Re: [moose-generic] MOOSE_installation_problem

[Vadim A. <ast...@nc...>]

Hi.
Our python is GCC not intell
Only numpy was intell but we now install new numpy compiled by gnu. My question is should I add path to this new compiled numpy to your Make file ?
Thanks a lot in advance for clarification.
Vadim.


Subhasis Ray <ray...@gm...> wrote:

>Dear Vadim,
>
> I am not familiar with such cluster environment. But from what I gather on the Internet, it seems that the issue is possibly a mismatch of compilers and libraries. If your default compiler is intel, then loading python before gnu perhaps loads a Python compiled with intel compiler your default. Can you see if changing the order of loading modules helps? i.e.
>
>module load gnu/4.6.1
>module load python
>...
>
>
>Also, you can run `ldd` on generated _moose.so to list the linked libraries and add the paths to the directories containing those libraries to your LD_LIBRARY_PATH environment variable.
>
>hth,
>
>  Subha
>
>
>
>
>
>On Sat, Apr 6, 2013 at 12:35 AM, Vadim A <ast...@nc...> wrote:
>
>Hi,
>
>numpy has been compiled with gnu on our cluster and to access bumpy  we do the following:
>
>module load python
>module load gnu/4.6.1
>export
>PYTHONPATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$PYT
>HONPATH
>
>
>
>Should I also adjust   Makefile for MOOSE  to make sure that proper "numpy" library will be used during compilation step ?
>
>Thanks a lot in advance for information.
>
>Vadim.
>
>
>
>
>
>On Mar 28, 2013, at 2:13 AM, Subhasis Ray wrote:
>
>> First please confirm that Python and numpy were also compiled with gcc.
>>
>> If so, then best option could be to allow somebody from here (niraj or
>> me) to login to your system (via some portal as Amitava mentioned
>> earlier in this thread) and run gdb as we cannot reproduce the error
>> on our system.
>>
>> On 3/28/13, Vadim A <ast...@nc...> wrote:
>>>
>>>
>
>>> On Mar 28, 2013, at 12:15 AM, Subhasis Ray wrote:
>>>
>>>> Hi,
>>>> On 3/28/13, Vadim A <ast...@nc...> wrote:
>>>>> When I compile, I always see lines with g++
>>>>>
>>>>>
>>>>> g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC
>>>>> -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS
>>>>> -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I
>>>>> /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o msg/_msg.o
>>>>> shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>>>>> randnum/_randnum.o
>>>>> scheduling/_scheduling.o builtins/_builtins.o device/_device.o
>>>>> kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o
>>>>> utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o
>>>>> signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64
>>>>> -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl
>>>>> -lgslcblas
>>>>> -lm -o moose
>>>>>
>>>>>
>>>>>
>>>>> That tells me that I am using g++ (which is gcc) but not Intel compiler,
>>>>> right ?
>>>>
>>>> Yes, moose is being compiled by g++
>>>>
>>>>>
>>>>> So, I kind of confused what should I do here.
>>>>>
>>>>
>>>> But what about Python libs? In your previous mail
>>>>
>>>> ----8<----------------->8---
>>>> gdb -c core.8851 /home/diag/opt/python2.7/bin/python
>>>>
>>>> Reading symbols from
>>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no
>>>> debugging symbols found)...done.
>>>> Loaded symbols for
>>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
>>>> Reading symbols from
>>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no
>>>> debugging symbols found)...done.
>>>> Loaded symbols for
>>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
>>>> Reading symbols from
>>>> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging
>>>> symbols found)...done.
>>>> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5
>>>> Reading symbols from
>>>> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no
>>>> debugging symbols found)...done.
>>>> Loaded symbols for
>>>> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so
>>>> Reading symbols from
>>>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done.
>>>> Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0
>>>>
>>>> ----8<----------------->8---
>>>>
>>>> shows that several libraries from intel compiler are being loaded
>>>> before scipy/sparse/sparsetools/_coo.so and libpython2.7.so.
>>>>
>>>> Did you compile Python in
>>>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 and/or numpy/scipy
>>>> from source? In that case, did you use intel compiler to compile them?
>>>>
>>>> Though this could be red herring, I do not see any reason for the
>>>> control to reach basecode/SetGet.h:289. May be a debugging session
>>>> could help.
>>>>
>>>> Best,
>>>>  Subha
>>>>
>>>
>>>
>>
>
>