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 >>>
