Dear Niall,

On 1 Aug 2019, at 15:16, Madden, Niall <niall.madden@nuigalway.ie> wrote:

Hi all, I've been trying to install firedrake for some time on a (large) HPC system, without success.

Can you give us some details on this system? Is it a cray, for example?

As a humble user, I can't run the package manager. One of the sys admins has made a valiant effort to get in installed on anaconda. It was rather tortuous (re-engineering the install script), but has fallen short of actually working.

Without anaconda, after loading git, gcc, openmpi and lapack modules, I tried python3 firedrake-install --disable-ssh --no-package-manager It fails compiling PETSc. The final part of the output is:

File "/usr/lib64/python3.6/subprocess.py", line 438, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/MYOB/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py,randomgen', '--no-deps', '-vvv', '--ignore-installed', 'petsc/']' returned non-zero exit status 1.

where "MYOB" is the subdir of my home directory.

The final part of firedrake-install.log is Processing ./petsc Created temporary directory: /tmp/pip-req-build-628_7y3h ERROR: Could not install packages due to an EnvironmentError. Traceback (most recent call last): File "/MYOB/firedrake/lib64/python3.6/site-packages/pip/_internal/commands/install.py", line 345, in run resolver.resolve(requirement_set) File "/MYOB/firedrake/lib64/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 196, in resolve self._resolve_one(requirement_set, req) File "/MYOB/firedrake/lib64/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 359, in _resolve_one abstract_dist = self._get_abstract_dist_for(req_to_install) File "/MYOB/firedrake/lib64/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 307, in _get_abstract_dist_for self.require_hashes File "/MYOB/firedrake/lib64/python3.6/site-packages/pip/_internal/operations/prepare.py", line 199, in prepare_linked_requirement progress_bar=self.progress_bar File "/MYOB/firedrake/lib64/python3.6/site-packages/pip/_internal/download.py", line 1037, in unpack_url unpack_file_url(link, location, download_dir, hashes=hashes) File "/MYOB/firedrake/lib64/python3.6/site-packages/pip/_internal/download.py", line 942, in unpack_file_url shutil.copytree(link_path, location, symlinks=True) File "/usr/lib64/python3.6/shutil.py", line 365, in copytree raise Error(errors) shutil.Error: [('/MYOB/firedrake/src/petsc/.git/objects/pack/pack-411fdf97d273b4933195ac04e846e6825ec1d491.pack', '/tmp/pip-req-build-628_\ 7y3h/.git/objects/pack/pack-411fdf97d273b4933195ac04e846e6825ec1d491.pack', "[Errno 13] Permission denied: '/tmp/pip-req-build-628_7y3h/.git/objects/pack/pack-411f\ df97d273b4933195ac04e846e6825ec1d491.pack'"), ('/MYOB/firedrake/src/petsc/.git/objects/pack/pack-411fdf97d273b4933195ac04e846e6825ec1d491.\ idx', '/tmp/pip-req-build-628_7y3h/.git/objects/pack/pack-411fdf97d273b4933195ac04e846e6825ec1d491.idx', "[Errno 13] Permission denied: '/tmp/pip-req-build-628_7y3\ h/.git/objects/pack/pack-411fdf97d273b4933195ac04e846e6825ec1d491.idx'")] Cleaning up... Removed build tracker '/tmp/pip-req-tracker-ad7jx96o'

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. Cheers, Lawrence