[firedrake] (Even more) progress on installing PyOP2/firedrake on ARCHER

[Eike Mueller]

Dear all,

some more observations/issues encountered while running on ARCHER:

I think I have to set the path to petsc4py, ufl, fiat and ffc in firedrake.tpl, as otherwise it complains that it can't find the modules:

export PYTHONPATH=${FDRAKE_DIR}/petsc4py/lib/python2.7/site-packages:${PYTHONPATH}
export PYTHONPATH=${FDRAKE_DIR}/ufl/lib/python2.7/site-packages/:${PYTHONPATH}
export PYTHONPATH=${FDRAKE_DIR}/fiat/lib/python2.7/site-packages/:${PYTHONPATH}
export PYTHONPATH=${FDRAKE_DIR}/ffc/lib/python2.7/site-packages/:${PYTHONPATH}

Still, even though I think the ufl path is correct, it can't load ufl.algorithms.compute_form_data:

  File "firedrake_poisson.py", line 4, in <module>
    from firedrake import *
  File "/work/n02/n02/eike/firedrake/firedrake/firedrake/__init__.py", line 11, in <module>
    from bcs import *
  File "/work/n02/n02/eike/firedrake/firedrake/firedrake/bcs.py", line 9, in <module>
    import function
  File "/work/n02/n02/eike/firedrake/firedrake/firedrake/function.py", line 11, in <module>
    import projection
  File "/work/n02/n02/eike/firedrake/firedrake/firedrake/projection.py", line 6, in <module>
    import solving
  File "/work/n02/n02/eike/firedrake/firedrake/firedrake/solving.py", line 38, in <module>
    import ffc_interface
  File "/work/n02/n02/eike/firedrake/firedrake/firedrake/ffc_interface.py", line 13, in <module>
    from ufl.algorithms import compute_form_data, ReuseTransformer
ImportError: cannot import name compute_form_data

Does it need a more recent version of ufl? The directory 

/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages/ufl/algorithms/

on ARCHER does not contain the file compute_form_data.py, but the installation on my laptop does, so looks like something is missing there.

Also (I believe this is an unrelated problem), I had to replace

module swap python anaconda

by the two lines

module unload python
module add anaconda

If python is not loaded by default on the compute nodes, the swap command fails, and the firedrake python code later crashes with a segmentation fault since it can't load the anaconda library:

ModuleCmd_Switch.c(172):ERROR:152: Module 'python' is currently not loaded
fdrake-python-env(30):ERROR:102: Tcl command execution failed: prepend-path LD_LIBRARY_PATH "$env(ANACONDA_LIB)"

I will go ahead and edit the wiki.

Eike

--

Dr Eike Hermann Mueller
Research Associate (PostDoc)

Department of Mathematical Sciences
University of Bath
Bath BA2 7AY, United Kingdom

+44 1225 38 5803
e.mueller at bath.ac.uk
http://people.bath.ac.uk/em459/

On 8 Sep 2014, at 15:53, Eike Mueller <E.Mueller at bath.ac.uk> wrote:

> Hi Florian,
> 
> thanks a lot for your reply and for updating the wiki, I got a bit further now.
> 
>> 
>> You're exactly right again: it seems that anaconda contains a version of
>> the TCL libraries which are incompatible with those use by the
>> environment modules. I'm not sure how to work around this, since we need
>> the anaconda libs (as you figured out later) - will open a ticket.
> 
> ok, I will use the environment script as it is and not worry about the fact that the anaconda library breaks the module command at the moment. Let's see if the support can figure something out.
> 
>> 
>> I've changed the wiki page to clone via https, thanks!
> 
> It works with the updated instructions on the webpage. Strangely, if I clone a repository into a directory, delete this directory and then try to clone again with exactly the same command, nothing happens.
> 
>> This seems to happen because (for reasons I can't figure out) setuptools
>> doesn't detect that NumPy is already installed and builds it from
>> source. The primary cause of the error you're seeing is this:
>> https://stackoverflow.com/a/21621493
> 
> I will ignore this then, and just call the setup.py script twice in the PyOP2 directory.
> 
>> This is because you've removed the anaconda lib path, which also
>> contains the Python libraries themselves, from LD_LIBRARY_PATH
> 
> I tried a simpler hello-world script where I swap python -> anaconda and run a python script. This does work.
> Still trying to run the poisson example from the benchmark repository, but the ARCHER queues seem to be terribly slow, even if I just run on one node on the debug queue :-(
> 
>> 
>> Absolutely, feel free to edit the wiki if you find more errors or things
>> that are unclear.
>> 
> 
> I think I already have access to the repository, so will edit if necessary.
> 
> Thanks a lot,
> 
> Eike
> 
>> Florian
>> 
>>> Cheers,
>>> 
>>> Eike
>>> 
>>> *** content of firedrake.env ***
>>> 
>>> module swap PrgEnv-cray PrgEnv-gnu
>>> module unload python
>>> module add anaconda
>>> 
>>> # Add fdrake module path
>>> export FDRAKE_DIR=/work/y07/y07/fdrake
>>> module use "$FDRAKE_DIR/modules"
>>> 
>>> # Load build environment
>>> module load fdrake-build-env
>>> module load fdrake-python-env
>>> 
>>> LD_LIBRARY_PATH=`echo $LD_LIBRARY_PATH | sed 's/\/work\/y07\/y07\/cse\/anaconda\/1.9.2\/lib//g'`
>>> 
>>> export PYTHONPATH=$WORK/firedrake-bench:$WORK/firedrake-bench/pybench:$WORK/firedrake:$WORK/PyOP2:$PYTHONPATH
>>> 
>>> 
>>> --
>>> 
>>> Dr Eike Hermann Mueller
>>> Research Associate (PostDoc)
>>> 
>>> Department of Mathematical Sciences
>>> University of Bath
>>> Bath BA2 7AY, United Kingdom
>>> 
>>> +44 1225 38 5803
>>> e.mueller at bath.ac.uk <mailto:e.mueller at bath.ac.uk>
>>> http://people.bath.ac.uk/em459/
>> 
>> _______________________________________________
>> firedrake mailing list
>> firedrake at imperial.ac.uk
>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
> 
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