Yes, mumps will not be available, but we can try to add it back later. Johannes
On Tue, Aug 25, 2015 at 6:41 PM Johannes Neumann <[email protected]> wrote: > ok i will try it now. thanks for your help. this means that mumps for > example will not be available? I don't need it at the moment so just, that > I know. > > > Am 25.08.2015 um 18:35 schrieb Johannes Ring: > > Try to remove this part from the petsc build: > > download: | > mumps, scalapack, blacs, ml > > I think this could be the problem. > > Johannes > > On Tue, Aug 25, 2015 at 6:26 PM Johannes Neumann <[email protected]> > wrote: > > oh, all right ;) here it is. >> > >> >> Am 25.08.2015 um 18:24 schrieb Johannes Ring: >> > [Please keep fenics-support in Cc] >> >> Thanks Jo, but I was thinking about the yaml file, where you specify the >> packages you want to build. >> >> Johannes >> >> On Tue, Aug 25, 2015 at 6:13 PM Johannes Neumann <[email protected]> >> wrote: >> >> >>> >>> >>> >>> >>> I compressed the profile without most of the libs and shared >>> data/header files. If you need any of these, please let me know. You >>> can download it here: >>> >>> >>> >>> >>> https://drive.google.com/file/d/0BybZyFhAQBNMa3pYdGk5SURKWUk/view?usp=sharing >>> >>> >>> >>> The custom profile is the default linux profile plus scipy and >>> joblib. >>> >>> >>> >>> Best, >>> >>> Jo >>> >> >>> >>> >>> >>> Am 25.08.2015 um 14:06 schrieb Johannes >>> Ring: >>> >>> >>> >>> >>> Can you send us your hashdist profile? >>> >>> >>> >>> >>> Johannes >>> >>> >>> >>> >>> >>> On Tue, Aug 25, 2015 at 1:27 PM Johannes Neumann >>> <[email protected]> >>> >>> wrote: >>> >>> >>> >>>> >>>> Hello, >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> we use a compute cluster with shared home dir but different >>>> software >>>> >>>> running on some of the nodes. so I am using the >>>> hashdist/hashstack >>>> >>>> version of fenics with works great except for when I use >>>> other nodes >>>> >>>> with different library versions. The output it generates is >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> from dolfin import * >>>> >>>> >>>> >>>> File >>>> >>>> >>>> "$HOME/.hashdist/bld/profile/7tifyrwdwqtd/lib/python2.7/site-packages/dolfin/__init__.py", >>>> >>>> line 16, in <module> >>>> >>>> >>>> >>>> from . import cpp >>>> >>>> >>>> >>>> File >>>> >>>> >>>> "$HOME/.hashdist/bld/profile/7tifyrwdwqtd/lib/python2.7/site-packages/dolfin/cpp/__init__.py", >>>> >>>> line 42, in <module> >>>> >>>> >>>> >>>> exec("from . import %s" % module_name) >>>> >>>> >>>> >>>> File "<string>", line 1, in <module> >>>> >>>> >>>> >>>> File >>>> >>>> >>>> "$HOME/.hashdist/bld/profile/7tifyrwdwqtd/lib/python2.7/site-packages/dolfin/cpp/common.py", >>>> >>>> line 32, in <module> >>>> >>>> >>>> >>>> _common = swig_import_helper() >>>> >>>> >>>> >>>> File >>>> >>>> >>>> "$HOME/.hashdist/bld/profile/7tifyrwdwqtd/lib/python2.7/site-packages/dolfin/cpp/common.py", >>>> >>>> line 28, in swig_import_helper >>>> >>>> >>>> >>>> _mod = imp.load_module('_common', fp, pathname, >>>> description) >>>> >>>> >>>> >>>> ImportError: >>>> >>>> $HOME/.hashdist/bld/petsc/cgj5xhkahatd/lib/libpetsc.so.3.5: >>>> >>>> undefined symbol: ParMETIS_V3_Mesh2Dual >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> And indeed, when I ldd >>>> >>>> the petsc library I get >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> neumann@erhard-17:~/fenics/tests> ldd >>>> >>>> $HOME/.hashdist/bld/petsc/cgj5xhkahatd/lib/libpetsc.so.3.5 >>>> >>>> >>>> >>>> linux-vdso.so.1 (0x00007ffc359b3000) >>>> >>>> >>>> >>>> libHYPRE-2.9.1a.so >>>> => >>>> >>>> $HOME/.hashdist/bld/hypre/kh4vd5dptalu/lib/libHYPRE-2.9.1a.so >>>> >>>> (0x00002acfabca6000) >>>> >>>> >>>> >>>> libmpichcxx.so.10 => >>>> >>>> $HOME/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpichcxx.so.10 >>>> >>>> (0x00002acfac13c000) >>>> >>>> >>>> >>>> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 >>>> >>>> (0x00002acfac35f000) >>>> >>>> >>>> >>>> libopenblas.so.0 => >>>> >>>> $HOME/.hashdist/bld/lapack/vwdn72phzwm3/lib/libopenblas.so.0 >>>> >>>> (0x00002acfac667000) >>>> >>>> >>>> >>>> libparmetis.so => >>>> >>>> /usr/lib64/mpi/gcc/openmpi/lib64/libparmetis.so >>>> >>>> (0x00002acfad417000) >>>> >>>> >>>> >>>> libmetis..so => >>>> >>> >>>> >>>> $HOME/.hashdist/bld/parmetis/hbifmb4gf2ps/lib/libmetis.so >>>> >>>> (0x00002acfad61b000) >>>> >>>> >>>> >>>> libX11.so.6 => /usr/lib64/libX11.so.6 >>>> >>>> (0x00002acfad887000) >>>> >>>> >>>> >>>> libpthread.so.0 => /lib64/libpthread.so.0 >>>> >>>> (0x00002acfadbc5000) >>>> >>>> >>>> >>>> libm.so.6 => /lib64/libm.so.6 >>>> (0x00002acfadde2000) >>>> >>>> >>>> >>>> libmpichf90.so.10 => >>>> >>>> $HOME/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpichf90.so.10 >>>> >>>> (0x00002acfae0e3000) >>>> >>>> >>>> >>>> libgfortran.so.3 => /usr/lib64/libgfortran.so.3 >>>> >>>> (0x00002acfae2e6000) >>>> >>>> >>>> >>>> libquadmath.so.0 => /usr/lib64/libquadmath.so.0 >>>> >>>> (0x00002acfae600000) >>>> >>>> >>>> >>>> libdl.so..2 => /lib64/libdl.so.2 >>>> (0x00002acfae83c000) >>>> >>>> >>>> >>>> libmpich..so.10 => >>>> >>> >>>> >>>> $HOME/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpich.so.10 >>>> >>>> (0x00002acfaea40000) >>>> >>>> >>>> >>>> libopa.so.1 => >>>> >>>> $HOME/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libopa.so.1 >>>> >>>> (0x00002acfaeeaf000) >>>> >>>> >>>> >>>> libmpl.so.1 => >>>> >>>> $HOME/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpl.so.1 >>>> >>>> (0x00002acfaf0b1000) >>>> >>>> >>>> >>>> librt.so..1 => /lib64/librt.so.1 >>>> (0x00002acfaf2b7000) >>>> >>>> >>>> >>>> libgcc_s..so.1 => /lib64/libgcc_s.so.1 >>>> >>> >>>> >>>> (0x00002acfaf4bf000) >>>> >>>> >>>> >>>> libc.so.6 => /lib64/libc.so.6 >>>> (0x00002acfaf6d6000) >>>> >>>> >>>> >>>> /lib64/ld-linux-x86-64.so.2 (0x00002acfaa8ee000) >>>> >>>> >>>> >>>> libptscotch.so.0 => >>>> >>>> /usr/lib64/mpi/gcc/openmpi/lib64/libptscotch.so.0 >>>> >>>> (0x00002acfafa7d000) >>>> >>>> >>>> >>>> libptscotcherr.so.0 => >>>> >>>> /usr/lib64/mpi/gcc/openmpi/lib64/libptscotcherr.so.0 >>>> >>>> (0x00002acfafd5b000) >>>> >>>> >>>> >>>> libz.so.1 => /lib64/libz.so.1 >>>> (0x00002acfaff5d000) >>>> >>>> >>>> >>>> libmpi.so.1 => >>>> >>>> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.1 >>>> (0x00002acfb0173000) >>>> >>>> >>>> >>>> libxcb.so.1 => /usr/lib64/libxcb.so.1 >>>> >>>> (0x00002acfb0443000) >>>> >>>> >>>> >>>> libopen-rte.so.5 => >>>> >>>> /usr/lib64/mpi/gcc/openmpi/lib64/libopen-rte.so.5 >>>> >>>> (0x00002acfb0663000) >>>> >>>> >>>> >>>> libopen-pal.so.5 => >>>> >>>> /usr/lib64/mpi/gcc/openmpi/lib64/libopen-pal.so.5 >>>> >>>> (0x00002acfb08d2000) >>>> >>>> >>>> >>>> libXau.so.6 => /usr/lib64/libXau.so.6 >>>> >>>> (0x00002acfb0b92000) >>>> >>>> >>>> >>>> libutil.so.1 => /lib64/libutil.so.1 >>>> >>>> (0x00002acfb0d96000) >>>> >>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Checking in hashdist shows, that they are build but not used >>>> for >>>> >>>> some reason. I am now rebuilding with the dev version >>>> (stable gives >>>> >>>> me the urllib error) and I will see, if this results in >>>> correct >>>> >>>> linking. but at the moment I have a hard time getting a >>>> stable >>>> >>>> connection to github. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Best, >>>> >>>> >>>> >>>> Jo >>>> >>>> >>>> >>>> -- >>>> Dipl.-Math. Johannes Neumann >>>> Weierstraß-Institut für Angewandte >>>> Analysis und Stochastik >>>> Mohrenstraße 39 >>>> 10117 Berlin >>>> Tel. +49 (0)30 20372 567 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> >>>> >>>> >>>> fenics-support mailing list >>>> >>>> >>>> >>>> [email protected] >>>> >>>> >>>> >>>> http://fenicsproject.org/mailman/listinfo/fenics-support >>>> >>>> >>>> >>>> >>> >>> >>> >>> >>> -- >>> Dipl.-Math. Johannes Neumann >>> Weierstraß-Institut für Angewandte >>> Analysis und Stochastik >>> Mohrenstraße 39 >>> 10117 Berlin >>> Tel. +49 (0)30 20372 567 >>> >>> >>> >>> >>> >> >> -- >> Dipl.-Math. Johannes Neumann >> Weierstraß-Institut für Angewandte >> Analysis und Stochastik >> Mohrenstraße 39 >> 10117 Berlin >> Tel. +49 (0)30 20372 567 >> >> >> > -- > Dipl.-Math. Johannes Neumann > Weierstraß-Institut für Angewandte > Analysis und Stochastik > Mohrenstraße 39 > 10117 Berlin > Tel. +49 (0)30 20372 567 > >
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