Hi Niall, (adding in firedrake cc again)
On 1 Aug 2019, at 15:43, Madden, Niall <niall.madden@nuigalway.ie> wrote:
Hi Lawrence, Thanks for the swift reply. I don't want to reply to the whole list with too much specific information on the system
Please do reply with the list. That way others who might be able to help will see things.
Can you give us some details on this system? Is it a cray, for example? The system is ICHEC's "kay" - Ireland's national supercomputer for academic purposes: https://www.ichec.ie/about/infrastructure/kay
Normally we find when building on supercomputers (contrary to the one-shot "firedrake-install" unfortunately), that it is best to build PETSc by hand. One then sets the appropriate environment variables and runs firedrake-install --honour-petsc-dir. This might be the best step forward.
Thanks for the tip. I tried compiling PETSc myself:
git clone https://github.com/firedrakeproject/petsc.git (but should I be cloning fromhttps://bitbucket.org/petsc/petsc ?)
No, cloning from the firedrakeproject "fork" is correct. We keep a (reasonably up to date) version of petsc that is known good with all Firedrake components there: it isn't otherwise special.
./configure --with-c2html=0 --download-chaco --download-metis --download-parmetis --download-scalapack --download-hypre --download-mumps --download-netcdf --download-hdf5 --download-pnetcdf --download-exodusii --download-mpich --download-suitesparse=1 --download-petsc4py=1 --download-mpi4py=1 --download-fblaslapack --download-zlib
Then I set PETSC_DIR and PETSC_ARCH, and PYTHONPATH
Then I try to install Firedrake with python3 firedrake-install --no-package-manager -v --disable-ssh --honour-petsc-dir --honour-pythonpath
But it eventually fails compiling libspatialindex for reasons that seem to be related to the mpicxx , but it is a little opaque: undefined reference to `psm2_info_query@PSM2_1.0'
Can you attach the contents of firedrake-install.log (maybe gzip it since it is likely to be large). Thanks, Lawrence