date:20160427

Re: globalValue in parallel

2016-04-27 Thread Keller, Trevor (Fed)

Looking into the rest of the FiPy source, we're already calling 
allgather(sendobj) in several places, and rarely calling allgather(sendobj, 
recvobj). To preserve the existing function calls (all of which are lower-case) 
and mess with the code the least, removing the recvobj argument appears to be 
the right call after all.

Working on the PR.

Trevor


From: fipy-boun...@nist.gov  on behalf of Guyer, 
Jonathan E. Dr. (Fed) 
Sent: Wednesday, April 27, 2016 4:39:05 PM
To: FIPY
Subject: Re: globalValue in parallel

It sounds like you're volunteering to put together the pull request with 
appropriate tests

> On Apr 27, 2016, at 4:06 PM, Keller, Trevor (Fed)  
> wrote:
>
> The mpi4py commit mentions that the receive object is no longer needed for 
> the lower-case form of the commands. Browsing the full source shows that the 
> upper-case commands retain both the send and receive objects. To avoid 
> deviating too far from the MPI standard, I'd like to suggest changing the 
> case (Allgather instead of allgather), rather than dropping buffers, in our 
> mpi4pyCommWrapper.py.
>
> Trevor
>
>
> 
> From: fipy-boun...@nist.gov  on behalf of Guyer, 
> Jonathan E. Dr. (Fed) 
> Sent: Wednesday, April 27, 2016 3:53:39 PM
> To: FIPY
> Subject: Re: globalValue in parallel
>
> It looks like 'recvobj' was removed from mpi4py about two years ago:
>
> https://bitbucket.org/mpi4py/mpi4py/commits/3d8503a11d320dd1c3030ec0dbce95f63b0ba602
>
> but I'm not sure when it made it into the released version.
>
>
> It looks like you can safely edit fipy/tools/comms/mpi4pyCommWrapper.py to 
> remove the 'recvobj' argument.
>
>
> We'll do some tests and push a fix as soon as possible. Thanks for alerting 
> us to the issue.
>
> Filed as https://github.com/usnistgov/fipy/issues/491
>
>
>> On Apr 27, 2016, at 2:23 PM, Kris Kuhlman  
>> wrote:
>>
>> I built the trilinos-capable version of fipy. It seems to work for serial 
>> (even for a non-trivial case), but I am getting errors with more than one 
>> processor with a simple call to globalValue(), which I was trying to use to 
>> make a plot by gathering the results to procID==0
>>
>> I used the latest git version of mpi4py and trilinos. Am I doing something 
>> wrong (is there a different preferred way to gather things to a single 
>> processor to save or make plots?) or do I need to use a specific version of 
>> these packages and rebuild?  It seems the function is expecting something 
>> with a different interface or call structure.
>>
>> Kris
>>
>> python test.py
>> hello from 0 out of 1 [ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  
>> 1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.]
>>
>> `--> ~/local/trilinos-fipy/anaconda/bin/mpirun -np 1 python test.py
>> hello from 0 out of 1 [ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  
>> 1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.]
>>
>> --> ~/local/trilinos-fipy/anaconda/bin/mpirun -np 2 python test.py
>> hello from 1 out of 2
>> Traceback (most recent call last):
>>  File "test.py", line 6, in 
>>print 'hello from',fp.tools.parallel.procID,'out 
>> of',fp.tools.parallel.Nproc,p.globalValue
>>  File 
>> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/cellVariable.py",
>>  line 163, in globalValue
>>

Re: globalValue in parallel

2016-04-27 Thread Guyer, Jonathan E. Dr. (Fed)

It sounds like you're volunteering to put together the pull request with 
appropriate tests

> On Apr 27, 2016, at 4:06 PM, Keller, Trevor (Fed)  
> wrote:
> 
> The mpi4py commit mentions that the receive object is no longer needed for 
> the lower-case form of the commands. Browsing the full source shows that the 
> upper-case commands retain both the send and receive objects. To avoid 
> deviating too far from the MPI standard, I'd like to suggest changing the 
> case (Allgather instead of allgather), rather than dropping buffers, in our 
> mpi4pyCommWrapper.py.
> 
> Trevor
> 
> 
> 
> From: fipy-boun...@nist.gov  on behalf of Guyer, 
> Jonathan E. Dr. (Fed) 
> Sent: Wednesday, April 27, 2016 3:53:39 PM
> To: FIPY
> Subject: Re: globalValue in parallel
> 
> It looks like 'recvobj' was removed from mpi4py about two years ago:
> 
> https://bitbucket.org/mpi4py/mpi4py/commits/3d8503a11d320dd1c3030ec0dbce95f63b0ba602
> 
> but I'm not sure when it made it into the released version.
> 
> 
> It looks like you can safely edit fipy/tools/comms/mpi4pyCommWrapper.py to 
> remove the 'recvobj' argument.
> 
> 
> We'll do some tests and push a fix as soon as possible. Thanks for alerting 
> us to the issue.
> 
> Filed as https://github.com/usnistgov/fipy/issues/491
> 
> 
>> On Apr 27, 2016, at 2:23 PM, Kris Kuhlman  
>> wrote:
>> 
>> I built the trilinos-capable version of fipy. It seems to work for serial 
>> (even for a non-trivial case), but I am getting errors with more than one 
>> processor with a simple call to globalValue(), which I was trying to use to 
>> make a plot by gathering the results to procID==0
>> 
>> I used the latest git version of mpi4py and trilinos. Am I doing something 
>> wrong (is there a different preferred way to gather things to a single 
>> processor to save or make plots?) or do I need to use a specific version of 
>> these packages and rebuild?  It seems the function is expecting something 
>> with a different interface or call structure.
>> 
>> Kris
>> 
>> python test.py
>> hello from 0 out of 1 [ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  
>> 1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.]
>> 
>> `--> ~/local/trilinos-fipy/anaconda/bin/mpirun -np 1 python test.py
>> hello from 0 out of 1 [ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  
>> 1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
>>  1.  1.]
>> 
>> --> ~/local/trilinos-fipy/anaconda/bin/mpirun -np 2 python test.py
>> hello from 1 out of 2
>> Traceback (most recent call last):
>>  File "test.py", line 6, in 
>>print 'hello from',fp.tools.parallel.procID,'out 
>> of',fp.tools.parallel.Nproc,p.globalValue
>>  File 
>> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/cellVariable.py",
>>  line 163, in globalValue
>>self.mesh._globalNonOverlappingCellIDs)
>>  File 
>> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/meshVariable.py",
>>  line 171, in _getGlobalValue
>>globalIDs = 
>> numerix.concatenate(self.mesh.communicator.allgather(globalIDs))
>>  File 
>> "/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/tools/comms/mpi4pyCommWrapper.py",
>>  line 75, in allgather
>>return self.mpi4py_comm.allgather(sendobj=sendobj, recvobj=recvobj)
>>  File "MPI/Comm.pyx", line 1288, in mpi4py.MPI.Comm.allgather 
>> (src/mpi4py.MPI.c:109141)
>>

Re: understanding convection terms

2016-04-27 Thread Daniel Wheeler

On Tue, Apr 26, 2016 at 10:57 AM, Kris Kuhlman
 wrote:
> Daniel,
>
> Thank you. I am a bit surprised that the CentralDifference basically matches
> the hybrid method, and is more accurate than upwind.

Remember that central difference is second order accurate. The other
schemes are first order. Of course it's unstable when the Peclet
number is above 2 that's why we use the other schemes. Basically, the
schemes (hybrid, exponential etc) are ways to swap between central
difference and upwind based on the local Peclet number.

-- 
Daniel Wheeler
___
fipy mailing list
fipy@nist.gov
http://www.ctcms.nist.gov/fipy
  [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]

globalValue in parallel

2016-04-27 Thread Kris Kuhlman

I built the trilinos-capable version of fipy. It seems to work for serial
(even for a non-trivial case), but I am getting errors with more than one
processor with a simple call to globalValue(), which I was trying to use to
make a plot by gathering the results to procID==0

I used the latest git version of mpi4py and trilinos. Am I doing something
wrong (is there a different preferred way to gather things to a single
processor to save or make plots?) or do I need to use a specific version of
these packages and rebuild?  It seems the function is expecting something
with a different interface or call structure.

Kris

python test.py
hello from 0 out of 1 [ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.]

`--> ~/local/trilinos-fipy/anaconda/bin/mpirun -np 1 python
test.py
hello from 0 out of 1 [ 1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.  1.
  1.  1.]

--> ~/local/trilinos-fipy/anaconda/bin/mpirun -np 2 python test.py
hello from 1 out of 2
Traceback (most recent call last):
  File "test.py", line 6, in 
print 'hello from',fp.tools.parallel.procID,'out
of',fp.tools.parallel.Nproc,p.globalValue
  File
"/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/cellVariable.py",
line 163, in globalValue
self.mesh._globalNonOverlappingCellIDs)
  File
"/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/meshVariable.py",
line 171, in _getGlobalValue
globalIDs =
numerix.concatenate(self.mesh.communicator.allgather(globalIDs))
  File
"/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/tools/comms/mpi4pyCommWrapper.py",
line 75, in allgather
return self.mpi4py_comm.allgather(sendobj=sendobj, recvobj=recvobj)
  File "MPI/Comm.pyx", line 1288, in mpi4py.MPI.Comm.allgather
(src/mpi4py.MPI.c:109141)
TypeError: allgather() got an unexpected keyword argument 'recvobj'
hello from 0 out of 2
Traceback (most recent call last):
  File "test.py", line 6, in 
print 'hello from',fp.tools.parallel.procID,'out
of',fp.tools.parallel.Nproc,p.globalValue
  File
"/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/cellVariable.py",
line 163, in globalValue
self.mesh._globalNonOverlappingCellIDs)
  File
"/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/variables/meshVariable.py",
line 171, in _getGlobalValue
globalIDs =
numerix.concatenate(self.mesh.communicator.allgather(globalIDs))
  File
"/home/klkuhlm/local/trilinos-fipy/anaconda/lib/python2.7/site-packages/fipy/tools/comms/mpi4pyCommWrapper.py",
line 75, in allgather
return self.mpi4py_comm.allgather(sendobj=sendobj, recvobj=recvobj)
  File "MPI/Comm.pyx", line 1288, in mpi4py.MPI.Comm.allgather
(src/mpi4py.MPI.c:109141)
TypeError: allgather() got an unexpected keyword argument 'recvobj'
---
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
---
--
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:

  Process name: [[1719,1],1]
  Exit code:1
--
import fipy as fp

m = fp.Grid2D(nx=10,ny=20)
p =

Re: globalValue in parallel

Re: globalValue in parallel

Re: understanding convection terms

globalValue in parallel

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