On 01/09/10 11:12, Anders Logg 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? >
It would be good if these paths could somehow be set on the code at compile/install since CMake has already done the work of finding them. 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
