[Libmesh-users] metis and libmesh installed

[Mauro C. <ca...@gf...>]

Dear all,

I am trying to install libmesh (as a part of the MOOSE framework) on a 
cluster (no root). The problem is that I am continuously having this 
error message:

"/ld: gk_cur_jbufs: TLS definition 
in*/usr/local/lib/libmetis.a(error.c.o)* section .tdata mismatches 
non-TLS definition in /cluster/petsc/petsc-3.9.3/lib///libmetis.so 
<http://libmetis.so>//section .data//
//*/cluster/petsc/petsc-3.9.3/lib/*/*/libmetis.so 
<http://libmetis.so>/*/: error adding symbols: Bad value//
//make[1]: *** [meshid-opt] Error 1//
//make[1]: *** Waiting for unfinished jobs..../"

The problem is that there is a conflict of libraries (metis shared and 
static). The PETSc version installed (against which I would like to 
link) does provide a so library (under cluster/petsc/petsc-3.9.3/lib). 
However, libmesh always tries always to further link to an existing old 
static libraries in the common path (under /usr/local/lib/).

I already asked on the MOOSE user group, and received this answer:

/"//The issue seems to be that there are two libmetis libraries under 
consideration by the linker, and because their thread-local storage 
("TLS") declarations disagree, the linker throws an error. The only way 
we have been able to fix this in the past is to remove the system 
libmetis (the one in /usr/local/lib) completely, but this is obviously 
not acceptable in all situations, so it would be nice to come up with a 
better solution. It would be nice, for example if the "first" 
//libmetis.so <http://libmetis.so>//could somehow take precedence and 
the second one could be ignored...//"/

The IT administrator asks whether it is possible to exclude the static 
library from the making (I think it would not be possible to delete it). 
However, it is not clear to me if that is possible at all, and where.

Any suggestion/help/way out would be really appreciated.

Thanks,

Mauro


-- 
Dr. Mauro Cacace
Department 6 Geotechnologies
Section 6.1 Basin Modelling
Phone : +49(0)331/288-1783
Fax : +49(0)331/288-1349
Email : ca...@gf...
_________________________________________

Helmholtz Centre Potsdam
*GFZ German Research Centre for Geosciences*
Foundation under public law of the federal state
of Brandenburg
Telegrafenberg, D-14473 Potsdam