[petsc-users] Need to create $PREFIX/include explicitly

Thu Jan 29 21:12:13 CST 2015

>    Hmm, this is because I intentionally turned off the installation of the sowing tools when installing PETSc; I didn't think of SLEPc using them.

Yes, that would be the culprit. The installation can possibly be
avoided if SLEPc also downloads Sowing wherein this particular
dependency on PETSc can be decoupled. Not sure whether that fits
SLEPc's workflow though.

>    End users who do not get the source code from the repository get a tarball with the Fortran already built hence they do not need the sowing tools.

It will be an issue for cases where a user installs PETSc source from
tarball and uses SLEPc source from repo only to find bfort not
available in the path. Perhaps this combination is already discouraged
?

Vijay

On Thu, Jan 29, 2015 at 8:01 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>    Hmm, this is because I intentionally turned off the installation of the sowing tools when installing PETSc; I didn't think of SLEPc using them.
>
>    End users who do not get the source code from the repository get a tarball with the Fortran already built hence they do not need the sowing tools.
>
>    I guess we should install them.
>
>    Barry
>
>> On Jan 29, 2015, at 7:10 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>
>> Found another related issue although not directly affected when
>> working with PETSc alone. I can created a new thread for this if
>> needed.
>>
>> When configuring SLEPc with an installed version of PETSc, the
>> operation fails due to not finding bfort. The issue seems to be that
>> for some reason, PETSc failed to install the bin files that are
>> clearly present in the source configuration i.e., they are under
>> $PETSC_DIR/$PETSC_ARCH/bin but not in $PREFIX/bin. I can rectify this
>> by manually copying the executables in $PETSC_DIR/$PETSC_ARCH/bin to
>> $PREFIX/bin which then makes SLEPc configure happy.
>>
>> Here are the offending outputs.
>>
>> SLEPc configure:=
>> vijaysm at tachyon ~/code/slepc (master) >
>> PETSC_DIR=/usr/software/petsc/dev/ubuntu_standalone_dbg PETSC_ARCH=""
>> ./configure --prefix=/usr/software/slepc/dev/ubuntu_standalone_dbg
>> --with-arpack=1 --with-arpack-dir=/usr/software/arpack/lib
>> --with-arpack-flags="-lparpack_ubuntu_x86_64 -larpack_ubuntu_x86_64"
>> Checking environment...
>> Checking PETSc installation...
>> Checking ARPACK library...
>> Checking LAPACK library...
>> Traceback (most recent call last):
>>  File "./configure", line 10, in <module>
>>    execfile(os.path.join(os.path.dirname(__file__), 'config', 'configure.py'))
>>  File "./config/configure.py", line 427, in <module>
>>    generatefortranstubs.main(slepcdir,petscconf.BFORT,os.getcwd(),0)
>>  File "/home/vijaysm/code/slepc/bin/maint/generatefortranstubs.py",
>> line 208, in main
>>    os.path.walk(dir, processDir, [petscdir, bfort,verbose])
>>  File "/usr/lib/python2.7/posixpath.py", line 246, in walk
>>    walk(name, func, arg)
>>  File "/usr/lib/python2.7/posixpath.py", line 238, in walk
>>    func(arg, top, names)
>>  File "/home/vijaysm/code/slepc/bin/maint/generatefortranstubs.py",
>> line 165, in processDir
>>    raise RuntimeError('Error running bfort\n'+cmd+'\n'+output)
>> RuntimeError: Error running bfort
>> cd /home/vijaysm/code/slepc/include;
>> BFORT_CONFIG_PATH=/home/vijaysm/code/slepc/lib/slepc-conf
>> /usr/software/petsc/dev/ubuntu_standalone_dbg/bin/bfort -dir
>> /home/vijaysm/code/slepc/include/ftn-auto -mnative -ansi -nomsgs
>> -noprofile -anyname -mapptr -mpi -mpi2 -ferr -ptrprefix Petsc -ptr64
>> PETSC_USE_POINTER_CONVERSION -fcaps PETSC_HAVE_FORTRAN_CAPS -fuscore
>> PETSC_HAVE_FORTRAN_UNDERSCORE -f90mod_skip_header -f90modfile
>> f90module.f90 slepcsc.h slepcsvd.h slepcmfn.h slepcpep.h slepcbv.h
>> slepcst.h slepcsys.h slepc.h slepceps.h slepcblaslapack.h slepcnep.h
>> slepcmath.h slepcversion.h slepcvec.h slepcrg.h slepcds.h slepcfn.h
>> slepcrgtypes.h
>> sh: 1: /usr/software/petsc/dev/ubuntu_standalone_dbg/bin/bfort: not found
>>
>> vijaysm at tachyon ~/code/slepc (master) > ls
>> /usr/software/petsc/dev/ubuntu_standalone_dbg/bin/
>> petsc-mpiexec.uni  petsc-pythonscripts
>>
>> vijaysm at tachyon ~/code/slepc (master) > ls
>> /usr/software/petsc/dev/ubuntu_standalone_dbg/bin/petsc-pythonscripts/
>> PetscBinaryIO.py  PetscBinaryIO_tests.py  petsc_conf.py
>> petsc_gen_xdmf.py  petsclogformat.py  petscnagupgrade.py
>> petscnagupgrade.pyc
>>
>> Again, let me know if you need any of the log files for either PETSc
>> or SLEPc. Thanks,
>>
>> Vijay
>>
>> On Wed, Jan 28, 2015 at 10:30 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>>> BTW: I also updated some routines in moab.cxx for changes in how we handle setfromoptions in master
>>>
>>> Thanks Barry, I'll take a look at it. Will be spending time next
>>> couple of weeks on DMMoab to add some geometric multigrid hooks and
>>> more examples.
>>>
>>> Vijay
>>>
>>> On Wed, Jan 28, 2015 at 9:29 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>  Fixed in master and next. Thanks for reporting it.
>>>>
>>>>   Barry
>>>>
>>>> BTW: I also updated some routines in moab.cxx for changes in how we handle setfromoptions in master
>>>>
>>>>> On Jan 28, 2015, at 7:39 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>>>>
>>>>> With the current master, when using a prefix, configuration fails with
>>>>> the following error message. I've not attached configure.log since its
>>>>> around 7MB (but definitely can send that if that helps further
>>>>> deciphering the issue). The problem here seems to be that
>>>>> $PREFIX/include is not created (while $PREFIX/lib is created
>>>>> explicitly with mkdir -p). If I manually create $PREFIX/include and
>>>>> rerun configure, everything proceeds fine. Minor annoyance.
>>>>>
>>>>> I am not sure whether I just pulled in between merges though. My
>>>>> latest hash: c04667f413dc6e46059f28faddb2b19f70ad4cfd.
>>>>>
>>>>> Command:
>>>>> ./configure --CFLAGS="-O2 -mtune=generic"
>>>>> --CPPFLAGS=-I/usr/software/metis-5.1.0/include --CXXFLAGS="-O2
>>>>> -mtune=generic" --FFLAGS="-O2 -mtune=generic"
>>>>> --LDFLAGS="-L/usr/software/moab/dev/optimized/lib
>>>>> -L/usr/software/pnetcdf-1.3.1/lib -L/usr/software/zoltan-3.6/lib
>>>>> -L/usr/software/ptscotch-6.0/lib -L/usr/software/parmetis-4.0.3/lib
>>>>> -L/usr/software/metis-5.1.0/lib" --LIBS="-lpnetcdf -lparmetis -lmetis
>>>>> -lm" --download-hypre=yes --download-mumps=yes
>>>>> --download-scalapack=yes --download-suitesparse=yes
>>>>> --prefix=/usr/software/petsc/dev/ubuntu_standalone_opt
>>>>> --with-blas-lapack-dir=/usr
>>>>> --with-boost-dir=/usr/software/boost/current --with-clanguage=C++
>>>>> --with-cmake=/usr/software/cmake/bin/cmake --with-cuda=0
>>>>> --with-debugging=0 --with-fortran-interfaces=1
>>>>> --with-fortran-kernels=1 --with-fortran=1
>>>>> --with-hdf5-dir=/usr/software/hdf5-1.8.11
>>>>> --with-metis-dir=/usr/software/metis-5.1.0
>>>>> --with-moab-include=/usr/software/moab/dev/optimized/include
>>>>> --with-moab-lib="-lMOAB -liMesh -lmbcoupler -lzoltan -lptscotch
>>>>> -lptscotcherr -lptscotcherrexit -lscotch -lscotcherr -lscotcherrexit
>>>>> -lz -lm " --with-mpi-dir=/usr/software/mpich-3.0.4
>>>>> --with-netcdf-dir=/usr/software/netcdf-4.3.0 --with-openmp=0
>>>>> --with-parmetis-dir=/usr/software/parmetis-4.0.3 --with-pic=1
>>>>> --with-ptscotch-include=/usr/software/ptscotch-6.0/include
>>>>> --with-ptscotch-lib="-lptesmumps -lptscotch -lptscotcherr
>>>>> -lptscotcherrexit -lscotch -lscotcherr -lscotcherrexit -lz -lm"
>>>>> --with-shared-libraries=1 PETSC_ARCH=ubuntu_standalone_opt
>>>>>
>>>>> Error:
>>>>> *******************************************************************************
>>>>>        UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log
>>>>> for details):
>>>>> -------------------------------------------------------------------------------
>>>>> Error running make on MUMPS: Could not execute "mkdir -p
>>>>> /usr/software/petsc/dev/ubuntu_standalone_opt/lib && cd
>>>>> /home/vijaysm/code/petsc/ubuntu_standalone_opt/externalpackages/MUMPS
>>>>> && cp -f lib/*.* /usr/software/petsc/dev/ubuntu_standalone_opt/lib/.
>>>>> && cp -f include/*.*
>>>>> /usr/software/petsc/dev/ubuntu_standalone_opt/include/.":
>>>>> cp: target '/usr/software/petsc/dev/ubuntu_standalone_opt/include/.'
>>>>> is not a directory
>>>>> *******************************************************************************
>>>>>
>>>>> Vijay
>>>>
>