Hi Michael,
In that case I suggest creating your own local module file for the python env, starting from fdrake-python-env as a template, where you can explicitly select the branch builds you require. The central module, however, should always always be self-contained.
I've done that now, and it all works fine again. I.e. if I use my locally build firedrake installation I can run the 3d solver code for the gravity wave system. I still use decorator-3.4.0, instant, psutil and scientificpython from the central firedrake installation since I can't be bothered to reinstall these locally, and it doesn't seem necessary.
Yes, it should work without this line now. I don't know why these components had been disabled in the central module.
I took the firedrake.env and firedrake.tpl from the webpage (https://github.com/firedrakeproject/firedrake-bench/wiki/Archer) and removed the references to the local PyOP2, petsc4py, firedrake, ufl, fiat and ffc. To be precise, the files I use are attached. I then tried to run the Poisson testcase as described on the webpage and it goes through fine. Note that I had to add export LD_LIBRARY_PATH=$ANACONDA_LIB:${LD_LIBRARY_PATH} in firedrake.tpl, otherwise I get python: error while loading shared libraries: libpython2.7.so.1.0: cannot open shared object file: No such file or directory Application 12817509 exit codes: 127 Application 12817509 resources: utime ~0s, stime ~0s, Rss ~4296, inblocks ~15, outblocks ~19 Do you have to uncomment prepend-path LD_LIBRARY_PATH $env(ANACONDA_LIB) in the central fdrake-python-env again? That's what I did in my local module file (i.e. the one I use to run with my local firedrake installation) and it doesn't seem to break the module command any more. Are you happy for me to go ahead and update the firedrake.tpl and firedrake.env on the webpage? Thanks, Eike
Thanks,
Eike
On 30/01/15 07:21, Michael Lange wrote:
Hi Eike,
I just updated the "firedrake" module on Archer and it should be fully functional again. Can you please give this a try and let me know if it works for you?
The PETSc problem was due to fdrake-build-env pointing at a very old petsc build (petsc/dev), not the one Florian re-built yesterday (petsc/shared). I also pulled the entire mapdes stack forward, so we should be up-to-date with current master versions.
Also, as a heads up, I am currently working with Tim Bond and Rupert Nash from EPCC on rolling out separate petsc-master and petsc4py-master packages that use the centrally installed (and supported) Python stack. This is possible after several updates to the Python environment on Archer and should allow us to get off the relatively unsupported Anaconda module to avoid more binary incompatibilities in the future. I'll post to the list once we're ready to switch.
Thanks, Michael
On 29/01/15 22:54, Florian Rathgeber wrote:
On 1/29/2015 12:04 PM, Eike Mueller wrote:
Hi Florian,
I recall having similar issues with incompatible MPI versions before, but can't find anything in my emails which points to a solution. I think the reason in my case was that the CRAY MPICH was updated at some point after the original /work/y07/y07/fdrake installation, but before I installed my own version. I would have expected something like this, but afaict we were using mpich 7.0.3 throughout.
Could it be that mpi4py is still using the old MPICH and needs to be reinstalled? That is indeed a possibility. I wonder if you could get access to the fdrake account since you're pretty much the main user. Michael?
Florian
Cheers,
Eike
On 29/01/15 11:51, Florian Rathgeber wrote:
On 29/01/15 10:23, Eike Mueller wrote: > I need to install my own version of FFC, since the one already > installed > in /work/y07/y07/fdrake appears not to be compatible with the > firedrake > version I use I had a go at updating the "official" firedrake package on ARCHER and dependencies. I updated PETSc and petsc4py to the latest revision of the respective firedrake branch. Then I failed however building the firedrake extension modules due to the following error:
/work/y07/y07/fdrake/petsc/include/petscsys.h:124:6: error: #error "PETSc was configured with one MPICH mpi.h v ersion but now appears to be compiling using a different MPICH mpi.h version"
afaict we always use cray-mpich/7.0.3 for building petsc and everything else. No idea what triggers this error.
On another note: I *really* don't have time to continue maintaining the fdrake modules on ARCHER and appreciate if someone else (Michael? Lawrence?) could take on this task. I also don't have time to sort out this current issue, sorry about that.
Florian
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