Indeed there seems to have a mix during the compilation of SuiteSparse (compiled with foss/2016a).
I had the file /opt/intel/parallel_studio_xe_2016/bin/iccvars.sh intel64 sourced in my profile because we have intel compiler installed system wide outside of eb. Not sourcing this file and recompiling SuiteSparse did the trick. Thanks 2017-03-21 17:23 GMT+01:00 Yann Sagon <[email protected]>: > I'm trying to build PETSc using this eb: > > PETSc-3.7.3-foss-2016a-Python-2.7.11.eb > > It's failing with this message: > > ************************************************************ > ******************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > ------------------------------------------------------------ > ------------------- > --with-suitesparse-lib=['/opt/ebsofts/MPI/GCC/4.9.3-2.25/ > OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/UMFPACK/Lib/libumfpack.a', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/KLU/Lib/libklu.a', '/opt/ebsofts/MPI/GCC/4.9.3-2. > 25/OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/CHOLMOD/Lib/libcholmod.a', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/BTF/Lib/libbtf.a', '/opt/ebsofts/MPI/GCC/4.9.3-2. > 25/OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/CCOLAMD/Lib/libccolamd.a', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/COLAMD/Lib/libcolamd.a', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/CAMD/Lib/libcamd.a', '/opt/ebsofts/MPI/GCC/4.9.3-2. > 25/OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/AMD/Lib/libamd.a', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/SuiteSparse_config/libsuitesparseconfig.a'] and > --with-suitesparse-include=['/opt/ebsofts/MPI/GCC/4.9.3-2. > 25/OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/UMFPACK/Include', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/KLU/Include', '/opt/ebsofts/MPI/GCC/4.9.3-2. > 25/OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/CHOLMOD/Include', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/BTF/Include', '/opt/ebsofts/MPI/GCC/4.9.3-2. > 25/OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/CCOLAMD/Include', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/COLAMD/Include', '/opt/ebsofts/MPI/GCC/4.9.3-2. > 25/OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/CAMD/Include', > '/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/AMD/Include', '/opt/ebsofts/MPI/GCC/4.9.3-2. > 25/OpenMPI/1.10.2/SuiteSparse/4.5.3-ParMETIS-4.0.3/SuiteSparse_config'] > did not work > ************************************************************ > ******************* > > In configure.log, > > I see this kind of error: > > opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/UMFPACK/Lib/libumfpack.a(umf_dl_solve.o):umf_solve.c:function > umfdl_solve: error: undefined reference to '_intel_fast_memcpy' > /opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/UMFPACK/Lib/libumfpack.a(umf_dl_solve.o):umf_solve.c:function > umfdl_solve: error: undefined reference to '_intel_fast_memcpy' > /opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/UMFPACK/Lib/libumfpack.a(umf_dl_solve.o):umf_solve.c:function > umfdl_solve: error: undefined reference to '_intel_fast_memcpy' > /opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/UMFPACK/Lib/libumfpack.a(umf_dl_solve.o):umf_solve.c:function > umfdl_solve: error: undefined reference to '_intel_fast_memcpy' > /opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/UMFPACK/Lib/libumfpack.a(umf_dl_solve.o):umf_solve.c:function > umfdl_solve: error: undefined reference to '_intel_fast_memset' > /opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/CHOLMOD/Lib/libcholmod.a(cholmod_l_ > common.o):cholmod_common.c:function cholmod_l_allocate_work: error: > undefined reference to '_intel_fast_memset' > /opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/CHOLMOD/Lib/libcholmod.a(cholmod_l_ > dense.o):cholmod_dense.c:function cholmod_l_ones: error: undefined > reference to '_intel_fast_memset' > /opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/SuiteSparse/ > 4.5.3-ParMETIS-4.0.3/CHOLMOD/Lib/libcholmod.a(cholmod_l_ > dense.o):cholmod_dense.c:function cholmod_l_zeros: error: undefined > reference to '_intel_fast_memset' > collect2: error: ld returned 1 exit status > > any clue? > > Thanks > > -- > Yann SAGON > Ingénieur système HPC > 24 Rue du Général-Dufour > 1211 Genève 4 - Suisse > Tél. : +41 (0)22 379 7737 <022%20379%2077%2037> > [email protected] - www.unige.ch > -- Yann SAGON Ingénieur système HPC 24 Rue du Général-Dufour 1211 Genève 4 - Suisse Tél. : +41 (0)22 379 7737 [email protected] - www.unige.ch
