Re: [Pypar-developers] PyPar installation

[Jay L. <jw...@rs...>]

Hi Ole,

Thanks for the rapid response...and on the weekend--wow!

Since we are all in Canberra, we should meet up sometime and I will buy you some drinks. 

All the Best,
               Jay

Sent from Jay's BlackBerry®

-----Original Message-----
From: Ole Nielsen <ole...@gm...>
Date: Sat, 19 Dec 2009 12:26:50 
To: Romesh Abeysuriya<rom...@gm...>
Cc: Dr. Jay Larson (ANU)<jay...@an...>; Pypar-developers<Pyp...@li...>
Subject: Re: PyPar installation

Hi Romesh

When I build pypar on our 64 bit Intel cluster (Ubuntu 9.04) with OpenMPI,
the compile string looks like this:

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/lib/openmpi/include
-I/usr/lib/openmpi/include/openmpi
-I/usr/lib/python2.6/dist-packages/numpy/core/include
-I/usr/include/python2.6 -c mpiext.c -o build/temp.linux-x86_64-2.6/mpiext.o
-fPIC
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
build/temp.linux-x86_64-2.6/mpiext.o -L/usr/lib/openmpi/lib -lmpi -lopen-rte
-lopen-pal -ldl -lnsl -lutil -lm -o
build/lib.linux-x86_64-2.6/pypar/mpiext.so

and all is well. The same is true on a 32 bit Ubuntu 9.10 system.


Could I ask you to try to run
python compile_pypar_locally.py

That will compile the mpiext.so using mpicc directly (bypassing distutils)
and the compile output should look something like this.

nielso@alamba:~/sandpit/pypar/source$ python compile_pypar_locally.py
mpicc -c mpiext.c -I/usr/include/python2.6
-I/usr/lib/python2.6/dist-packages/numpy/core/include -o mpiext.o -Wall
-fPIC
mpicc -shared mpiext.o  -o mpiext.so -mcmodel=medium
MPI initialised OK


Then you should be able to run the unit tests
mpirun -np 2 python test_pypar.py

Please let us know how you go.

Cheers
Ole




un...@in...

On Fri, Dec 18, 2009 at 3:26 PM, Romesh Abeysuriya <rom...@gm...>wrote:

> Hi Ole,
>
> We are trying to build PyPar on a couple of platforms, and are encountering
> the same problem.
>
> The two architectures are:  64-bit intels (one Linux, the other OS X Snow
> Leopard).  The common
> error we encounter in both is associated with this message:
>
> gcc -pthread -shared build/temp.linux-x86_64-2.4/mpiext.o
> -L/users/prl/rga112/mpich2-install-scucomp1/lib -lmpich -lopa -lpthread -lrt
> -lopa' -o build/lib.linux-x86_64-2.4/pypar/mpiext.so
> sh: -c: line 0: unexpected EOF while looking for matching `''
> sh: -c: line 1: syntax error: unexpected end of file
> _exec_command_posix failed (status=512)
> /usr/bin/bash: -c: line 0: unexpected EOF while looking for matching `''
> /usr/bin/bash: -c: line 1: syntax error: unexpected end of file
> /usr/bin/bash: -c: line 0: unexpected EOF while looking for matching `''
> /usr/bin/bash: -c: line 1: syntax error: unexpected end of file
> error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.4/mpiext.o
> -L/users/prl/rga112/mpich2-install-scucomp1/lib -lmpich -lopa -lpthread -lrt
> -lopa' -o build/lib.linux-x86_64-2.4/pypar/mpiext.so" failed with exit
> status 2
>
> The main problem stems from this -lopa' element.  Grepping around your
> source for "lopa" or "opa" didn't give us a clue how to fix this problem.
>
> Additionally, on Snow Leopard, problems arise because PyPar is trying to
> create a Universal Binary, when only x86_64 MPICH libraries have been
> compiled, so we are looking for a way to remove the extra -arch switches.
>
> We really would like to use PyPar in our project, so if you could please
> advise us how to fix these problems, we'd be really grateful.
>
> For reference, here's some version information on our software stack we're
> using to build PyPar:
>
> MPICH2-1.2.1
> Python 2.6.1 (OS X)
> Numpy 1.0.1 (current rpmforge repository version), latest SVN (OS X)
> GCC 4.1.2 (Linux), 4.2.1 (OS X)
> PyPar 2.1.0.66
>
>
> Thanks and all the best...
>
> Romesh Abeysuriya
> Jay Larson
>
>
>