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. Garth > -- > Anders > > _______________________________________________ > Mailing list: https://launchpad.net/~dorsal > Post to : [email protected] > Unsubscribe : https://launchpad.net/~dorsal > More help : https://help.launchpad.net/ListHelp _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
