[petsc-users] compile petsc with intel compiler
Satish Balay
balay at mcs.anl.gov
Wed Jul 10 10:12:05 CDT 2013
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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