hi folks, made some progress on this. Built petsc manually, still fails with same permission error. Found this bug report for pip install on panfs: https://github.com/pypa/pip/issues/2941 Turns out setting write flags on the git pack idx and .pack files works on lustre too. I could then (within the activated firedrake venv) do the pip install. Without the write flags, I got the same error when running pip install manually within the venv. I'll hack the firedrake-install script to do the chmod once petsc4py has been cloned and hopefully this will work for a full install. Will let you know if that works. Cheers, J. On 07/02/2019 09:50, Ham, David A wrote:
Hi Jon,
One option is to compile petsc separately and point firedrake at it. This is a common strategy many users adopt on slightly uncooperative systems. You can get the correct set of configure options from: firedrake-install --show-petsc-configure-options and you'll want to use the firedrake fork from https://github.com/firedrakeproject/petsc .
I would normally think that compiling on the backend is the Right Thing. Can you post the error from that? (I think the error you posted was from a front end compilation).
Cheers,
David
On 07/02/2019, 08:53, "firedrake-bounces@imperial.ac.uk on behalf of Jon Hill" <firedrake-bounces@imperial.ac.uk on behalf of jon.hill@york.ac.uk> wrote:
Hi folks,
I'm having issues compiling on York's new supercomputer (Viking - cool name). I have successfully compiled on the machine, but in the frontend /users space which is not available on the backend.
When I compile on he backend filesystem, I get the error attached - basically a permission error when moving files
The drive available on the backend is called scratch. I've tried a few things: - move the venv: virtualenv --relocatable firedrake, mv it, but this fails when running (just hangs somewhere in the simulation - probably mpipy)
These all fail compilation: - set the TMPDIR flag to /user during compilation - compile on the back end - compile on the frontend directly on /scratch
I suspect it's something to do with the Lustre filesystem as I can compile on the frontend space.
Thanks in advance for any advice!
Jon
-- Dr Jon Hill Senior Lecturer in Physical Geography Department of Environment and Geography University of York M: +44(0)7748254812 P: +44(0)1904 324480 Twitter: @jonxhill Web: https://jonxhill.wordpress.com/ Web: https://envmodellinggroup.github.io/
-- Dr Jon Hill Senior Lecturer in Physical Geography Department of Environment and Geography University of York M: +44(0)7748254812 P: +44(0)1904 324480 Twitter: @jonxhill Web: https://jonxhill.wordpress.com/ Web: https://envmodellinggroup.github.io/