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 >
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