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

[Barry Smith]

   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
>>>