installation SLEPc et slepc4py

indie · Le 14/01/2018, à 08:32

Bonjour,

j'ai besoin d'installer slepc4py, (je dois installer aussi SLEPc) pour faire simple j'ai utilisé la commande "pip installe slepc slepc4py" sans succès:

root@user-UX331UN:/home/user/slepc-3.8.2# pip install slepc slepc4py
Requirement already satisfied: slepc in /usr/local/lib/python2.7/dist-packages/slepc-3.8.0-py2.7.egg
Collecting slepc4py
  Using cached slepc4py-3.8.0.tar.gz
Requirement already satisfied: petsc<3.9,>=3.8 in /usr/local/lib/python2.7/dist-packages (from slepc)
Requirement already satisfied: petsc4py<3.9,>=3.8 in /usr/local/lib/python2.7/dist-packages (from slepc4py)
Requirement already satisfied: numpy in /usr/lib/python2.7/dist-packages (from petsc4py<3.9,>=3.8->slepc4py)
Building wheels for collected packages: slepc4py
  Running setup.py bdist_wheel for slepc4py ... error
  Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-dLsWId/slepc4py/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpNqtBxppip-wheel- --python-tag cp27:
  running bdist_wheel
  running build
  running build_src
  running build_py
  creating build
  creating build/lib.linux-x86_64-2.7
  creating build/lib.linux-x86_64-2.7/slepc4py
  copying src/__main__.py -> build/lib.linux-x86_64-2.7/slepc4py
  copying src/SLEPc.py -> build/lib.linux-x86_64-2.7/slepc4py
  copying src/__init__.py -> build/lib.linux-x86_64-2.7/slepc4py
  creating build/lib.linux-x86_64-2.7/slepc4py/lib
  copying src/lib/__init__.py -> build/lib.linux-x86_64-2.7/slepc4py/lib
  creating build/lib.linux-x86_64-2.7/slepc4py/include
  creating build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
  copying src/include/slepc4py/slepc4py.h -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
  copying src/include/slepc4py/slepc4py.SLEPc.h -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
  copying src/include/slepc4py/slepc4py.SLEPc_api.h -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
  copying src/include/slepc4py/slepc4py.i -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
  copying src/include/slepc4py/__init__.pxd -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
  copying src/include/slepc4py/SLEPc.pxd -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
  copying src/include/slepc4py/__init__.pyx -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
  copying src/SLEPc.pxd -> build/lib.linux-x86_64-2.7/slepc4py
  copying src/lib/slepc.cfg -> build/lib.linux-x86_64-2.7/slepc4py/lib
  running build_ext
  SLEPC_DIR:   /usr/local/lib/python2.7/dist-packages/slepc-3.8.0-py2.7.egg/slepc
  PETSC_DIR:    /usr/local/lib/python2.7/dist-packages/petsc
  PETSC_ARCH:
  version:      3.8.1 release
  integer-size: 32-bit
  scalar-type:  real
  precision:    double
  language:     CONLY
  compiler:     /usr/bin/mpicc
  linker:       /usr/bin/mpicc
  building 'SLEPc' extension
  creating build/temp.linux-x86_64-2.7
  creating build/temp.linux-x86_64-2.7/src
  /usr/bin/mpicc -pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -DPETSC_DIR=/usr/local/lib/python2.7/dist-packages/petsc -DSLEPC_DIR=/usr/local/lib/python2.7/dist-packages/slepc-3.8.0-py2.7.egg/slepc -I/usr/local/lib/python2.7/dist-packages/slepc-3.8.0-py2.7.egg/slepc/include -I/usr/local/lib/python2.7/dist-packages/petsc/include -Isrc/include -I/usr/local/lib/python2.7/dist-packages/petsc4py/include -I/usr/include/python2.7 -c src/SLEPc.c -o build/temp.linux-x86_64-2.7/src/SLEPc.o
  In file included from src/SLEPc.c:3:0:
  src/slepc4py.SLEPc.c:515:19: fatal error: slepc.h: Aucun fichier ou dossier de ce type
  compilation terminated.
  error: command '/usr/bin/mpicc' failed with exit status 1
  
  ----------------------------------------
  Failed building wheel for slepc4py
  Running setup.py clean for slepc4py
Failed to build slepc4py
Installing collected packages: slepc4py
  Running setup.py install for slepc4py ... error
    Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-dLsWId/slepc4py/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-YaVIIJ-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_src
    running build_py
    creating build
    creating build/lib.linux-x86_64-2.7
    creating build/lib.linux-x86_64-2.7/slepc4py
    copying src/__main__.py -> build/lib.linux-x86_64-2.7/slepc4py
    copying src/SLEPc.py -> build/lib.linux-x86_64-2.7/slepc4py
    copying src/__init__.py -> build/lib.linux-x86_64-2.7/slepc4py
    creating build/lib.linux-x86_64-2.7/slepc4py/lib
    copying src/lib/__init__.py -> build/lib.linux-x86_64-2.7/slepc4py/lib
    creating build/lib.linux-x86_64-2.7/slepc4py/include
    creating build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
    copying src/include/slepc4py/slepc4py.h -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
    copying src/include/slepc4py/slepc4py.SLEPc.h -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
    copying src/include/slepc4py/slepc4py.SLEPc_api.h -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
    copying src/include/slepc4py/slepc4py.i -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
    copying src/include/slepc4py/__init__.pxd -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
    copying src/include/slepc4py/SLEPc.pxd -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
    copying src/include/slepc4py/__init__.pyx -> build/lib.linux-x86_64-2.7/slepc4py/include/slepc4py
    copying src/SLEPc.pxd -> build/lib.linux-x86_64-2.7/slepc4py
    copying src/lib/slepc.cfg -> build/lib.linux-x86_64-2.7/slepc4py/lib
    running build_ext
    SLEPC_DIR:   /usr/local/lib/python2.7/dist-packages/slepc-3.8.0-py2.7.egg/slepc
    PETSC_DIR:    /usr/local/lib/python2.7/dist-packages/petsc
    PETSC_ARCH:
    version:      3.8.1 release
    integer-size: 32-bit
    scalar-type:  real
    precision:    double
    language:     CONLY
    compiler:     /usr/bin/mpicc
    linker:       /usr/bin/mpicc
    building 'SLEPc' extension
    creating build/temp.linux-x86_64-2.7
    creating build/temp.linux-x86_64-2.7/src
    /usr/bin/mpicc -pthread -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g -O -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -DPETSC_DIR=/usr/local/lib/python2.7/dist-packages/petsc -DSLEPC_DIR=/usr/local/lib/python2.7/dist-packages/slepc-3.8.0-py2.7.egg/slepc -I/usr/local/lib/python2.7/dist-packages/slepc-3.8.0-py2.7.egg/slepc/include -I/usr/local/lib/python2.7/dist-packages/petsc/include -Isrc/include -I/usr/local/lib/python2.7/dist-packages/petsc4py/include -I/usr/include/python2.7 -c src/SLEPc.c -o build/temp.linux-x86_64-2.7/src/SLEPc.o
    In file included from src/SLEPc.c:3:0:
    src/slepc4py.SLEPc.c:515:19: fatal error: slepc.h: Aucun fichier ou dossier de ce type
    compilation terminated.
    error: command '/usr/bin/mpicc' failed with exit status 1
    
    ----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-dLsWId/slepc4py/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-YaVIIJ-record/install-record.txt --single-ver

J'ai testé "easy_install slepc4py" mais ca ne fonctionne pas non plus:

root@user-UX331UN:/home/user/slepc-3.8.2# easy_install slepc4py
Searching for slepc4py
Reading [pypi.python.org]
Best match: slepc4py 3.8.0
Downloading [pypi.python.org]
Processing slepc4py-3.8.0.tar.gz
Writing /tmp/easy_install-sym1PW/slepc4py-3.8.0/setup.cfg
Running slepc4py-3.8.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-sym1PW/slepc4py-3.8.0/egg-dist-tmp-G7hz0H
In file included from src/SLEPc.c:3:0:
src/slepc4py.SLEPc.c:515:19: fatal error: slepc.h: Aucun fichier ou dossier de ce type
compilation terminated.
error: Setup script exited with error: command '/usr/bin/mpicc' failed with exit status 1

Je précise que j'ai installé aussi slepc-dev.
Je ne sais plus quoi tester pour avancer, pouvez vous m'aider svp?

inbox · Le 14/01/2018, à 09:48

Salut,

Que donne cette commande ?

locate slepc.h

Si locate n'est pas installé, voir locate.

A+

indie · Le 14/01/2018, à 11:05

Merci, ceci:

:~$ locate slepc.h
/home/user/slepc-3.8.2/include/slepc.h
/home/user/slepc-3.8.2/include/slepc.h.html
/home/user/slepc-3.8.2/include/slepc/finclude/slepc.h
/home/user/slepc-3.8.2/include/slepc/finclude/slepc.h.html
/home/user/slepc-3.8.2/include/slepc/private/vecimplslepc.h
/home/user/slepc-3.8.2/include/slepc/private/vecimplslepc.h.html
/usr/lib/slepcdir/3.6.1/x86_64-linux-gnu-real/include/slepc.h
/usr/lib/slepcdir/3.6.1/x86_64-linux-gnu-real/include/slepc/finclude/slepc.h
/usr/lib/slepcdir/3.6.1/x86_64-linux-gnu-real/include/slepc/finclude/slepc.h90
/usr/lib/slepcdir/3.6.1/x86_64-linux-gnu-real/include/slepc/private/vecimplslepc.h

inbox · Le 14/01/2018, à 11:14

Cela veut donc probablement dire, que le script d'installation ne cherche pas le fichier "slepc.h" la ou il se trouve.

indie · Le 14/01/2018, à 11:43

Ok, mais comment faire pour lui dire?

inbox · Le 14/01/2018, à 14:09

Je n'en sait rien, il faut savoir ou il le cherche en analysant le script d'installation.

indie · Le 14/01/2018, à 14:27

J'ai essayé de fouiller dans quelques fichiers mais je ne vois pas.

SInon j'ai essayé d'installer d'abord slepc-3.8.2 en faisant ./configure comme indiqué ici doc, mais c'est encore pire:

:slepc-3.8.2$ ./configure
Checking environment...
ERROR: SLEPC_DIR enviroment variable is not valid

J'ai essayé de changé SLEPC_DIR mais ca ne marche pas pourtant le chemin me semble bon...

inbox · Le 14/01/2018, à 15:12

As-tu bien appliqué ce qui est indiqué dans cette procédure d'installation ?

indie · Le 14/01/2018, à 16:11

Oui, j'ai déjà installé mpi4py et numpy.
J'ai également installé PETSc et petcs4py, testé et ca marche.

Mais pour SLEPC et slepc4py je coince. J'avais aussi testé sans succès
$ pip install --no-deps git+https://bitbucket.org/slepc/slepc
$ pip install --no-deps git+https://bitbucket.org/slepc/slepc4py

:~$ pip install --no-deps git+https://bitbucket.org/slepc/slepc
Collecting git+https://bitbucket.org/slepc/slepc
  Cloning https://bitbucket.org/slepc/slepc to /tmp/pip-jf9J9u-build
Installing collected packages: slepc
  Running setup.py install for slepc ... error
    Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-jf9J9u-build/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-bRdRZY-record/install-record.txt --single-version-externally-managed --compile:
    running install
    SLEPc: configure
    configure options:
        --prefix=/usr/local/lib/python2.7/dist-packages/slepc
    Checking environment... done
    Checking PETSc installation...
    ERROR: Cannot mix release and development versions of SLEPc and PETSc
    ERROR: See "installed-arch-python-linux-x86_64/lib/slepc/conf/configure.log" file for details
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-jf9J9u-build/setup.py", line 277, in <module>
        **metadata)
      File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/tmp/pip-jf9J9u-build/setup.py", line 193, in run
        config(prefix, self.dry_run)
      File "/tmp/pip-jf9J9u-build/setup.py", line 131, in config
        if status != 0: raise RuntimeError(status)
    RuntimeError: 256
    
    ----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-jf9J9u-build/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-bRdRZY-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-jf9J9u-build/

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#1 Le 14/01/2018, à 08:32

installation SLEPc et slepc4py

#2 Le 14/01/2018, à 09:48

Re : installation SLEPc et slepc4py

#3 Le 14/01/2018, à 11:05

Re : installation SLEPc et slepc4py

#4 Le 14/01/2018, à 11:14

Re : installation SLEPc et slepc4py

#5 Le 14/01/2018, à 11:43

Re : installation SLEPc et slepc4py

#6 Le 14/01/2018, à 14:09

Re : installation SLEPc et slepc4py

#7 Le 14/01/2018, à 14:27

Re : installation SLEPc et slepc4py

#8 Le 14/01/2018, à 15:12

Re : installation SLEPc et slepc4py

#9 Le 14/01/2018, à 16:11

Re : installation SLEPc et slepc4py

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