[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 > > >
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