On Wed, Sep 1, 2010 at 12:50 PM, Anders Logg <[email protected]> wrote: > On Wed, Sep 01, 2010 at 12:43:12PM +0200, Anders Logg wrote: >> On Wed, Sep 01, 2010 at 12:33:40PM +0200, Johannes Ring wrote: >> > On Wed, Sep 1, 2010 at 12:12 PM, Anders Logg <[email protected]> wrote: >> > > On Wed, Sep 01, 2010 at 12:09:20PM +0200, Johannes Ring wrote: >> > >> On Wed, Sep 1, 2010 at 12:03 PM, Anders Logg <[email protected]> wrote: >> > >> > On Wed, Sep 01, 2010 at 11:36:11AM +0200, Johannes Ring wrote: >> > >> >> On Wed, Sep 1, 2010 at 11:13 AM, Harish Narayanan >> > >> >> <[email protected]> wrote: >> > >> >> > On 9/1/10 2:35 PM, Harish Narayanan wrote: >> > >> >> >> On 9/1/10 2:09 PM, Johannes Ring wrote: >> > >> >> >>> On Wed, Sep 1, 2010 at 9:17 AM, Johannes Ring >> > >> >> >>> <[email protected]> wrote: >> > >> >> >>>> On Wed, Sep 1, 2010 at 8:39 AM, Harish Narayanan >> > >> >> >>>> <[email protected]> wrote: >> > >> >> >>>>> On 9/1/10 12:02 PM, Harish Narayanan wrote: >> > >> >> >>>>>> On 9/1/10 2:44 AM, Marie Rognes wrote: >> > >> >> >>>>>>> On 31. aug. 2010 22:56, Anders Logg wrote: >> > >> >> >>>>>>>> On Tue, Aug 31, 2010 at 04:28:32PM +0200, Marie Rognes >> > >> >> >>>>>>>> wrote: >> > >> >> >>>>>>>> >> > >> >> >>>>>>>>> On 31. aug. 2010 16:22, Johannes Ring wrote: >> > >> >> >>>>>>>>> >> > >> >> >>>>>>>>>> On Tue, Aug 31, 2010 at 4:13 PM, Marie Rognes >> > >> >> >>>>>>>>>> <[email protected]> wrote: >> > >> >> >>>>>>>>>> >> > >> >> >>>>>>>>>> >> > >> >> >>>>>>>>>>> I having some issues with PETSc (surprise) as of today. >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> Dorsal tells me that (full log attached): >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> [\snip] >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> -- The following optional packages were found: >> > >> >> >>>>>>>>>>> -- (OK) MPI >> > >> >> >>>>>>>>>>> -- (OK) PETSC >> > >> >> >>>>>>>>>>> -- (OK) SLEPC >> > >> >> >>>>>>>>>>> -- (OK) UMFPACK >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> [\snap] >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> But: >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>>>>> from dolfin import * >> > >> >> >>>>>>>>>>>>>> has_la_backend("PETSc") >> > >> >> >>>>>>>>>>>>>> >> > >> >> >>>>>>>>>>>>>> >> > >> >> >>>>>>>>>>> False >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>>>>> A = PETScMatrix() >> > >> >> >>>>>>>>>>>>>> >> > >> >> >>>>>>>>>>>>>> >> > >> >> >>>>>>>>>>> Traceback (most recent call last): >> > >> >> >>>>>>>>>>> File "<stdin>", line 1, in <module> >> > >> >> >>>>>>>>>>> NameError: name 'PETScMatrix' is not defined >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>>>>> >> > >> >> >>>>>>>>>>> Help? >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>>> >> > >> >> >>>>>>>>>> There is no -DHAS_PETSC in your log. Try to clean >> > >> >> >>>>>>>>>> up/remove the >> > >> >> >>>>>>>>>> dorsal_build_dir inside the DOLFIN source directory. >> > >> >> >>>>>>>>>> >> > >> >> >>>>>>>>> >> > >> >> >>>>>>>>> Removed. Check. >> > >> >> >>>>>>>>> >> > >> >> >>>>>>>>> >> > >> >> >>>>>>>>> >> > >> >> >>>>>>>>>> Then rerun Dorsal >> > >> >> >>>>>>>>>> and see if the PETSc test passes. >> > >> >> >>>>>>>>>> >> > >> >> >>>>>>>>>> >> > >> >> >>>>>>>>> -- The following optional packages were found: >> > >> >> >>>>>>>>> -- (OK) MPI >> > >> >> >>>>>>>>> -- (OK) PETSC >> > >> >> >>>>>>>>> -- (OK) SLEPC >> > >> >> >>>>>>>>> -- (OK) UMFPACK >> > >> >> >>>>>>>>> -- (OK) PARMETIS >> > >> >> >>>>>>>>> -- (OK) GMP >> > >> >> >>>>>>>>> -- (OK) CGAL >> > >> >> >>>>>>>>> -- (OK) ZLIB >> > >> >> >>>>>>>>> -- (OK) PYTHON >> > >> >> >>>>>>>>> -- The following optional packages could not be found: >> > >> >> >>>>>>>>> -- (**) TRILINOS >> > >> >> >>>>>>>>> -- (**) MTL4 >> > >> >> >>>>>>>>> -- (**) CHOLMOD >> > >> >> >>>>>>>>> -- (**) SCOTCH >> > >> >> >>>>>>>>> -- Configuring done >> > >> >> >>>>>>>>> -- Generating done >> > >> >> >>>>>>>>> -- Build files have been written to: >> > >> >> >>>>>>>>> /home/meg/local/dorsal_downloads/dolfin >> > >> >> >>>>>>>>> make: *** No rule to make target `install'. Stop. >> > >> >> >>>>>>>>> Failure with exit status: 2 >> > >> >> >>>>>>>>> Exit message: There was a problem building dolfin. >> > >> >> >>>>>>>>> >> > >> >> >>>>>>>> I had the same problem (I think). It turned out to be a >> > >> >> >>>>>>>> problem with my >> > >> >> >>>>>>>> PETSC_ARCH variable which was set to linux-gnu-c-opt >> > >> >> >>>>>>>> instead of >> > >> >> >>>>>>>> linux-gnu-cxx-opt. >> > >> >> >>>>>>>> >> > >> >> >>>>>>>> >> > >> >> >>>>>>> >> > >> >> >>>>>>> Doesn't solve the problem for me :( >> > >> >> >>>>>>> >> > >> >> >>>>>>> - My PETSC_ARCH is set to linux-gnu-cxx-opt (cf >> > >> >> >>>>>>> gentoo.platform) >> > >> >> >>>>>>> - cmake reports: -- PETSC_ARCH is linux-gnu-cxx-opt >> > >> >> >>>>>>> - Still get same problem. >> > >> >> >>>>>>> >> > >> >> >>>>>>>> I think this changed in Dorsal at some point recently. >> > >> >> >>>>>>>> >> > >> >> >>>>>>>> >> > >> >> >>>>>>> >> > >> >> >>>>>>> Everything updated as of 20 seconds ago ... >> > >> >> >>>>>> >> > >> >> >>>>>> I too am now seeing strange things such as this: >> > >> >> >>>>>> >> > >> >> >>>>>> >> > >> >> >>>>>> . >> > >> >> >>>>>> . >> > >> >> >>>>>> . >> > >> >> >>>>>> >> > >> >> >>>>>> -- PETSC_DIR is /Users/harish/Work/FEniCS/dev/src/petsc-3.1-p4 >> > >> >> >>>>>> -- PETSC_ARCH is darwin10.0.0-cxx-opt >> > >> >> >>>>>> -- Found petscconf.h >> > >> >> >>>>>> -- PETSc test failed >> > >> >> >>>>>> -- PETSc could not be found. Be sure to set PETSC_DIR and >> > >> >> >>>>>> PETSC_ARCH. >> > >> >> >>>>>> (missing: PETSC_TEST_RUNS) >> > >> >> >>>>>> >> > >> >> >>>>>> . >> > >> >> >>>>>> . >> > >> >> >>>>>> . >> > >> >> >>>>>> >> > >> >> >>>>>> -- (OK) MPI >> > >> >> >>>>>> -- (OK) MTL4 >> > >> >> >>>>>> -- (OK) UMFPACK >> > >> >> >>>>>> -- (OK) CHOLMOD >> > >> >> >>>>>> -- (OK) SCOTCH >> > >> >> >>>>>> -- (OK) PARMETIS >> > >> >> >>>>>> -- (OK) GMP >> > >> >> >>>>>> -- (OK) CGAL >> > >> >> >>>>>> -- (OK) ZLIB >> > >> >> >>>>>> -- (OK) PYTHON >> > >> >> >>>>>> -- The following optional packages could not be found: >> > >> >> >>>>>> -- (**) PETSC >> > >> >> >>>>>> -- (**) SLEPC >> > >> >> >>>>>> -- (**) TRILINOS >> > >> >> >>>>> >> > >> >> >>>>> Following which (and independently), CMake fails >> > >> >> >>>>> catastrophically: >> > >> >> >>>>> >> > >> >> >>>>> Building CXX object >> > >> >> >>>>> dolfin/CMakeFiles/dolfin.dir/ale/HarmonicSmoothing.cpp.o >> > >> >> >>>>> [ 1%] cd /foo/dolfin/dorsal_build_dir/dolfin && >> > >> >> >>>>> /opt/local/bin/c++ >> > >> >> >>>>> -Ddolfin_EXPORTS -DPACKAGE_VERSION=\"0.9.8\" >> > >> >> >>>>> -DBOOST_UBLAS_NDEBUG >> > >> >> >>>>> -DHAS_MTL4 -DMTL_HAS_BLAS -DHAS_UMFPACK -DHAS_CHOLMOD >> > >> >> >>>>> -DHAS_SCOTCH >> > >> >> >>>>> -DHAS_PARMETIS -DHAS_CGAL -DHAS_GMP -DHAS_ZLIB -DHAS_CPPUNIT >> > >> >> >>>>> -DHAS_MPI >> > >> >> >>>>> -DMPICH_IGNORE_CXX_SEEK -frounding-math;-D_REENTRANT -O2 -g >> > >> >> >>>>> -fPIC >> > >> >> >>>>> -I/foo/dolfin -I/opt/local/include/libxml2 >> > >> >> >>>>> -I/Users/harish/Work/FEniCS/dev/include -I/opt/local/include >> > >> >> >>>>> -I/Users/harish/Work/FEniCS/dev/src/mtl4 >> > >> >> >>>>> -I/opt/local/include/ufsparse >> > >> >> >>>>> -I/opt/local/include/cppunit -o >> > >> >> >>>>> CMakeFiles/dolfin.dir/ale/HarmonicSmoothing.cpp.o -c >> > >> >> >>>>> /foo/dolfin/dolfin/ale/HarmonicSmoothing.cpp >> > >> >> >>>>> i686-apple-darwin10-g++-4.2.1: no input files >> > >> >> >>>>> i686-apple-darwin10-g++-4.2.1: no input files >> > >> >> >>>>> Building CXX object >> > >> >> >>>>> dolfin/CMakeFiles/dolfin.dir/ale/TransfiniteInterpolation.cpp.o >> > >> >> >>>>> cd /foo/dolfin/dorsal_build_dir/dolfin && /opt/local/bin/c++ >> > >> >> >>>>> -Ddolfin_EXPORTS -DPACKAGE_VERSION=\"0.9.8\" >> > >> >> >>>>> -DBOOST_UBLAS_NDEBUG >> > >> >> >>>>> -DHAS_MTL4 -DMTL_HAS_BLAS -DHAS_UMFPACK -DHAS_CHOLMOD >> > >> >> >>>>> -DHAS_SCOTCH >> > >> >> >>>>> -DHAS_PARMETIS -DHAS_CGAL -DHAS_GMP -DHAS_ZLIB -DHAS_CPPUNIT >> > >> >> >>>>> -DHAS_MPI >> > >> >> >>>>> -DMPICH_IGNORE_CXX_SEEK -frounding-math;-D_REENTRANT -O2 -g >> > >> >> >>>>> -fPIC >> > >> >> >>>>> -I/foo/dolfin -I/opt/local/include/libxml2 >> > >> >> >>>>> -I/Users/harish/Work/FEniCS/dev/include -I/opt/local/include >> > >> >> >>>>> -I/Users/harish/Work/FEniCS/dev/src/mtl4 >> > >> >> >>>>> -I/opt/local/include/ufsparse >> > >> >> >>>>> -I/opt/local/include/cppunit -o >> > >> >> >>>>> CMakeFiles/dolfin.dir/ale/TransfiniteInterpolation.cpp.o -c >> > >> >> >>>>> /foo/dolfin/dolfin/ale/TransfiniteInterpolation.cpp >> > >> >> >>>>> Building CXX object >> > >> >> >>>>> dolfin/CMakeFiles/dolfin.dir/common/real.cpp.o >> > >> >> >>>>> /bin/sh: -D_REENTRANT: command not found >> > >> >> >>>>> /bin/sh: -D_REENTRANT: command not found >> > >> >> >>>> >> > >> >> >>>> I made a fix for this yesterday. Maybe you just need to clean >> > >> >> >>>> up the >> > >> >> >>>> CMake cache (remove the dorsal_build_dir folder)? >> > >> >> >>> >> > >> >> >>> My fix was reverted but it should be fixed again now. >> > >> >> >> >> > >> >> >> This problem is fixed, leaving only the petsc/slepc error. >> > >> >> > >> > >> >> > I spoke too soon. I now receive the following during the linking >> > >> >> > stage >> > >> >> > (too). >> > >> >> > >> > >> >> > Undefined symbols: >> > >> >> > "_METIS_mCPartGraphRecursive2", referenced from: >> > >> >> > _ParMETIS_V3_PartKway in libparmetis.a(kmetis.o) >> > >> >> > _PartitionSmallGraph__ in libparmetis.a(weird.o) >> > >> >> > _Mc_InitPartition_RB__ in libparmetis.a(initpart.o) >> > >> >> > _Mc_InitPartition_RB__ in libparmetis.a(initpart.o) >> > >> >> > _Balance_Partition__ in libparmetis.a(initbalance.o) >> > >> >> > _Balance_Partition__ in libparmetis.a(initbalance.o) >> > >> >> > ld: symbol(s) not found >> > >> >> > collect2: ld returned 1 exit status >> > >> >> > make[2]: *** [dolfin/libdolfin.0.9.8.dylib] Error 1 >> > >> >> > make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2 >> > >> >> > make: *** [all] Error 2 >> > >> >> >> > >> >> I also got this on the Mac buildbot. The problem is that there is a >> > >> >> file /opt/local/lib/libmetis.dylib that is used instead of the one >> > >> >> that comes with ParMETIS (that Dorsal builds). I worked around this >> > >> >> by >> > >> >> configuring DOLFIN with >> > >> >> -DMETIS_LIBRARY=/Users/fenicsslave2/Work/FEniCS/lib/libmetis.a (the >> > >> >> one that Dorsal installed with ParMETIS). >> > >> >> >> > >> >> This problem only shows up when PETSc is not found because >> > >> >> PETSC_LIBRARIES contains the correct link flags >> > >> >> (-L/path/to/libmetis.a >> > >> >> -lmetis). >> > >> >> >> > >> >> Johannes >> > >> > >> > >> > Everything seems to work fine except BOOST_DIR is missing when I run >> > >> > the demos. >> > >> >> > >> /sw (Fink) was the default BOOST_DIR. I have changed this to >> > >> /opt/local (MacPorts) now. >> > > >> > > It works fine when I set BOOST_DIR to /opt/local >> > > >> > > Should we write BOOST_DIR to dolfin.conf? >> > >> > Yes, that might be a good idea, however, it might not always be defined. >> >> Your latest fix seems to have done the trick. It's working fine now. >> >> So, clean install from Dorsal on Mac OS X without any extra tweaks >> seems to work perfectly now, at least for me. >> >> Anyone else still having trouble? >> >> I'll try removing some PETSc files next to see if it breaks cleanly. > > One thing that's still missing on OS X is SLEPc. It has worked before > but the test program fails during configuration with the following message: > > Undefined symbols: > "_ompi_mpi_comm_self"
I'm having a similar problem with PETSc on the Mac buildbot: http://fenics.org:8080/builders/dolfin-mac-osx/builds/721/steps/dolfin%20build/logs/CMakeError.log > I think I remember seeing this in a discussion recently. Is there a > solution for this? It has worked before. One solution will be to set CXX=mpic++ before running cmake. I guess the reason it worked before might be that the test was not required to work in order for PETSc and SLEPc to be found. This was changed a few days back. Johannes _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
