Problem building libmesh

[hsheldon]

I'm having trouble building libmesh. Here's what I'm getting:

libtool: warning: '/apps/gcc/9.2.0/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../lib64/libstdc++.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libgfortran.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libquadmath.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libquadmath.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libgfortran.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libquadmath.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libquadmath.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libgfortran.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libquadmath.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libquadmath.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libquadmath.la' seems to be moved
libtool: warning: '/apps/gcc/4.9.3/lib/../lib64/libquadmath.la' seems to be moved
CXXLD fparser_parse-opt
./.libs/libmesh_opt.so: error: undefined reference to 'GOMP_loop_nonmonotonic_dynamic_start'
./.libs/libmesh_opt.so: error: undefined reference to 'GOMP_loop_nonmonotonic_dynamic_next'
collect2: error: ld returned 1 exit status
Makefile:13596: recipe for target 'fparser_parse-opt' failed
make[1]: *** [fparser_parse-opt] Error 1
make[1]: Leaving directory '/scratch1/projects/moose/moose/libmesh/build'
Makefile:32290: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1

In those warnings it seems to be looking for gcc/4.9.3 but I have gcc/9.2.0 loaded. Does that have something to do with it? Or is the error completely unrelated to the warnings?
Cheers,
Heather

[GiudGiud]

Hello

Seems like remnants of a previous compilation are being used. Could you please clean the repo (save your work then git clean -xfd) then try again.

How are you building libmesh? With scripts/update_and_rebuild_libmesh?

Guillaume

[hsheldon]

/apps/openmpi/3.1.4-ofed45-gcc/bin/mpicxx

[milljm]

Can you list all your loaded modules? And a printout of an env would also be helpful:

module purge
module load <the modules you are attempting to use>
module list
env

Thanks!

[hsheldon]

I seem to have fixed the problem by switching from gcc/9.2.0 to gcc/6.1.0. I have the following modules loaded:

Currently Loaded Modulefiles:

1. SC 4) openmpi/3.1.4-ofed45-gcc 7) netcdf/4.3.3.1 10) hdf5/1.8.16-gcc 13) git/2.30.0 16) paraview/5.5.0
2. slurm/current 5) petsc/3.10.5-gcc-mpi314-moose 8) glpk/4.60 11) eigen/3.3.7 14) python/2.7.13
3. hpc-x/2.4.0 6) intel-mkl/11.3.2 9) gcc/6.1.0 12) moose/master 15) mesa/17.2.4_gallium

Maybe there's something in there that explains why gcc/6.1.0 works?

[GiudGiud]

As long as all of these were compiled with gcc 6.1.0 (or 9.2 previously)
Why are you loading moose/master though? You are compiling your own libmesh, you should compile your own moose too

[hsheldon]

I am compiling moose as well - which works now that I've managed to build libmesh. I have module load moose in my .profile.
Thanks for your help!