On Wed, Sep 1, 2010 at 1:30 PM, Anders Logg <[email protected]> wrote: > On Wed, Sep 01, 2010 at 12:22:27PM +0100, Garth N. Wells wrote: >> >> >> On 01/09/10 12:17, Anders Logg wrote: >> > On Wed, Sep 01, 2010 at 01:13:30PM +0200, Anders Logg wrote: >> >> On Wed, Sep 01, 2010 at 12:58:36PM +0200, Johannes Ring wrote: >> >>> 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. >> >> >> >> Did we have CXX=mpic++ or similar in the Dorsal platform file for Snow >> >> Leopard? >> > >> > We used to have this in dolfin.package: >> > >> > package_specific_setup () { >> > export CC=mpicc >> > export CXX=mpic++ >> > } >> > >> > Can we add it back? SLEPc works again for me on OS X when I add it. >> > >> >> Best would be to get the MPI flags right in dolfin/CMakeLists.txt. There >> are a few FIXME related the link flags. >> >> If we use the MPI wrappers, we should somehow test for this and then not >> add the MPI compiler flags in dolfin/CMakeLists.txt. > > I don't understand. That seems like a secondary issue, that we would > add flags we don't really need if we are using the MPI wrappers. > > Does anyone know which extra flag is needed to get things to run?
I guess that these should do it: -lmpi -lopen-rte -lopen-pal The problem (in my case with PETSc) is that these are missing from PETSC_LIBRARIES so the test program in FindPETSc.cmake fails. Johannes > Otherwise, I suggest adding the above to dolfin.platform and also a > FIXME to dolfin/CMakeLists.txt about needing to figure out how to get > those libraries on Mac. At least that would get things working now. > > -- > Anders > _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
