-1.3.0rc2-py2.6.egg/easybuild/framework/easyblock.py", line 1721, in run_all_steps
    self.run_step(stop_name, step_methods, skippable=skippable)
  File "/home/users/fgeorgatos/.local/lib/python2.6/site-packages/easybuild_framework-1.3.0rc2-py2.6.egg/easybuild/framework/easyblock.py", line 1604, in run_step
    m(self)
  File "/home/users/fgeorgatos/.local/lib/python2.6/site-packages/easybuild_framework-1.3.0rc2-py2.6.egg/easybuild/framework/easyblock.py", line 1655, in <lambda>
    configure_step_spec = ('configure', 'configuring', [lambda x: x.configure_step()], True)
  File "/home/users/fgeorgatos/.local/lib/python2.6/site-packages/easybuild_easyblocks-1.3.0rc1-py2.6.egg/easybuild/easyblocks/d/dolfin.py", line 172, in configure_step
    self.log.error("Optional packages could not be found, this should not happen...")
  File "/home/users/fgeorgatos/.local/lib/python2.6/site-packages/easybuild_framework-1.3.0rc2-py2.6.egg/easybuild/tools/build_log.py", line 88, in error
    raise EasyBuildError(newMsg)
EasyBuildError: 'EasyBuild crashed with an error (at easybuild/easyblocks/d/dolfin.py:172 in configure_step): Optional packages could not be found, this should not happen...'
boegel commented 11 years ago

The relevant errors messages from the above:

SCOTCH should be compiled without SCOTCH_PTHREAD
(0): ERROR: SCOTCH_dgraphInit: Scotch compiled with SCOTCH_PTHREAD and program not launched with MPI_THREAD_MULTIPLE
...
-- Performing test SCOTCH_ZLIB_TEST_RUNS
-- Performing test SCOTCH_ZLIB_TEST_RUNS - Failed

I don't know what's causing these because we're not seeing any problems like this on our side, although the mention of zlib makes me shiver (cfr. https://github.com/hpcugent/easybuild-framework/issues/108).

Will figure this out post v1.3.0, I don't consider this to be a blocker.

fgeorgatos commented 11 years ago

zlib makes me shiver

Shiver not: something is seriously fishy in relation to zlib/zlib-devel/DOLFIN/Boost and friends. It may be needed to find out in a hackathon expedition, most likely.

Will figure this out post v1.3.0, I don't consider this to be a blocker.

It never was: I doubt anybody outside of the RHEL* family ever built it successfully until now, so there is no backward compatibility issue at all, AFAIK :-P

JensTimmerman commented 11 years ago

hmm, SCOTCH_PTHREAD should be enabled in non intel mpi builds according to: see https://github.com/hpcugent/easybuild-easyblocks/blob/develop/easybuild/easyblocks/s/scotch.py 

if not self.toolchain.mpi_family() == toolchain.INTELMPI:  #@UndefinedVariable
            cflags += " -DSCOTCH_PTHREAD"

So I'm not sure why this is the case. I can faintly remember I needed to add thi

The zlib test runs are just failing because the scotch test runs failed...

boegel commented 11 years ago

@JensTimmerman: Where did you get that -DSCOTCH_PTHREAD is only required for Intel builds? Maybe it should always be included, but we just don't notice?

JensTimmerman commented 11 years ago

Boegel, it's enabled in all non intel builds, I don't know why this is failing now, is the MPI_THREAD_MULTIPLE option somehow removed in dolfin?

Anyway, fotis, maybe you should look into building dolfin 1.0.1, it is shipping 2 of our patches by default now, and iirc it had some SCOTCH fix in its somwhere aswell.

boegel commented 11 years ago

This needs to be revisited for v1.4. Is this still an issue?

boegel commented 11 years ago

@fgeorgatos: Any updates on this?

fgeorgatos commented 11 years ago

Hi Ken,

On Thu, May 23, 2013 at 10:40 PM, Kenneth Hoste notifications@github.comwrote:

@fgeorgatos https://github.com/fgeorgatos: Any updates on this?

I suspect a little bit of libboost saga still going on; in one of our systems we see:

sw@d-cluster1-1:~$ time echo easyconfigs/d/DOLFIN/*eb|xargs -n1 eb
...
== sanity checking...
ERROR: EasyBuild encountered an exception (at easybuild/main.py:817 in
build_and_install_software): autoBuild Failed (last 300 chars):
ftware/DOLFIN/1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3/lib/libdolfin.so:
undefined reference to 'boost::system::generic_category()'
collect2: ld returned 1 exit status
make[2]: *** [demo_stokes-iterative] Error 1
make[1]: *** [CMakeFiles/demo_stokes-iterative.dir/all] Error 2
make: *** [all] Error 2
== sanity checking...
ERROR: EasyBuild encountered an exception (at easybuild/main.py:817 in
build_and_install_software): autoBuild Failed (last 300 chars):
ftware/DOLFIN/1.0.0-goolf-1.4.10-Python-2.7.3/lib/libdolfin.so: undefined
reference to 'boost::system::generic_category()'
collect2: error: ld returned 1 exit status
make[2]: *** [demo_stokes-iterative] Error 1
make[1]: *** [CMakeFiles/demo_stokes-iterative.dir/all] Error 2
make: *** [all] Error 2
== sanity checking...
ERROR: EasyBuild encountered an exception (at easybuild/main.py:817 in
build_and_install_software): autoBuild Failed (last 300 chars): t'
/opt/apps/HPCBIOS.20130517/software/DOLFIN/1.0.0-ictce-4.0.6-Python-2.7.3/lib/libdolfin.so:
undefined reference to 'boost::filesystem3::path::parent_path() const'
make[2]: *** [demo_stokes-iterative] Error 1
make[1]: *** [CMakeFiles/demo_stokes-iterative.dir/all] Error 2
make: *** [all] Error 2

ps. We have no DOLFIN users over here, but we may care about this as part of the PRACE prereqs; (see fenics) ie. low priority so far for us but, eventually it would be nice to get it ironed out.

boegel commented 11 years ago

(I tried fixing the comment above w.r.t. formatting, but GitHub isn't doing what it's supposed to be doing, very weird, so pasted below)

Hi Ken,

On Thu, May 23, 2013 at 10:40 PM, Kenneth Hoste notifications@github.comwrote:

@fgeorgatos https://github.com/fgeorgatos: Any updates on this?

I suspect a little bit of libboost saga still going on; in one of our systems we see:

sw@d-cluster1-1:~$ time echo easyconfigs/d/DOLFIN/*eb|xargs -n1 eb
...
== sanity checking...
ERROR: EasyBuild encountered an exception (at easybuild/main.py:817 in
build_and_install_software): autoBuild Failed (last 300 chars):
ftware/DOLFIN/1.0.0-goalf-1.1.0-no-OFED-Python-2.7.3/lib/libdolfin.so:
undefined reference to 'boost::system::generic_category()'
collect2: ld returned 1 exit status
make[2]: *** [demo_stokes-iterative] Error 1
make[1]: *** [CMakeFiles/demo_stokes-iterative.dir/all] Error 2
make: *** [all] Error 2
== sanity checking...
ERROR: EasyBuild encountered an exception (at easybuild/main.py:817 in
build_and_install_software): autoBuild Failed (last 300 chars):
ftware/DOLFIN/1.0.0-goolf-1.4.10-Python-2.7.3/lib/libdolfin.so: undefined
reference to 'boost::system::generic_category()'
collect2: error: ld returned 1 exit status
make[2]: *** [demo_stokes-iterative] Error 1
make[1]: *** [CMakeFiles/demo_stokes-iterative.dir/all] Error 2
make: *** [all] Error 2
== sanity checking...
ERROR: EasyBuild encountered an exception (at easybuild/main.py:817 in
build_and_install_software): autoBuild Failed (last 300 chars): t'
/opt/apps/HPCBIOS.20130517/software/DOLFIN/1.0.0-ictce-4.0.6-Python-2.7.3/lib/libdolfin.so:
undefined reference to 'boost::filesystem3::path::parent_path() const'
make[2]: *** [demo_stokes-iterative] Error 1
make[1]: *** [CMakeFiles/demo_stokes-iterative.dir/all] Error 2
make: *** [all] Error 2

ps. We have no DOLFIN users over here, but we may care about this as part of the PRACE prereqs; (see fenics) ie. low priority so far for us but, eventually it would be nice to get it ironed out.

boegel commented 11 years ago

@fgeorgatos: Can you check whether that system as a system-wide Boost installed? And if so, which version?

fgeorgatos commented 11 years ago

hm... yes, I discovered an interesting situation as regards packages provided libboost: v1.42.0-4 for libs AND headers, along with some extra headers from v1.42.0.1 (debian provides distinct packages for that). In theory, building DOLFIN should be independent from that, but I'm well aware of the mess that can arise out of it...

boegel commented 11 years ago

It's possible that EB isn't properly specifying Boost paths during the DOLFIN build, and thus is able to resort to the system-provided Boost libs/includes.

We'll have to look into this (maybe in combination with testing the build of DOLFIN 1.0)...

fgeorgatos commented 11 years ago

this has to be retargeted for v1.6 or even later.

fgeorgatos commented 10 years ago

Just reporting that DOLFIN is still tricky over here, this is nothing of urgency though:

sw@gaia-43:~$ time eb DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb --strict=ignore -r
== temporary log file in case of crash /tmp/easybuild-srLuh9.log
== resolving dependencies ...
== processing EasyBuild easyconfig /opt/apps/HPCBIOS.20131117/software/EasyBuild/1.9.0/lib/python2.6/site-packages/easybuild_easyconfigs-1.9.0.0-py2.6.egg/easybuild/easyconfigs/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb
== building and installing DOLFIN/1.0.0-goolf-1.4.10-Python-2.7.3...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== packaging...
== postprocessing...
== sanity checking...
ERROR: EasyBuild encountered an exception (at easybuild/main.py:770 in build_and_install_software): autoBuild Failed (last 300 chars): 10-Python-2.7.3/share/dolfin/demo/pde/stokes-iterative/cpp'
make[1]: *** [CMakeFiles/demo_stokes-iterative.dir/all] Error 2
make[1]: Leaving directory `/mnt/nfs/apps/HPCBIOS.20131117/software/DOLFIN/1.0.0-goolf-1.4.10-Python-2.7.3/share/dolfin/demo/pde/stokes-iterative/cpp'
make: *** [all] Error 2
)

real    7m28.507s
user    17m4.584s
sys     1m26.717s
sw@gaia-43:~$
fgeorgatos commented 10 years ago

ImportError: /dev/shm/DOLFIN/1.0.0/goolf-1.4.10-Python-2.7.3/dolfin-1.0.0/dolfin/libdolfin.so.1.0: undefined symbol: _ZN5boost11filesystem36detail6statusERK

If somebody could dump his output of the (equivalent of the) following command, it could be interesting: ldd /opt/apps/HPCBIOS.20131117/software/DOLFIN/1.0.0-goolf-1.4.10-Python-2.7.3/lib/libdolfin.so|grep -i boost

boegel commented 10 years ago

@fgeorgatos:

$ ldd /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/DOLFIN/1.0.0-goolf-1.4.10-Python-2.7.3/lib/libdolfin.so | grep -i boost
/user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/DOLFIN/1.0.0-goolf-1.4.10-Python-2.7.3/lib/libdolfin.so: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libxml2/2.8.0-goolf-1.4.10/lib/libxml2.so.2)
    libboost_filesystem.so.1.49.0 => /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_filesystem.so.1.49.0 (0x00002ad0500f4000)
    libboost_program_options.so.1.49.0 => /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_program_options.so.1.49.0 (0x00002ad050314000)
    libboost_system.so.1.49.0 => /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_system.so.1.49.0 (0x00002ad050574000)
    libboost_thread.so.1.49.0 => /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_thread.so.1.49.0 (0x00002ad050778000)
    libboost_iostreams.so.1.49.0 => /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_iostreams.so.1.49.0 (0x00002ad050993000)
    libboost_math_tr1.so.1.49.0 => /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_math_tr1.so.1.49.0 (0x00002ad050bbb000)
    libboost_mpi.so.1.49.0 => /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_mpi.so.1.49.0 (0x00002ad050df7000)
    libboost_serialization.so.1.49.0 => /user/scratchdelcatty/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Boost/1.49.0-goolf-1.4.10-Python-2.7.3/lib/libboost_serialization.so.1.49.0 (0x00002ad051026000)