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

Thu Jan 29 19:10:03 CST 2015

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
>>