Den 07-02-2015 kl. 12:00 skrev [email protected]:
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Today's Topics:
1. Re: libmshr1.5 install error on update to dolfin1.5
(Benjamin Kehlet)
2. Re: Fenics on Ubuntu 12.04 cluster, using fenics-install.sh
(Birgitte Maria Elisabeth Brydso)
3. cannot assemble a mixed form (since version 1.4) (Jan Heiland)
----------------------------------------------------------------------
Message: 1
Date: Fri, 6 Feb 2015 12:30:11 +0100
From: Benjamin Kehlet <[email protected]>
To: "[email protected]" <[email protected]>
Cc: "[email protected]"
<[email protected]>
Subject: Re: [FEniCS-support] libmshr1.5 install error on update to
dolfin1.5
Message-ID:
<caks4ypxhk6v2dmmat4q35w+qrz1eu654tk6wzblx0ray0fg...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Den fredag 6. februar 2015 skrev <[email protected]> f?lgende:
On Friday, February 06, 2015 03:28 PM, Henrik Garde wrote:
Hi, I am using Ubuntu 14.04 64-bit. I just updated from dolfin 1.4 to
dolfin 1.5 via the PPA, and I got the following error:
Preparing to unpack .../libmshr1.5_1.5.0~git20150116-1~ppa1~trusty1_amd64.deb
...
Unpacking libmshr1.5 (1.5.0~git20150116-1~ppa1~trusty1) ...
dpkg: error processing archive /var/cache/apt/archives/
libmshr1.5_1.5.0~git20150116-1~ppa1~trusty1_amd64.deb (--unpack):
trying to overwrite '/usr/lib/x86_64-linux-gnu/libmshr.so.1.4.0',
which is also in package libmshr1.4 1.4.0~git201411123-1~ppa1~trusty1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Errors were encountered while processing:
/var/cache/apt/archives/libmshr1.5_1.5.0~git20150116-
1~ppa1~trusty1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
Running "sudo apt-get -f install" results in the same error. Any
suggestions?
Best regards
Henrik Garde
Hi Henrik,
I recalled encountering this.
You can try manually removing libmshr1.4 (and also libmshr-dev if you have
it.) first. You may have to use "sudo dpkg --force-depends -r" instead of
"sudo apt-get remove" because of dependencies problems.
Regards,
ST
--
Johannes: Do you know if this is an issue with the package? Wrongly named
file or a file should be deleted?
Benjamin
Hi Benjamin
I can confirm that removing libmshr1.4 and libmshr-dev like ST suggested
did indeed get it to install correctly.
/Henrik Garde
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Message: 2
Date: Fri, 6 Feb 2015 13:28:10 +0100 (CET)
From: Birgitte Maria Elisabeth Brydso <[email protected]>
To: [email protected]
Subject: Re: [FEniCS-support] Fenics on Ubuntu 12.04 cluster, using
fenics-install.sh
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-15"; Format="flowed"
On Thu, 5 Feb 2015, Birgitte Maria Elisabeth Brydso wrote:
now. It starts building dolfin, actually, but does not complete. This
is the tail of build.sh:
2015/02/05 15:07:00 - INFO: [package:run_job] [ 95%] Building CXX
object dolfin/CMakeFiles/dolfin.dir/refinement/RivaraRefinement.cpp.o
2015/02/05 15:07:03 - INFO: [package:run_job] [ 96%] Building CXX
object
dolfin/CMakeFiles/dolfin.dir/refinement/UniformMeshRefinement.cpp.o
2015/02/05 15:07:05 - INFO: [package:run_job] [ 96%] Building CXX
object dolfin/CMakeFiles/dolfin.dir/refinement/refine.cpp.o
2015/02/05 15:07:06 - INFO: [package:run_job] Linking CXX shared
library libdolfin.so 2015/02/05 15:07:13 - INFO: [package:run_job]
[ 96%] Built target dolfin 2015/02/05 15:07:13 - INFO:
[package:run_job] Scanning dependencies of target copy_swig_files
2015/02/05 15:07:14 - INFO: [package:run_job] [ 96%] Built target
copy_swig_files
2015/02/05 15:07:14 - INFO: [package:run_job] [ 96%] Swig source
2015/02/05 15:07:31 - INFO: [package:run_job] Scanning dependencies
of target _mesh
2015/02/05 15:07:31 - INFO: [package:run_job] [ 96%] Building CXX
object
dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o
2015/02/05 15:07:49 - INFO: [package:run_job] make[2]: *** No rule to
make target
`/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/python/vocgqpztn6ne/lib/libpython2.7.so',
hashdist tries to link DOLFIN against libpython built by hashdist
although you instructed it to use system python. Is there libpython on
your system? Try maybe
$ locate libpython2.7.so
Maybe Johannes will know how to debug it.
Jan
There is libpython on the system:
t-mn01 [/usr/lib]$ ls -la libpython2.7.*
lrwxrwxrwx 1 root root 31 Dec 18 20:46 libpython2.7.a ->
python2.7/config/libpython2.7.a
lrwxrwxrwx 1 root root 17 Dec 18 20:46 libpython2.7.so ->
libpython2.7.so.1
lrwxrwxrwx 1 root root 19 Dec 18 20:46 libpython2.7.so.1 ->
libpython2.7.so.1.0
-rw-r--r-- 1 root root 3059040 Dec 18 20:46 libpython2.7.so.1.0
Could there be some problem with 32bit vs. 64bit? What is hashdist expecting
to find?
t-mn01 [/usr/lib]$ ldd libpython2.7.so.1.0
linux-vdso.so.1 => (0x00007fff7c600000)
libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0
(0x00002b94b2b20000)
libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
(0x00002b94b2d80000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00002b94b3160000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00002b94b3378000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002b94b3598000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
(0x00002b94b37a0000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b94b39a8000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b94b3ca8000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00002b94b4068000)
/lib64/ld-linux-x86-64.so.2 (0x00002b94b23e0000)
Thanks! I will try and see what happens if I instead ask hashdist to use its
own libpython.
needed by `dolfin/swig/modules/mesh/_mesh.so'. Stop. 2015/02/05
15:07:49 - INFO: [package:run_job] make[1]: ***
[dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2
2015/02/05 15:07:49 - INFO: [package:run_job] make: *** [all] Error 2
2015/02/05 15:07:49 - ERROR: [package:run_job] Command
'[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status
2 2015/02/05 15:07:49 - ERROR: [package:run_job] command failed
(code=2); raising
I tried letting hashdist build python and swig, but it did not help:
2015/02/06 13:07:19 - INFO: [package:run_job] [ 96%] Swig source
2015/02/06 13:07:46 - INFO: [package:run_job] Scanning dependencies of
target _mesh
2015/02/06 13:07:46 - INFO: [package:run_job] [ 96%] Building CXX object
dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o
2015/02/06 13:08:08 - INFO: [package:run_job] make[2]: *** No rule to make
target
`/pfs/nobackup/home/b/bbrydsoe/fenics_install/bld/python/5eydw745avpo/lib/libpython2.7.so',
needed by `dolfin/swig/modules/mesh/_mesh.so'. Stop.
2015/02/06 13:08:08 - INFO: [package:run_job] make[1]: ***
[dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2
2015/02/06 13:08:08 - INFO: [package:run_job] make: *** [all] Error 2
2015/02/06 13:08:08 - ERROR: [package:run_job] Command '[u'/bin/bash',
'_hashdist/build.sh']' returned non-zero exit status 2
2015/02/06 13:08:08 - ERROR: [package:run_job] command failed (code=2);
raising
Anyone have any idea why I am still getting the complaint about libpython
with hashdist built python?
Thanks,
Birgitte
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