Hi Christoph, thanks for your help.
Sorry for the missing information. I am indeed installing on a Linux
(Ubuntu 20.04). Mumps and scotch were compiled manually in /opt,
following instructions in the readmes.
As you correctly pointed out, Mumps was compiled without -fPIC. This was
fixed by adding the flag to both OPTF and OPTC in Makefile.inc, and
recompiling. Then, recompiling kwant was smooth.
The install target for kwant in a virtualenv also located in
/opt/python3-venv. After installation though, when importing kwant, I
still have the message:
/opt/python3-venv/lib/python3.8/site-packages/kwant-1.4.2-py3.8-linux-x86_64.egg/kwant/solvers/default.py:16:
RuntimeWarning: MUMPS is not available, SciPy built-in solver will be
used as a fallback. Performance can be very poor in this case.
It is caused by the following import error:
/opt/python3-venv/lib/python3.8/site-packages/kwant-1.4.2-py3.8-linux-x86_64.egg/kwant/linalg/_mumps.cpython-38-x86_64-linux-gnu.so:
undefined symbol: GOMP_loop_nonmonotonic_dynamic_start
This points again to my hand-built Mumps, so again not a kwant issue per se.
Etienne
On 17/01/2022 16:00, Christoph Groth wrote:
Etienne Fayen wrote :
I am trying to build kwant and its dependencies from sources.
A first build without Mumps succeeded. When adding Mumps however, the
linker returns the following error:
/usr/bin/ld: /opt/mumps-5.4.1/lib/libzmumps.a(ztools.o): relocation
R_X86_64_PC32 against symbol `.gomp_critical_user_critical_old_ooc' can
not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
I suppose that this is on some kind of Linux? Since mumps and friends
are located in /opt I guess they were compiled manually? In which way?
Would adding -fPIC flag as suggested by the error message solve the
issue ? If so, how can this flag be added with the python build
setup ?
Please check the whole log of compilation (you can also post it here).
For example, run
python3 setup.py clean -a
followed by
python3 setup.py build_ext -i
During the build process the commands that are executed are echoed. So
when you see an error, the command that caused it is immediately above.
Would adding -fPIC flag as suggested by the error message solve the
issue ? If so, how can this flag be added with the python build
setup ?
On my machine the -fPIC flag is present in all invocations of gcc by
setup.py. That should be also the case for you (please check).
My first guess is that the problem you experience might be due to
mumps/scotch (and not Kwant) being compiled without -fPIC.
Hope this helps a bit
Christoph
