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

[Jose E. Roman]

The easiest thing for SLEPc would be that PETSc installs Sowing binaries, as was done a few weeks ago. But, as you suggest, maybe it makes more sense that SLEPc is capable of downloading Sowing itself. I will have a look at it in the next days.

Jose


El 30/01/2015, a las 04:12, Vijay S. Mahadevan escribió:

>>   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
>>>>> 
>>