On 20 Jun 2019, at 14:24, Simone Puel <spuel@utexas.edu> wrote:
Hi Matt,
Thank you so much for your email. Do you mean remove the entire Anaconda, or removing some directories in the firedrake folder? Thanks in advance. Have a wonderful day.
Your anaconda environment has installed a version of HDF5 in: /home/simone/anaconda3/lib/libhdf5.so.103 When we build h5py, we attempt to link it agains the (parallel) version of HDF5 built by PETSc. Looking back at your firedrake-install.log I see: gcc -pthread -shared -B /home/simone/anaconda3/compiler_compat -L/home/simone/anaconda3/lib -Wl,-rpath=/home/simone/anaconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/home/simone/firedrake/src/h5py/h5py/h5ac.o -L/home/simone/firedrake/lib/python3.6/site-packages/petsc/lib -Wl,-R/home/simone/firedrake/lib/python3.6/site-packages/petsc/lib -lhdf5 -lhdf5_hl -o /home/simone/firedrake/src/h5py/h5py/h5ac.cpython-36m-x86_64-linux-gnu.so We (firedrake-install) arranged for this bit: -L/home/simone/firedrake/lib/python3.6/site-packages/petsc/lib -Wl,-R/home/simone/firedrake/lib/python3.6/site-packages/petsc/lib Which is the "right" place. But anaconda (I guess) has added. -L/home/simone/anaconda3/lib -Wl,-rpath=/home/simone/anaconda3/lib Which is what is being used to resolve libhdf5.so I don't know enough about anaconda to know why it adds these extra link lines. Perhaps you should start in a new conda "environment" that doesn't have hdf5 installed? Thanks, Lawrence
Best regards, Simone
On Thu, Jun 20, 2019 at 2:40 AM Matthew Knepley <knepley@gmail.com> wrote: On Wed, Jun 19, 2019 at 9:50 AM Simone Puel <spuel@utexas.edu> wrote: Hi Lawrence and Matt,
Thank you so much for your email. Thanks Matt, what can I do? I was wondering that the problem might be related to have installed most of the packages with both anaconda and directly on my computer. This is the output:
I think the easiest thing to do is not let Firedrake see the Anaconda libraries. I think this should be easy by just removing those directories from the environment variables. Does this make sense?