[firedrake] Locally installed FFC not found on ARCHER

[Eike Mueller]

Hi Michael,

ok, so you suggest I still use the central fdrake-build-env (which adds 
swig to PYTHONPATH), but create my own copy of fdrake-python-env, where 
I replace $root by my installation directory?

Would it make sense to still use some of the centrally installed 
packages such as

prepend-path PYTHONPATH "$root/decorator-3.4.0/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/instant/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/mpi4py/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/psutil/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/scientificpython/lib/python2.7/site-packages"

(and swig)

and only install the following locally:

prepend-path PYTHONPATH "$root/ffc/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/fiat/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/ufl/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/coffee/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/PyOP2/lib/python2.7/site-packages"
prepend-path PYTHONPATH "$root/firedrake/lib/python2.7/site-packages"

?

Why are there two files (fdrake-build-env and fdrake-python-env) in the 
first place, if they are always loaded together? Wouldn't it make sense 
if I just create one file (i.e. add everything in fdrake-build-env at 
the top of my local fdrake-python-env?

Thanks,

Eike

On 30/01/15 10:29, Michael Lange wrote:
> On 30/01/15 10:13, Eike Mueller wrote:
>> Hi Michael,
>>
>> I'm using quite a few non-standard branches
>> (petsc->knepley/fix-plex-1d-refinement, PyOP2->columnwise_kernels,
>> firedrake->multigrid-extrusion) to get my extruded multigrid working.
>> The dependency on the non-default PETSc required me to install both
>> this and petsc4py locally. I also installed FFC, UFL, FIAT and COFFEE
>> locally, since the central versions were still out-out-of-date yesterday.
> 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.
>>
>> But to test your changes, I can try running a basic firedrake code and
>> use the centrally installed firdrake version.
>>
>> Just to be clear: You updated both PyOP2 and firdrake centrally, so in
>> the instructions here
>> https://github.com/firedrakeproject/firedrake-bench/wiki/Archer I do
>> not need to build a local firedrake version and can leave out the
>> following in firedrake.env and my jobscript:
>>
>> export
>> PYTHONPATH=$WORK/firedrake-bench:$WORK/pybench:$WORK/firedrake:$WORK/PyOP2:$PYTHONPATH
>>
> Yes, it should work without this line now. I don't know why these
> components had been disabled in the central module.
>
> Thanks,
> Michael
>
>>
>> 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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>>>
>>>
>>>
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>>
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