[petsc-users] compile petsc with intel compiler
Satish Balay
balay at mcs.anl.gov
Wed Jul 10 09:41:01 CDT 2013
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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