Thread: [Pypar-developers] Fwd: Problems with pypar & MPICH2
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From: Ole N. <ole...@gm...> - 2009-12-21 12:45:41
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Hi guys This sounds like the problem you had? Is this something with recent MPICH versions perhaps? Cheers Ole ---------- Forwarded message ---------- From: Jussi Lehtola <jus...@fe...> Date: Mon, Dec 21, 2009 at 11:34 PM Subject: Problems with pypar & MPICH2 To: ole...@gm... Hi, I'm trying to add MPICH2 support to the Fedora package of pypar, however the compilation fails with mpicc -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fPIC -I/usr/include/mpich2-x86_64 -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c mpiext.c -o build/temp.linux-x86_64-2.6/mpiext.o -fPIC mpiext.c: In function 'type_map': mpiext.c:127: warning: return makes integer from pointer without a cast mpiext.c: In function 'op_map': mpiext.c:168: warning: return makes integer from pointer without a cast gcc -pthread -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic build/temp.linux-x86_64-2.6/mpiext.o -L/usr/lib64/mpich2/lib -L/usr/lib64 -lmpich -lopa -lpthread -lrt -lopa' -lpython2.6 -o build/lib.linux-x86_64-2.6/pypar/mpiext.so /usr/bin/ld: cannot find -lopa' collect2: ld returned 1 exit status so it seems that an extra ' is picked up somewhere. Do you have any idea where this might come out from? Also, although I've defined CC=mpicc, the file is compiled with gcc.. -- Jussi Lehtola Fedora Project Contributor jus...@fe... |
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From: Ole N. <ole...@gm...> - 2009-12-21 18:29:53
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OK - then the problem might be with mpicc --showme Could I bother you to issue that command (using mpicc from MPICH2) and paste the results in. With OpenMPI it is o@desktop:~/sandpit/pypar$ mpicc --showme gcc -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -pthread -L/usr/lib/openmpi/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl and this works fine. Cheers Ole On Mon, Dec 21, 2009 at 11:42 PM, Jussi Lehtola < jus...@fe...> wrote: > On Mon, 2009-12-21 at 23:38 +1100, Ole Nielsen wrote: > > Hi Jussi - this compiles fine where I am, but I am using OpenMPI. > > The compiler flags are generated mpicc. > > I'm, too, a Open MPI user myself. > > > Does it work if you run python compile_pypar_locally.py - just as a > > test. > > Yes, it works just fine with MPICH2. > > -- > Jussi Lehtola > Fedora Project Contributor > jus...@fe... > > |
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From: Ole N. <ole...@gm...> - 2009-12-21 18:33:40
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Or as it is, it appears that with MPICH the command to get the compiler string is mpicc -compile_info -link_info Could I bother you to paste that in? Thanks Ole On Tue, Dec 22, 2009 at 5:29 AM, Ole Nielsen <ole...@gm...>wrote: > OK - then the problem might be with mpicc --showme > Could I bother you to issue that command (using mpicc from MPICH2) and > paste the results in. > With OpenMPI it is > > o@desktop:~/sandpit/pypar$ mpicc --showme > gcc -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -pthread > -L/usr/lib/openmpi/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic > -lnsl -lutil -lm -ldl > > and this works fine. > > Cheers > Ole > > > On Mon, Dec 21, 2009 at 11:42 PM, Jussi Lehtola < > jus...@fe...> wrote: > >> On Mon, 2009-12-21 at 23:38 +1100, Ole Nielsen wrote: >> > Hi Jussi - this compiles fine where I am, but I am using OpenMPI. >> > The compiler flags are generated mpicc. >> >> I'm, too, a Open MPI user myself. >> >> > Does it work if you run python compile_pypar_locally.py - just as a >> > test. >> >> Yes, it works just fine with MPICH2. >> >> -- >> Jussi Lehtola >> Fedora Project Contributor >> jus...@fe... >> >> > |
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From: Jay L. <jw...@rs...> - 2009-12-21 21:33:49
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Hi Ole, The -lopa' problem is certainly the same. Jay Sent from Jay's BlackBerry® -----Original Message----- From: Ole Nielsen <ole...@gm...> Date: Mon, 21 Dec 2009 23:37:01 To: Dr. Jay Larson (ANU)<jay...@an...>; Pypar-developers<Pyp...@li...>; Romesh Abeysuriya<rom...@gm...>; Jussi Lehtola<jus...@fe...> Subject: Fwd: Problems with pypar & MPICH2 Hi guys This sounds like the problem you had? Is this something with recent MPICH versions perhaps? Cheers Ole ---------- Forwarded message ---------- From: Jussi Lehtola <jus...@fe...> Date: Mon, Dec 21, 2009 at 11:34 PM Subject: Problems with pypar & MPICH2 To: ole...@gm... Hi, I'm trying to add MPICH2 support to the Fedora package of pypar, however the compilation fails with mpicc -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fPIC -I/usr/include/mpich2-x86_64 -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c mpiext.c -o build/temp.linux-x86_64-2.6/mpiext.o -fPIC mpiext.c: In function 'type_map': mpiext.c:127: warning: return makes integer from pointer without a cast mpiext.c: In function 'op_map': mpiext.c:168: warning: return makes integer from pointer without a cast gcc -pthread -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic build/temp.linux-x86_64-2.6/mpiext.o -L/usr/lib64/mpich2/lib -L/usr/lib64 -lmpich -lopa -lpthread -lrt -lopa' -lpython2.6 -o build/lib.linux-x86_64-2.6/pypar/mpiext.so /usr/bin/ld: cannot find -lopa' collect2: ld returned 1 exit status so it seems that an extra ' is picked up somewhere. Do you have any idea where this might come out from? Also, although I've defined CC=mpicc, the file is compiled with gcc.. -- Jussi Lehtola Fedora Project Contributor jus...@fe... |
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From: Romesh A. <rom...@gm...> - 2009-12-21 23:32:17
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Hi Ole,
Here is the latest from compiling on my OS X machine
pypar-2.1.0_66 : has the -lopa' problem, but if I run compile_pypar_locally,
it installs and runs (but fails tests as discussed previously)
pypar-2.1.2_87 : 'python setup.py install' runs and finishes without errors,
although it complains about the library architecture (as previously
discussed re. building universal binary as opposed to a single
architecture). However, if I try to import pypar in python, I get this:
>>> import pypar
ERROR: C extension mpiext could not be imported.
Please compile mpiext.c e.g. by running
python compile_pypar_manually.py
in the pypar directory, or by using
python setup.py install
WARNING: MPI library could not be initialised - running sequentially
>>>
By the way, should this error message read
"Please compile mpiext.c e.g. by running
python compile_pypar_locally.py"
rather than "python compile_pypar_manually.py" ?
If I run compile_pypar_locally, it compiles. However, Python then does this:
>>> import pypar
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "pypar.py", line 863, in <module>
mpi = CDLL('libmpi.so.0', RTLD_GLOBAL)
File
"/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/ctypes/__init__.py",
line 345, in __init__
self._handle = _dlopen(self._name, mode)
OSError: dlopen(libmpi.so.0, 10): image not found
>>>
pypar-2.1.3_91 : 'python setup.py install' quits with the following error
message
...
running build_ext
building 'pypar.mpiext' extension
creating build/temp.macosx-10.6-universal-2.6
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os
-Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64
-pipe
-I/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy/core/include
-I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
-c mpiext.c -o build/temp.macosx-10.6-universal-2.6/mpiext.o
gcc-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -arch i386 -arch ppc -arch
x86_64 build/temp.macosx-10.6-universal-2.6/mpiext.o -L/usr/opt/mpi -lmpi
-lelan -o build/lib.macosx-10.6-universal-2.6/pypar/mpiext.so
ld: library not found for -lelan
collect2: ld returned 1 exit status
ld: library not found for -lelan
collect2: ld returned 1 exit status
ld: library not found for -lelan
collect2: ld returned 1 exit status
lipo: can't open input file:
/var/folders/eW/eWXFeb8cGoKDvOMgR+R4Q++++TI/-Tmp-//cciaX7u5.out (No such
file or directory)
error: command 'gcc-4.2' failed with exit status 1
Running compile_pypar_locally gives exactly the same error message in python
as 2.1.2_87
Thanks for the speedy updates!
Romesh
2009/12/22 Jay Larson <jw...@rs...>
> Hi Ole,
>
> The -lopa' problem is certainly the same.
>
> Jay
>
> Sent from Jay's BlackBerry®
> ------------------------------
> *From: * Ole Nielsen <ole...@gm...>
> *Date: *Mon, 21 Dec 2009 23:37:01 +1100
> *To: *Dr. Jay Larson (ANU)<jay...@an...>; Pypar-developers<
> Pyp...@li...>; Romesh Abeysuriya<
> rom...@gm...>; Jussi Lehtola<jus...@fe...>
> *Subject: *Fwd: Problems with pypar & MPICH2
>
> Hi guys
>
> This sounds like the problem you had?
>
> Is this something with recent MPICH versions perhaps?
>
> Cheers
> Ole
>
> ---------- Forwarded message ----------
> From: Jussi Lehtola <jus...@fe...>
> Date: Mon, Dec 21, 2009 at 11:34 PM
> Subject: Problems with pypar & MPICH2
> To: ole...@gm...
>
>
> Hi,
>
>
> I'm trying to add MPICH2 support to the Fedora package of pypar, however
> the compilation fails with
>
> mpicc -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> -D_GNU_SOURCE -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
> -mtune=generic -fPIC -I/usr/include/mpich2-x86_64
> -I/usr/lib64/python2.6/site-packages/numpy/core/include
> -I/usr/include/python2.6 -c mpiext.c -o
> build/temp.linux-x86_64-2.6/mpiext.o -fPIC
> mpiext.c: In function 'type_map':
> mpiext.c:127: warning: return makes integer from pointer without a cast
> mpiext.c: In function 'op_map':
> mpiext.c:168: warning: return makes integer from pointer without a cast
> gcc -pthread -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
> -mtune=generic build/temp.linux-x86_64-2.6/mpiext.o
> -L/usr/lib64/mpich2/lib -L/usr/lib64 -lmpich -lopa -lpthread -lrt -lopa'
> -lpython2.6 -o build/lib.linux-x86_64-2.6/pypar/mpiext.so
> /usr/bin/ld: cannot find -lopa'
> collect2: ld returned 1 exit status
>
> so it seems that an extra ' is picked up somewhere. Do you have any idea
> where this might come out from?
>
> Also, although I've defined CC=mpicc, the file is compiled with gcc..
>
> --
> Jussi Lehtola
> Fedora Project Contributor
> jus...@fe...
>
>
>
|
|
From: Ole N. <ole...@gm...> - 2009-12-22 07:25:37
Attachments:
setup.py
|
OK - try to use the attached setup.py and let me know how it goes.
Thanks
Ole
On Tue, Dec 22, 2009 at 6:31 AM, Romesh Abeysuriya <rom...@gm...>wrote:
> Hi Ole,
>
> Here is the latest from compiling on my OS X machine
>
> pypar-2.1.0_66 : has the -lopa' problem, but if I run
> compile_pypar_locally, it installs and runs (but fails tests as discussed
> previously)
>
> pypar-2.1.2_87 : 'python setup.py install' runs and finishes without
> errors, although it complains about the library architecture (as previously
> discussed re. building universal binary as opposed to a single
> architecture). However, if I try to import pypar in python, I get this:
>
> >>> import pypar
> ERROR: C extension mpiext could not be imported.
> Please compile mpiext.c e.g. by running
> python compile_pypar_manually.py
> in the pypar directory, or by using
> python setup.py install
>
> WARNING: MPI library could not be initialised - running sequentially
> >>>
>
> By the way, should this error message read
> "Please compile mpiext.c e.g. by running
>
> python compile_pypar_locally.py"
>
> rather than "python compile_pypar_manually.py" ?
>
> If I run compile_pypar_locally, it compiles. However, Python then does
> this:
>
> >>> import pypar
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "pypar.py", line 863, in <module>
> mpi = CDLL('libmpi.so.0', RTLD_GLOBAL)
> File
> "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/ctypes/__init__.py",
> line 345, in __init__
> self._handle = _dlopen(self._name, mode)
> OSError: dlopen(libmpi.so.0, 10): image not found
> >>>
>
> pypar-2.1.3_91 : 'python setup.py install' quits with the following error
> message
>
> ...
> running build_ext
> building 'pypar.mpiext' extension
> creating build/temp.macosx-10.6-universal-2.6
> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os
> -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64
> -pipe
> -I/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy/core/include
> -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
> -c mpiext.c -o build/temp.macosx-10.6-universal-2.6/mpiext.o
> gcc-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -arch i386 -arch ppc
> -arch x86_64 build/temp.macosx-10.6-universal-2.6/mpiext.o -L/usr/opt/mpi
> -lmpi -lelan -o build/lib.macosx-10.6-universal-2.6/pypar/mpiext.so
> ld: library not found for -lelan
>
> collect2: ld returned 1 exit status
> ld: library not found for -lelan
>
> collect2: ld returned 1 exit status
> ld: library not found for -lelan
>
> collect2: ld returned 1 exit status
> lipo: can't open input file:
> /var/folders/eW/eWXFeb8cGoKDvOMgR+R4Q++++TI/-Tmp-//cciaX7u5.out (No such
> file or directory)
> error: command 'gcc-4.2' failed with exit status 1
>
> Running compile_pypar_locally gives exactly the same error message in
> python as 2.1.2_87
>
> Thanks for the speedy updates!
>
> Romesh
>
> 2009/12/22 Jay Larson <jw...@rs...>
>
> Hi Ole,
>>
>> The -lopa' problem is certainly the same.
>>
>> Jay
>>
>> Sent from Jay's BlackBerry®
>> ------------------------------
>> *From: * Ole Nielsen <ole...@gm...>
>> *Date: *Mon, 21 Dec 2009 23:37:01 +1100
>> *To: *Dr. Jay Larson (ANU)<jay...@an...>; Pypar-developers<
>> Pyp...@li...>; Romesh Abeysuriya<
>> rom...@gm...>; Jussi Lehtola<jus...@fe...>
>> *Subject: *Fwd: Problems with pypar & MPICH2
>>
>> Hi guys
>>
>> This sounds like the problem you had?
>>
>> Is this something with recent MPICH versions perhaps?
>>
>> Cheers
>> Ole
>>
>> ---------- Forwarded message ----------
>> From: Jussi Lehtola <jus...@fe...>
>> Date: Mon, Dec 21, 2009 at 11:34 PM
>> Subject: Problems with pypar & MPICH2
>> To: ole...@gm...
>>
>>
>> Hi,
>>
>>
>> I'm trying to add MPICH2 support to the Fedora package of pypar, however
>> the compilation fails with
>>
>> mpicc -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -D_GNU_SOURCE -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
>> -mtune=generic -fPIC -I/usr/include/mpich2-x86_64
>> -I/usr/lib64/python2.6/site-packages/numpy/core/include
>> -I/usr/include/python2.6 -c mpiext.c -o
>> build/temp.linux-x86_64-2.6/mpiext.o -fPIC
>> mpiext.c: In function 'type_map':
>> mpiext.c:127: warning: return makes integer from pointer without a cast
>> mpiext.c: In function 'op_map':
>> mpiext.c:168: warning: return makes integer from pointer without a cast
>> gcc -pthread -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
>> -mtune=generic build/temp.linux-x86_64-2.6/mpiext.o
>> -L/usr/lib64/mpich2/lib -L/usr/lib64 -lmpich -lopa -lpthread -lrt -lopa'
>> -lpython2.6 -o build/lib.linux-x86_64-2.6/pypar/mpiext.so
>> /usr/bin/ld: cannot find -lopa'
>> collect2: ld returned 1 exit status
>>
>> so it seems that an extra ' is picked up somewhere. Do you have any idea
>> where this might come out from?
>>
>> Also, although I've defined CC=mpicc, the file is compiled with gcc..
>>
>> --
>> Jussi Lehtola
>> Fedora Project Contributor
>> jus...@fe...
>>
>>
>>
>
|
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