Hi all,
I'm writing just to let you know I finally got an execution with MPI. I'm
attaching a patch with the changes I've made to the code to make PyFR work
on a 32 bits platform (in this case, also ARM).
I found that the problem with the key error was caused by some other "bug"
in numpy. Here how you can reproduce it:
>>> import numpy as np
>>> np.dtype('P').type
<class 'numpy.uint32'>
>>> np.uint32
<class 'numpy.uint32'>
>>> np.dtype('P').type == np.uint32
False
This also happens with 'i' dtype (int32), so when trying to access to a map
that has numpy types as keys, the comparison fails and the key error
exception happens.
Thanks for all the help provided.
Best regards,
-Dani
El miércoles, 1 de julio de 2015, 11:06:03 (UTC+2), Dani Ruiz escribió:
>
> Hi Freddie,
>
> Your change leaded again to the error with pickle... So I added the
> "np.intp = np.int32" line to every file importing numpy module and that
> solved the issue.
>
> Anyhow, now I'm facing another problem with MPI (most probably related
> with mpi4py Python module) which I'm trying to solve right now.
>
> Thanks a lot for all the help :-)
>
> Best regards,
> -Dani
>
> El martes, 30 de junio de 2015, 16:47:11 (UTC+2), Freddie Witherden
> escribió:
>>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA256
>>
>> On 30/06/2015 14:41, Dani Ruiz wrote:
>> > Hi,
>> >
>> > Regarding the issue Miquel had, chaning the intp instances by
>> > int32 solves the problem with pickle on ARM 32 bits and, therefore,
>> > the application runs correctly with OpenMP backend.
>> >
>> > However, when running MPI+OpenMP it crashes again due to some key
>> > error with int32. Below the specific error:
>> >
>> > After this message, OpenMPI invokes on rank 1 an MPI_ABORT,
>> > finishing the execution. Could this be related with the
>> > modifications made before? I also noticed that he MPI_ABORT is
>> > never invoked on the MPI process with rank 0, not pretty sure if
>> > this could help.
>>
>> It seems to be related to the same numpy issue that breaks regular
>> PyFR on 32-bit systems. As a workaround can you try, against a stock
>> copy of PyFR, opening up pyfr/__main__.py and before
>>
>> import pyfr.scripts.main
>>
>> insert
>>
>> import numpy as np
>> np.intp = np.int32
>>
>> and see if that works. The good news is that if it solves the problem
>> it should solve it everywhere and with only minor code modifications.
>>
>> Regards, Freddie.
>>
>> -----BEGIN PGP SIGNATURE-----
>> Comment: GPGTools - http://gpgtools.org
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>
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diff --git a/tmp/PyFR-1.0.0/pyfr/nputil.py b/home/druiz/python/pyfr/PyFR-1.0.0/pyfr/nputil.py
index d1bd5e8..a8b6fd2 100644
--- a/tmp/PyFR-1.0.0/pyfr/nputil.py
+++ b/home/druiz/python/pyfr/PyFR-1.0.0/pyfr/nputil.py
@@ -119,5 +119,9 @@ def npdtype_to_ctypestype(dtype):
# Special-case None which otherwise expands to np.float
if dtype is None:
return None
+ elif dtype is 'P':
+ return ct.c_uint32
+ elif dtype is 'i':
+ return ct.c_int32
return _ctypestype_map[np.dtype(dtype).type]
diff --git a/tmp/PyFR-1.0.0/pyfr/util.py b/home/druiz/python/pyfr/PyFR-1.0.0/pyfr/util.py
index af71f5c..2aeeaaf 100644
--- a/tmp/PyFR-1.0.0/pyfr/util.py
+++ b/home/druiz/python/pyfr/PyFR-1.0.0/pyfr/util.py
@@ -7,6 +7,7 @@ import itertools as it
import os
import pickle
import shutil
+import numpy as np
from pyfr.ctypesutil import find_libc
@@ -26,6 +27,7 @@ class memoize(object):
except AttributeError:
cache = instance._memoize_cache = {}
+ np.intp = np.int32
key = (self.func, pickle.dumps(args[1:], 1), pickle.dumps(kwargs, 1))
try:
