On 01. sep. 2010 12:43, 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? > >
After removing everything that involves dolfin, branching a fresh copy and running dorsal -- I am happy again (including PETSc/SLEPc) :) -- Marie _______________________________________________ Mailing list: https://launchpad.net/~dorsal Post to : [email protected] Unsubscribe : https://launchpad.net/~dorsal More help : https://help.launchpad.net/ListHelp
