[petsc-users] compile petsc with intel compiler
Michael Povolotskyi
mpovolot at purdue.edu
Wed Jul 10 10:05:11 CDT 2013
Hi Satish,
it looks like I have this file but not in "standard" location:
locate bits/c++config.h
/usr/include/x86_64-linux-gnu/c++/4.7/bits/c++config.h
/usr/share/gccxml-0.9/GCC/4.4/bits/c++config.h
/usr/share/gccxml-0.9/GCC/4.6/bits/c++config.h
/usr/share/gccxml-0.9/GCC/4.7/bits/c++config.h
Should I try to add -I usr/include/x86_64-linux-gnu/c++/4.7/ to the CPPLAGS?
Michael.
On 07/10/2013 10:41 AM, Satish Balay wrote:
> Perhaps stuff is not installed correctly on this machine?
>
> [petsc:~] petsc> dpkg -S /usr/include/c++/4.6/bits/stl_algobase.h
> libstdc++6-4.6-dev: /usr/include/c++/4.6/bits/stl_algobase.h
> [petsc:~] petsc> dpkg -S /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h
> libstdc++6-4.6-dev: /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h
> [petsc:~] petsc>
>
>
> So both bits/stl_algobase.h and bits/c++config.h are installed by libstdc++ package.
>
> What do you have for:
>
> ls /usr/include/c++/4.7/bits/stl_algobase.h
> ls /usr/include/c++/4.7/x86_64-linux-gnu/bits/c++config.h
> dpkg -S /usr/include/c++/4.7/bits/stl_algobase.h
> dpkg -S /usr/include/c++/4.7/x86_64-linux-gnu/bits/c++config.h
>
> [perhaps the files exist - but the intel compiler is not finding it?]
>
> Satish
>
>
> On Wed, 10 Jul 2013, Michael Povolotskyi wrote:
>
>> Thank you Matt.
>> Unfortunately 'make all-legacy' gives the same error:
>> =========================================
>> libfast in: /home/mpovolot/Code_intel/libs/petsc/build-real/src
>> libfast in: /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys
>> libfast in: /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/classes
>> libfast in:
>> /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/classes/viewer
>> libfast in:
>> /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/classes/viewer/impls
>> libfast in:
>> /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/classes/viewer/impls/socket
>> /usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic error: cannot open
>> source file "bits/c++config.h"
>> #include <bits/c++config.h>
>> ^
>>
>> compilation aborted for send.c (code 4)
>>
>>
>>
>> Michael.
>>
>> On 07/10/2013 08:05 AM, Matthew Knepley wrote:
>>> On Wed, Jul 10, 2013 at 12:00 AM, Michael Povolotskyi <mpovolot at purdue.edu
>>> <mailto:mpovolot at purdue.edu>> wrote:
>>>
>>> Hello everybody,
>>> unfortunately building petsc without fortran cannot work for me
>>> because I need MUMPs that requires Scalapack that needs fortran. I
>>> played with the options. As result the configuration runs okay,
>>> the build gives an error that does not seem to be related to fortran:
>>>
>>>
>>> Quit building with CMake. It complicates everything. Use the legacy build.
>>>
>>> Matt
>>>
>>> [ 0%] Building CXX object
>>> CMakeFiles/petscsys.dir/src/sys/totalview/tv_data_display.c.o
>>> Building Fortran object
>>> CMakeFiles/petscsys.dir/src/sys/f90-mod/petscsysmod.F.o
>>> Building CXX object
>>> CMakeFiles/petscsys.dir/src/sys/python/pythonsys.c.o
>>> [ 0%] /usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic
>>> error: cannot open source file "bits/c++config.h"
>>> #include <bits/c++config.h>
>>> ^
>>>
>>> /usr/include/c++/4.7/bits/stl_algobase.h(60): catastrophic error:
>>> cannot open source file "bits/c++config.h"
>>> #include <bits/c++config.h>
>>> ^
>>>
>>> compilation aborted for
>>> /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/info/verboseinfo.c
>>> (code 4)
>>> compilation aborted for
>>> /home/mpovolot/Code_intel/libs/petsc/build-real/src/sys/logging/plog.c
>>> (code 4)
>>>
>>> I attach here the log files.
>>> Any advise is highly appreciated.
>>> Michael.
>>>
>>> On 7/9/2013 4:34 PM, Matthew Knepley wrote:
>>>> On Tue, Jul 9, 2013 at 3:32 PM, Michael Povolotskyi
>>>> <mpovolot at purdue.edu <mailto:mpovolot at purdue.edu>> wrote:
>>>>
>>>> If I do not need to use petsc in fortran programs, can I
>>>> build petsc without fortran and thus avoid this situation?
>>>> Michael.
>>>>
>>>>
>>>> On 07/09/2013 04:31 PM, Satish Balay wrote:
>>>>
>>>> For some reason this issue comes up with mpi.mod provided
>>>> by intel
>>>> mpi.
>>>>
>>>> We have a configure test for it - but looks like its not
>>>> sufficient to
>>>> catch this issue.
>>>>
>>>> satish
>>>>
>>>>
>>>> On Tue, 9 Jul 2013, Matthew Knepley wrote:
>>>>
>>>> On Tue, Jul 9, 2013 at 3:11 PM, Michael Povolotskyi
>>>> <mpovolot at purdue.edu <mailto:mpovolot at purdue.edu>>wrote:
>>>>
>>>> Dear Petsc users and developers,
>>>> I'm trying to build petsc with Intel compiler.
>>>>
>>>> 1) First, ask yourself whether you really want to
>>>> build with the Intel
>>>> compiler. Then ask again.
>>>>
>>>> 2) Do you need Fortran? If not, turn it off --with-fc=0.
>>>>
>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>>>
>>>> Matt
>>>>
>>>> 3) If you want Fortran and Intel (and have a hatred
>>>> of free time), try the
>>>> legacy build
>>>>
>>>> make all-legacy
>>>>
>>>> 4) If this is still broken, send the new make.log
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>> The configuration process runs okay (I attach the
>>>> log here),
>>>> but I get an error when I build it:
>>>> -- Configuring done
>>>> -- Generating done
>>>> -- Build files have been written to:
>>>> /home/mpovolot/Code_intel/**
>>>> libs/petsc/build-real/linux
>>>> Scanning dependencies of target petscsys
>>>> [ 0%] [ 0%] [ 0%] Building CXX object
>>>> CMakeFiles/petscsys.dir/src/**
>>>> sys/info/verboseinfo.c.o
>>>> Building Fortran object
>>>> CMakeFiles/petscsys.dir/src/**
>>>> sys/f90-mod/petscsysmod.F.o
>>>> Building CXX object CMakeFiles/petscsys.dir/src/**
>>>> sys/totalview/tv_data_display.**c.o
>>>> Building CXX object
>>>> CMakeFiles/petscsys.dir/src/**sys/python/pythonsys.c.o
>>>> Building CXX object
>>>> CMakeFiles/petscsys.dir/src/**sys/logging/plog.c.o
>>>> /home/mpovolot/Code_intel/**libs/petsc/build-real/src/sys/**
>>>> f90-mod/petscsysmod.F:6.11:
>>>>
>>>> use mpi
>>>> 1
>>>> Fatal Error: File 'mpi.mod' opened at (1) is not
>>>> a GFORTRAN module file
>>>> make[6]: ***
>>>> [CMakeFiles/petscsys.dir/src/**sys/f90-mod/petscsysmod.F.o]
>>>> Error 1
>>>> make[6]: *** Waiting for unfinished jobs....
>>>> make[5]: *** [CMakeFiles/petscsys.dir/all] Error 2
>>>> make[4]: *** [all] Error 2
>>>> make[3]: *** [ccmake] Error 2
>>>> make[2]: *** [cmake] Error 2
>>>> ****************************ERROR**************************************
>>>> Error during compile, check linux/conf/make.log
>>>> Send it and linux/conf/configure.log to
>>>> petsc-maint at mcs.anl.gov
>>>> <mailto:petsc-maint at mcs.anl.gov>
>>>> ************************************************************************
>>>>
>>>> I attach here the make.log
>>>> What is strange to me that it has something to do
>>>> with Gfortran, while I
>>>> want to build everything with Intel.
>>>> Thank you for help,
>>>> Michael.
>>>>
>>>> --
>>>> Michael Povolotskyi, PhD
>>>> Research Assistant Professor
>>>> Network for Computational Nanotechnology
>>>> 207 S Martin Jischke Drive
>>>> Purdue University, DLR, room 441-10
>>>> West Lafayette, Indiana 47907
>>>>
>>>> phone: +1-765-494-9396 <tel:%2B1-765-494-9396>
>>>> fax: +1-765-496-6026 <tel:%2B1-765-496-6026>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -- What most experimenters take for granted before they begin
>>>> their
>>>> experiments is infinitely more interesting than any results to
>>>> which their experiments lead.
>>>> -- Norbert Wiener
>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their experiments
>>> is infinitely more interesting than any results to which their experiments
>>> lead.
>>> -- Norbert Wiener
>>
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