On Wed, Sep 1, 2010 at 1:02 PM, Garth N. Wells <[email protected]> wrote: > > > On 01/09/10 11:58, 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. >> > > I changed the order a few days back to reduce the number of duplicate > libraries, with package with the most dependencies at the top, and > package with the fewest dependencies at the bottom. > > I'm still unsure if the line > > list(REMOVE_DUPLICATES DOLFIN_TARGET_LINK_LIBRARIES) > > will mess we any carefully order libraries.
I don't see why it should, but maybe it's best to remove it just to be sure. Johannes _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
