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
>
>
>
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