[firedrake] Locally installed FFC not found on ARCHER

Fri Jan 30 10:33:44 GMT 2015

Hi Michael,

my current configuration broke with the recent update of the central 
installation. The centrally installed modules end up in the Python path 
in front of the locally installed ones:

sys.path=['/fs2/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source', 
'/fs2/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages/decorator-3.4.0-py2.7.egg', 
'/work/y07/y07/fdrake/PyOP2/lib/python2.7/site-packages/PyOP2-0.11.0_153_g63f5afb_dirty-py2.7-linux-x86_64.egg', 
'/fs2/y07/y07/fdrake/coffee/lib/python2.7/site-packages/COFFEE-0.1.0-py2.7.egg', 
'/work/y07/y07/fdrake/coffee/lib/python2.7/site-packages/COFFEE-0.1.0-py2.7.egg', 
'/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/FFC-1.5.0_-py2.7-linux-x86_64.egg', 
'/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages/decorator-3.4.0-py2.7.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/python_hostlist-1.14-py2.7.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/GridDataFormats-0.2.4-py2.7.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/extasy.coco-0.1-py2.7.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/MDAnalysis-0.8.1-py2.7-linux-x86_64.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/python_hostlist-1.14-py2.7.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/GridDataFormats-0.2.4-py2.7.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/apache_libcloud-0.15.1-py2.7.egg', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg', 
'/work/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source', 
'/work/n02/n02/eike/git_workspace/ufl/build/lib', 
'/work/n02/n02/eike/git_workspace/fiat/build/lib', 
'/work/n02/n02/eike/git_workspace/ffc/build/lib.linux-x86_64-2.7', 
'/work/n02/n02/eike/git_workspace/COFFEE/build/lib', 
'/work/n02/n02/eike/git_workspace/firedrake', 
'/work/n02/n02/eike/git_workspace/PyOP2', 
'/work/n02/n02/eike/git_workspace/petsc4py/cray-gnu-shared/lib/python2.7/site-packages', 
'/work/n02/n02/eike/Library/mpi4py/lib/python2.7/site-packages', 
'/work/n02/n02/eike/git_workspace/pybench', 
'/work/n02/n02/eike/git_workspace/firedrake-bench', 
'/work/y07/y07/fdrake/firedrake/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/PyOP2/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/coffee/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/instant/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages', 
'/work/y07/y07/fdrake/petsc/cray-gnu-shared/lib/python2.7/site-packages', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7', 
'/opt/cray/sdb/1.0-1.0501.48084.4.48.ari/lib64/py', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python27.zip', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/plat-linux2', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-tk', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-old', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-dynload', 
'/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/PIL', 
'/opt/cray/sdb/1.0-1.0501.48084.4.48.ari/lib64/py']

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
>>
>>
>> _______________________________________________
>> firedrake mailing list
>> firedrake at imperial.ac.uk
>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>
>
>
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