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
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