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
