On 19/06/2015 08:43, Johannes Ring wrote:
On Fri, Jun 19, 2015 at 9:15 AM Michal Rybinski
<[email protected] <mailto:[email protected]>>
wrote:
Hi Fenics team,
I am facing a Fenics installation problem on Debian 8. I have checked
archives back to half of 2014 before writing here, but couldn't find
similar topic that could help me.
In Debian there is the Fenics package from debian repos, but it is in
version 1.4.0.1, whereas I would like to install 1.5, hence I am
installing from source.
Yes, 1.5.0 did not make it into Jessie, but it is available in Debian
unstable.
When executing via "curl -s
http://fenicsproject.org/fenics-install.sh |
bash" I have encountered a few problems, but was able to fix them
on my
own so far. Unfortunately the one I am dealing with now, looks like a
bit above my head so I am asking kindly for help.
During "boost" package compilation there is an error thrown in the
build.log:
2015/06/18 21:34:29 - INFO: [package:run_job] gcc.link.dll
_build/boost/bin.v2/libs/mpi/build/gcc-4.9.2/release/address-model-64/threading-multi/libboost_mpi.so.1.55.0
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: skipping
incompatible /root/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpich.so when
searching for -lmpich
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: skipping
incompatible /root/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpich.a when
searching for -lmpich
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: cannot find
-lmpich
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: skipping
incompatible /root/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpichcxx.so
when searching for -lmpichcxx
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: skipping
incompatible
/root/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpichcxx.a when
searching for -lmpichcxx
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: cannot find
-lmpichcxx
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: skipping
incompatible /root/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpl.so when
searching for -lmpl
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: skipping
incompatible /root/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libmpl.a when
searching for -lmpl
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: cannot
find -lmpl
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: skipping
incompatible /root/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libopa.so when
searching for -lopa
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: skipping
incompatible /root/.hashdist/bld/mpi/gmkx3ftk3tz2/lib/libopa.a when
searching for -lopa
2015/06/18 21:34:29 - INFO: [package:run_job] /usr/bin/ld: cannot
find -lopa
2015/06/18 21:34:29 - INFO: [package:run_job] collect2: error: ld
returned 1 exit status
The whole build.log attached.
It looks like a problem with lack of libmpich or libmpl or libopa
libraries, but all of this is installed:
root@deb8-fenics-gbac-x86:/3# dpkg -l | grep -E 'libmpich|mpich'
ii libmpich-dev 3.1-5+b2 i386
Development files for MPICH
ii libmpich12:i386 3.1-5+b2 i386
Shared libraries for MPICH
ii mpich 3.1-5+b2 i386
Implementation of the MPI Message Passing Interface standard
ii mpich2 3.1-5+b2 i386
Transitional dummy package
root@deb8-fenics-gbac-x86:/3# dpkg -l | grep libmpl
ii libmpl-dev 3.1-5+b2 i386
Development files for mpl part of MPICH
ii libmpl1:i386 3.1-5+b2 i386
Shared libraries for mpl part of MPICH
root@deb8-fenics-gbac-x86:/3# dpkg -l | grep libopa
ii libopa-dev 3.1-5+b2 i386
Development files for opa part of MPICH
ii libopa1:i386 3.1-5+b2 i386
Shared libraries for opa part of MPICH
so I was thinking about problems caused by the i386 architecture and
installed all available multilib libraries for gcc:
root@deb8-fenics-gbac-x86:/3# dpkg -l | grep multilib
ii g++-4.9-multilib 4.9.2-10 i386
GNU C++ compiler (multilib files)
ii g++-multilib 4:4.9.2-2 i386 GNU
C++ compiler (multilib files)
ii gcc-4.9-multilib 4.9.2-10 i386
GNU C compiler (multilib files)
ii gcc-multilib 4:4.9.2-2 i386
GNU C
compiler (multilib files)
ii gccgo-4.9-multilib 4.9.2-10 i386
GNU Go compiler (multilib files)
ii gccgo-multilib 4:4.9.2-2 i386 Go
compiler, based on the GCC backend (multilib files)
ii gobjc++-4.9-multilib 4.9.2-10
i386 GNU Objective-C++ compiler (multilib files)
ii gobjc++-multilib 4:4.9.2-2 i386
GNU Objective-C++ compiler (multilib files)
ii gobjc-4.9-multilib 4.9.2-10 i386
GNU Objective-C compiler (multilib files)
ii gobjc-multilib 4:4.9.2-2 i386 GNU
Objective-C compiler (multilib files)
I see you are using i386. The problem is that the script assumes that
you are on a 64-bit OS and there is currently no check for if you are
using 32-bit. For now, you will have to download
fenics-developer-tools and modify the hashdist profile. Here are the
steps:
git clone https://bitbucket.org/fenics-project/fenics-developer-tools.git
cd fenics-developer-tools
sed -i 's/address_model: 64/address_model: 32/'
install/profiles/fenics.Linux.yaml
./install/fenics-install.sh install/profiles/fenics.Linux.yaml
Let us know if that works for you.
Johannes
Hi Johannes,
Thank you very much for your prompt response.
I tried your solution during this weekend and it worked beautifully.
Thanks again!
Michal
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