Do you need Fortran? Since you are using PETSc from python. If you do not need it then change --with-fc=mpif90 to --with-fc=0
Looks like something is wrong with the mpi Fortran 90 module > Fatal Error: Reading module mpi at line 1 column 2: Unexpected EOF > On Dec 18, 2016, at 1:54 PM, Aurelien Ponte <[email protected]> wrote: > > Here is what I am trying now: > > setenv MPICC mpiicc > pip install --user --upgrade --ignore-installed --no-cache-dir mpi4py > pip install --user --upgrade --ignore-installed --no-cache-dir numpy > setenv PETSC_CONFIGURE_OPTIONS '--with-64-bit-indices --with-fc=mpif90 > --download-fblaslapack' > pip install --user --upgrade --ignore-installed --no-cache-dir petsc petsc4py > > I get now the following error message (I'll send the logs to > [email protected] as suggested): > > CC arch-python-linux-x86_64/obj/src/vec/is/is/interface/index.o > Fatal Error: Reading module mpi at line 1 column 2: Unexpected EOF > gmake[2]: *** [arch-python-linux-x86_64/obj/src/sys/f90-mod/petscsysmod.o] > Error 1 > gmake[2]: *** Waiting for unfinished jobs.... > /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/client.c(3): warning #161: > unrecognized #pragma > #pragma clang diagnostic ignored "-Wdeprecated-declarations" > ^ > > /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/client.c(4): warning #161: > unrecognized #pragma > #pragma gcc diagnostic ignored "-Wdeprecated-declarations" > ^ > > /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/google.c(3): warning #161: > unrecognized #pragma > #pragma clang diagnostic ignored "-Wdeprecated-declarations" > ^ > > /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/google.c(4): warning #161: > unrecognized #pragma > #pragma gcc diagnostic ignored "-Wdeprecated-declarations" > ^ > > /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/box.c(3): warning #161: > unrecognized #pragma > #pragma clang diagnostic ignored "-Wdeprecated-declarations" > ^ > > /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/box.c(4): warning #161: > unrecognized #pragma > #pragma gcc diagnostic ignored "-Wdeprecated-declarations" > ^ > > /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/globus.c(2): warning #161: > unrecognized #pragma > #pragma clang diagnostic ignored "-Wdeprecated-declarations" > ^ > > /tmp/pip-build-t7pV1u/petsc/src/sys/webclient/globus.c(3): warning #161: > unrecognized #pragma > #pragma gcc diagnostic ignored "-Wdeprecated-declarations" > ^ > > gmake[2]: Leaving directory `/tmp/pip-build-t7pV1u/petsc' > gmake[1]: *** [gnumake] Error 2 > gmake[1]: Leaving directory `/tmp/pip-build-t7pV1u/petsc' > **************************ERROR************************************* > Error during compile, check > arch-python-linux-x86_64/lib/petsc/conf/make.log > Send it and arch-python-linux-x86_64/lib/petsc/conf/configure.log to > [email protected] > ******************************************************************** > make: *** [all] Error 1 > Traceback (most recent call last): > File "<string>", line 1, in <module> > File "/tmp/pip-build-t7pV1u/petsc/setup.py", line 302, in <module> > **metadata) > File > "/appli/python/2.7.10_gcc-4.9.2/python-2.7.10/lib/python2.7/distutils/core.py", > line 151, in setup > dist.run_commands() > File > "/appli/python/2.7.10_gcc-4.9.2/python-2.7.10/lib/python2.7/distutils/dist.py", > line 953, in run_commands > self.run_command(cmd) > File > "/appli/python/2.7.10_gcc-4.9.2/python-2.7.10/lib/python2.7/distutils/dist.py", > line 972, in run_command > cmd_obj.run() > File "/tmp/pip-build-t7pV1u/petsc/setup.py", line 219, in run > build(self.dry_run) > File "/tmp/pip-build-t7pV1u/petsc/setup.py", line 164, in build > if status != 0: raise RuntimeError(status) > RuntimeError: 512 > > ---------------------------------------- > Command "/appli/python/2.7.10_gcc-4.9.2/python-2.7.10/bin/python -u -c > "import setuptools, > tokenize;__file__='/tmp/pip-build-t7pV1u/petsc/setup.py';f=getattr(tokenize, > 'open', open)(__file__);code=f.read().replace('\r\n', > '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record > /tmp/pip-ebXwB3-record/install-record.txt --single-version-externally-managed > --compile --user --prefix=" failed with error code 1 in > /tmp/pip-build-t7pV1u/petsc/ > > > > > Le 18/12/2016 à 16:52, Satish Balay a écrit : >> How about using --download-fblaslapack instead of MKL? >> >> Satish >> >> On Sun, 18 Dec 2016, Aurelien Ponte wrote: >> >>> Allright I got the following to complete: >>> >>> ### install pip: >>> module load python/2.7.10_gnu-4.9.2 >>> wget https://bootstrap.pypa.io/get-pip.py >>> python get-pip.py --user >>> # edit .cshrc: set path = ($path $home/.local/bin) + setenv LD_LIBRARY_PATH >>> /home1/caparmor/aponte/.local/lib:${LD_LIBRARY_PATH} >>> >>> # >>> setenv MPICC mpiicc >>> pip install --user --upgrade mpi4py >>> pip install --user --upgrade numpy >>> setenv PETSC_CONFIGURE_OPTIONS '--with-64-bit-indices >>> --with-blas-lapack-dir=/appli/intel/Compiler/11.1/073/mkl/lib/em64t' >>> pip install --user petsc petsc4py >>> >>> But now I get the following at run time: >>> *** libmkl_mc3.so *** failed with error : >>> /appli/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_mc3.so: undefined >>> symbol: >>> mkl_dft_commit_descriptor_s_c2c_md_omp >>> *** libmkl_def.so *** failed with error : >>> /appli/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_def.so: undefined >>> symbol: >>> mkl_dft_commit_descriptor_s_c2c_md_omp >>> MKL FATAL ERROR: Cannot load neither libmkl_mc3.so nor libmkl_def.so >>> MKL FATAL ERROR: Cannot load neither libmkl_mc3.so nor libmkl_def.so >>> >>> >>> Any ideas? >>> >>> I will also try the other approach (from source). >>> >>> thanks >>> >>> aurelien >>> >>> >>> >>> >>> Le 17/12/2016 à 22:36, Lawrence Mitchell a écrit : >>>>> On 17 Dec 2016, at 19:19, Barry Smith <[email protected]> wrote: >>>>> >>>>> Looks like --install-option= are options for pip not the underlying >>>>> package. >>>>> >>>>> Lisandro, how does one do what seems to be a simple request? >>>> Set PETSC_CONFIGURE_OPTIONS to any additional flags you want to pass to >>>> configure during pip install >>> >>> > > > -- > Aurélien Ponte > Tel: (+33) 2 98 22 40 73 > Fax: (+33) 2 98 22 44 96 > UMR 6523, IFREMER > ZI de la Pointe du Diable > CS 10070 > 29280 Plouzané >
