Hello Johannes,
thank you for your answer. I disabled ipython and it goes much more further.
I encounter an other problem in parmetis : some file were not compiled
with the -fPIC" flag and It was a problem, so I modify CXX in 'icpc
-fPIC' and after recompiling it was solved.
After this, there is a linking error in superlu_dist :
[superlu_dist] Building superlu_dist/vkqads73ax76, follow log with:
[superlu_dist] tail -f
/work/mdsip/fenics/1.6.0_intel/tmp/superlu_dist-vkqads73ax76/_hashdist/build.log
[superlu_dist|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']'
returned non-zero exit status 2
[superlu_dist|ERROR] command failed (code=2); raising
2015/11/19 16:13:46 - INFO: [package:run_job] ar cr
/work/mdsip/fenics/1.6.0_intel/tmp/superlu_dist-vkqads73ax76/lib/libsuperlu_dist.a
\
2015/11/19 16:13:46 - INFO: [package:run_job] dcomplex.o
zlangs.o zgsequ.o zlaqgs.o zutil.o zmemory.o zmyblas2.o zsp_blas2.o
zsp_blas3.o pzgssvx.o pzgssvx_ABglobal.o zreadhb.o zreadrb.o
zreadtriple.o zreadMM.o pzgsequ.o pzlaqgs.o zldperm_dist.o pzlangs.o
pzutil.o pzsymbfact_distdata.o zdistribute.o pzdistribute.o pzgstrf.o
pzgstrf2.o pzgstrs.o pzgstrs1.o pzgstrs_lsum.o pzgstrs_Bglobal.o
pzgsrfs.o pzgsmv.o pzgsrfs_ABXglobal.o pzgsmv_AXglobal.o sp_ienv.o
etree.o sp_colorder.o get_perm_c.o mmd.o comm.o memory.o util.o
superlu_grid.o pxerbla.o superlu_timer.o GetDiagU.o symbfact.o
psymbfact.o psymbfact_util.o get_perm_c_parmetis.o mc64ad_dist.o
static_schedule.o
2015/11/19 16:13:46 - INFO: [package:run_job] ranlib
/work/mdsip/fenics/1.6.0_intel/tmp/superlu_dist-vkqads73ax76/lib/libsuperlu_dist.a
2015/11/19 16:13:46 - INFO: [package:run_job] make[1]: Leaving directory
`/work/mdsip/fenics/1.6.0_intel/tmp/superlu_dist-vkqads73ax76/SRC'
2015/11/19 16:13:46 - INFO: [package:run_job]
/work/mdsip/fenics/1.6.0_intel/bld/mpi/slodgw4kha73/bin/mpicc -O2 -fPIC
-std=c99
-I/work/mdsip/fenics/1.6.0_intel/bld/parmetis/c6afdimk3bho/include
-DAdd_ -DUSE_VENDOR_BLAS -I../SRC -c pddrive.c
2015/11/19 16:13:46 - INFO: [package:run_job]
/work/mdsip/fenics/1.6.0_intel/bld/mpi/slodgw4kha73/bin/mpicc -O2 -fPIC
-std=c99
-I/work/mdsip/fenics/1.6.0_intel/bld/parmetis/c6afdimk3bho/include
-DAdd_ -DUSE_VENDOR_BLAS -I../SRC -c dcreate_matrix.c
2015/11/19 16:13:47 - INFO: [package:run_job]
/work/mdsip/fenics/1.6.0_intel/bld/mpi/slodgw4kha73/bin/mpicc pddrive.o
dcreate_matrix.o
/work/mdsip/fenics/1.6.0_intel/tmp/superlu_dist-vkqads73ax76/lib/libsuperlu_dist.a
-Wl,-rpath,/work/mdsip/fenics/1.6.0_intel/bld/lapack/ekv3eggxdboh/lib
-L/work/mdsip/fenics/1.6.0_intel/bld/lapack/ekv3eggxdboh/lib -lopenblas
-Wl,-rpath,/work/mdsip/fenics/1.6.0_intel/bld/lapack/ekv3eggxdboh/lib
-L/work/mdsip/fenics/1.6.0_intel/bld/lapack/ekv3eggxdboh/lib -lopenblas
-Wl,-rpath,/work/mdsip/fenics/1.6.0_intel/bld/parmetis/c6afdimk3bho/lib
-L/work/mdsip/fenics/1.6.0_intel/bld/parmetis/c6afdimk3bho/lib
-lparmetis
-Wl,-rpath,/work/mdsip/fenics/1.6.0_intel/bld/parmetis/c6afdimk3bho/lib
-L/work/mdsip/fenics/1.6.0_intel/bld/parmetis/c6afdimk3bho/lib -lmetis
-lm -o pddrive
2015/11/19 16:13:47 - INFO: [package:run_job]
/work/mdsip/fenics/1.6.0_intel/bld/lapack/ekv3eggxdboh/lib/libopenblas.so:
undefined reference to `for_concat'
2015/11/19 16:13:47 - INFO: [package:run_job]
/work/mdsip/fenics/1.6.0_intel/bld/lapack/ekv3eggxdboh/lib/libopenblas.so:
undefined reference to `for_cpystr'
2015/11/19 16:13:47 - INFO: [package:run_job] make: *** [pddrive] Error 1
2015/11/19 16:13:47 - ERROR: [package:run_job] Command '[u'/bin/bash',
'_hashdist/build.sh']' returned non-zero exit status 2
2015/11/19 16:13:47 - ERROR: [package:run_job] command failed (code=2);
raising
If I look at the end of the "build.log" file of openblas installation,
it seems that it has been linked with Intel's fortran libraries.
2015/11/19 14:12:14 - INFO: [package:run_job] icc -fPIC -O2 -wd981
-DF_INTERFACE_INTEL -fPIC -DNO_WARMUP -DMAX_CPU_NUMBER=16 -DASMNAME=
-DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\"
-DNO_AFFINITY -I.. -w -o linktest linktest.c
../libopenblas_nehalem-r0.2.13.so
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/ipp/../compiler/lib/intel64
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/ipp/lib/intel64
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/tbb/lib/intel64/gcc4.1
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/daal/lib/intel64_lin
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/daal/../tbb/lib/intel64_lin/gcc4.4
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/daal/../compiler/lib/intel64_lin
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64_lin
-L/usr/lib64/gcc/x86_64-suse-linux/4.3/
-L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64
-L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/
-L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64
-L/usr/lib/../lib64/
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/ipp/../compiler/lib/intel64/
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/ipp/lib/intel64/
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64/
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/mkl/lib/intel64/
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/tbb/lib/intel64/gcc4.1/
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/daal/lib/intel64_lin/
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/daal/../tbb/lib/intel64_lin/gcc4.4/
-L/ccipl/logiciels/intel/compilers_and_libraries_2016.0.109/linux/daal/../compiler/lib/intel64_lin/
-L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/lib/ -L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../
-L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lifport -lifcore_pic -limf
-lsvml -lm -lipgo -lirc -lpthread -lsvml -lc -lirc_s -ldl -lc
-lgfortran && echo OK.
2015/11/19 14:12:15 - INFO: [package:run_job] OK.
Regards,
Guy
Le 18/11/2015 10:38, Johannes Ring a écrit :
Yes, I also had this problem when compiling with the Intel compiler. I
have made a bug report for this now:
https://github.com/hashdist/hashstack/issues/886. My current solution
is to disable ipython in the hashdist profile.
Johannes
Regards,
Guy
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