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 <[email protected]> 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 <[email protected]> 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@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@tachyon ~/code/slepc (master) > ls >>> /usr/software/petsc/dev/ubuntu_standalone_dbg/bin/ >>> petsc-mpiexec.uni petsc-pythonscripts >>> >>> vijaysm@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 <[email protected]> >>> 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 <[email protected]> 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 <[email protected]> >>>>>> 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 >>>>> >>
