Hello,
I have an update here as I ran into the problem again, where the wrong
parmetis is used by petsc. I tried a couple of different things (static
build, tell petsc to download parmetis on its own etc pp.) but this did
not help. I think the problem with this is connected to the following
warning that I get during the petsc buid in the log:
2015/10/05 15:09:41 - INFO: [package:run_job]
===============================================================================
2015/10/05 15:09:41 - INFO: [package:run_job] ***** WARNING: MPI_DIR
(set to /Home/flow/neumann/.hashdist/bld/mpi/gmkx3ftk3tz2) found in
environment variables - ignoring
2015/10/05 15:09:41 - INFO: [package:run_job] use ./configure
MPI_DIR=$MPI_DIR if you really want to use that value ******
2015/10/05 15:09:41 - INFO: [package:run_job]
===============================================================================
I couldn't find anything related to that variable in the petsc.yaml or
the accompanying .py script. So I gues that is why Petsc uses the system
parmetis and not the locally build one. As I understand, I will have to
add this in the py. script. I will try to do it myself locally but help
would be appreciated.
Best,
Jo
Am 25.08.2015 um 18:49 schrieb Johannes Ring:
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] <mailto:[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] <mailto:[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] <mailto:[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] <mailto:[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 <http://libHYPRE-2.9.1a.so>
=>
$HOME/.hashdist/bld/hypre/kh4vd5dptalu/lib/libHYPRE-2.9.1a.so
<http://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]
<mailto:[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
--
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
