[petsc-users] compile petsc with intel compiler
Klaus Zimmermann
klaus.zimmermann at physik.uni-freiburg.de
Wed Jul 10 10:50:38 CDT 2013
Hi Michael,
for what it's worth, I have built petsc 3.1 and 3.2 with the intel
compiler. It went smoothly ones I had the mpi environment set up. Your
output looks to me like your mpicc and/or mpiicc is still calling gcc.
Could you confirm your mpicc actually calls icc by looking at
mpicc --version
?
Best
Klaus
Am 10.07.2013 17:14, schrieb Michael Povolotskyi:
> Everything was installed by synaptic that calls dpkg.
> I'm reconfiguring and will let you know.
> Michael.
>
>
> On 07/10/2013 11:12 AM, Satish Balay wrote:
>> Hm - thats wierd. Was it installed by dpkg or something else?
>> On my ubuntu 12.04 box - I get:
>>
>> balay at petsc^~ $ locate bits/c++config.h
>> /usr/include/c++/4.4/x86_64-linux-gnu/32/bits/c++config.h
>> /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h
>> /usr/include/c++/4.6/x86_64-linux-gnu/32/bits/c++config.h
>> /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h
>>
>>
>> You can try specifing the include path with CXXCPPFLAGS [for the c++
>> compiler]
>>
>> Satish
>>
>> On Wed, 10 Jul 2013, Michael Povolotskyi wrote:
>>
>>> 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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