On 23 Apr 2018, at 20:57, Mohammad Sarraf Joshaghani <m.sarraf.j@gmail.com> wrote:
Dear Lawrence, I get:
$ ldd /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 => (0x00007ffc197fc000) libpetsc.so.3.8 => /lib64/libpetsc.so.3.8 (0x00007f0bfb6b8000)
This looks to be the problem, I think. Assuming that you got firedrake-install to install PETSc, it should be installed in: /home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib/.../petsc Whereas here it looks like the linker is picking up a system-installed PETSc. That dynamic library was linked as: gcc -pthread -shared -Wl,-z,relro -g build/temp.linux-x86_64-3.6/pyop2/sparsity.o -L/usr/lib64 -lpetsc -lpython3.6m -o /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so -L/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib -Wl,-rpath,/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib So we bake the rpath to PETSc in. But somehow when running, you don't pick that one up. Can you show the output of "env" in the same shell you ran "ldd" please? Cheers, Lawrence
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007f0bfb18f000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0bfaf73000) libc.so.6 => /lib64/libc.so.6 (0x00007f0bfabb0000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f0bfa88d000) libsuperlu.so.5.1 => /lib64/libsuperlu.so.5.1 (0x00007f0bfa618000) libumfpack.so.5 => /lib64/libumfpack.so.5 (0x00007f0bfa363000) libklu.so.1 => /lib64/libklu.so.1 (0x00007f0bfa12e000) libcholmod.so.2 => /lib64/libcholmod.so.2 (0x00007f0bf9e42000) libamd.so.2 => /lib64/libamd.so.2 (0x00007f0bf9c38000) libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007f0bf7767000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f0bf7429000) libm.so.6 => /lib64/libm.so.6 (0x00007f0bf7127000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f0bf6f22000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f0bf6c1a000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f0bf6a04000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f0bf6800000) /lib64/ld-linux-x86-64.so.2 (0x000055a8504ca000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f0bf65c4000) libsatlas.so.3 => /usr/lib64/atlas/libsatlas.so.3 (0x00007f0bf59af000) libsuitesparseconfig.so.4 => /lib64/libsuitesparseconfig.so.4 (0x00007f0bf57ac000) libcolamd.so.2 => /lib64/libcolamd.so.2 (0x00007f0bf55a4000) libbtf.so.1 => /lib64/libbtf.so.1 (0x00007f0bf53a0000) libcamd.so.2 => /lib64/libcamd.so.2 (0x00007f0bf5194000) libccolamd.so.2 => /lib64/libccolamd.so.2 (0x00007f0bf4f88000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f0bf4d60000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f0bf4b5b000)