[petsc-users] petsc installs okay, cannot install petsc4py

[Jérémy REKIER]

Dear support team,

I am trying to install petsc4py on top of my miniconda3 python environment. 

I recently filed an issue <https://bitbucket.org/petsc/petsc4py/issues/50/cannot-pass-runtestpy#comment-30006281> on bitbucket about the trouble that I was having with installing the development version of petsc4py. I have changed the status of this issue as invalid as this no longer corresponds to the trouble that I am having. 

Since I think that the problem I’m probably having comes from my—possibly broken—environment, I reckoned the best was to ask for support via e-mail.

I had previously succeeded in installing the development version of both petsc and petsc4py on my office computer running on MacOSX. But, when I try to do so on my laptop (using the same OS) using exactly the same command inputs, I keep on failing. 

Now, I seem to compile PETSc without trouble. Configuration step produces the following output:


jrek at MacJerem:petsc$ python2.7 ./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --with-scalar-type=complex --download-scalapack --download-mumps
===============================================================================
             Configuring PETSc to compile on your system                       
===============================================================================
Compilers:                                                                                                                                                                  
  C Compiler:         mpicc    -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3 
  C++ Compiler:       mpicxx  -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g     
  Fortran Compiler:   mpif90   -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g  
Linkers:
  Shared linker:   mpicc  -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress    -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3
  Dynamic linker:   mpicc  -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress    -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3
make:
BLAS/LAPACK: -llapack -lblas
MPI:
  Includes: -I/usr/local/Cellar/open-mpi/1.10.3/include
cmake:
  Arch:     
hwloc:
  Includes: -I/usr/local/include
  Library:  -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lhwloc
scalapack:
  Library:  -Wl,-rpath,/Users/jrek/softs/petsc/arch-darwin-c-opt/lib -L/Users/jrek/softs/petsc/arch-darwin-c-opt/lib -lscalapack
MUMPS:
  Includes: -I/Users/jrek/softs/petsc/arch-darwin-c-opt/include
  Library:  -Wl,-rpath,/Users/jrek/softs/petsc/arch-darwin-c-opt/lib -L/Users/jrek/softs/petsc/arch-darwin-c-opt/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord
X:
  Includes: -I/opt/X11/include
  Library:  -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -lX11
pthread:
sowing:
ssl:
  Includes: -I/usr/local/opt/openssl/include
  Library:  -Wl,-rpath,/usr/local/opt/openssl/lib -L/usr/local/opt/openssl/lib -lssl -lcrypto
PETSc:
  PETSC_ARCH: arch-darwin-c-opt
  PETSC_DIR: /Users/jrek/softs/petsc
  Scalar type: complex
  Precision: double
  Clanguage: C
  Integer size: 32
  shared libraries: enabled
  Memory alignment: 16
xxx=========================================================================xxx
 Configure stage complete. Now build PETSc libraries with (gnumake build):
   make PETSC_DIR=/Users/jrek/softs/petsc PETSC_ARCH=arch-darwin-c-opt all
xxx=========================================================================xxx

Then, everything works smoothly with building and testing until I get to the point of actually installing petsc4py. Then, the error I am having is this one:

jrek at MacJerem:petsc4py$ python setup.py install 
running install
running build
running build_src
running build_py
running build_ext
PETSC_DIR:    /Users/jrek/softs/petsc
PETSC_ARCH:   arch-darwin-c-opt
version:      3.7.3 development
integer-size: 32-bit
scalar-type:  complex
precision:    double
language:     CONLY
compiler:     mpicc
linker:       mpicc
building 'PETSc' extension
mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -g3 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/jrek/miniconda3/include -arch x86_64 -DPETSC_DIR=/Users/jrek/softs/petsc -I/usr/local/Cellar/open-mpi/1.10.3/include -I/usr/local/opt/openssl/include -I/opt/X11/include -I/usr/local/include -I/Users/jrek/softs/petsc/arch-darwin-c-opt/include -I/Users/jrek/softs/petsc/include -Isrc/include -I/Users/jrek/miniconda3/lib/python3.5/site-packages/numpy/core/include -I/Users/jrek/miniconda3/include/python3.5m -c src/PETSc.c -o build/temp.macosx-10.6-x86_64-3.5/arch-darwin-c-opt/src/PETSc.o
In file included from src/PETSc.c:3:
In file included from src/petsc4py.PETSc.c:271:
In file included from /usr/local/include/petsc.h:5:
In file included from /usr/local/include/petscbag.h:4:
/usr/local/include/petscsys.h:152:6: error: "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version"
#    error "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version"

Plus other errors which I think have good chances of being due to this one. 

I guess I must probably have conflicting OpenMPI installs but I do not understand why PETSc is cannot compile just as fine as it did a moment ago. 
How can be sure of the “mpi.h” that I am using and would specify one solve my problem ? 

Any help would be greatly appreciated as this is slowly driving me insane :)
Thanks very much in advance :D

Cheers,
Jerem 



 
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