[petsc-users] Compile petsc using intel mpi
Matthew Knepley
knepley at gmail.com
Thu Nov 29 07:19:35 CST 2018
On Thu, Nov 29, 2018 at 8:17 AM Edoardo alinovi <edoardo.alinovi at gmail.com>
wrote:
> Ok, this makes sense, but the reason to use sudo was this one:
>
sudo rm RDict.log
Matt
> [Errno 13] Permission denied: 'RDict.log'
> File "./config/configure.py", line 391, in petsc_configure
> framework =
> config.framework.Framework(['--configModules=PETSc.Configure','--optionsModule=config.compilerOptions']+sys.argv[1:],
> loadArgDB = 0)
> File
> "/home/edo/software/petsc_intel/config/BuildSystem/config/framework.py",
> line 80, in __init__
> argDB = RDict.RDict(load = loadArgDB)
> File "/home/edo/software/petsc_intel/config/BuildSystem/RDict.py", line
> 90, in __init__
> self.setupLogFile()
> File "/home/edo/software/petsc_intel/config/BuildSystem/RDict.py", line
> 145, in setupLogFile
> self.logFile = file(filename, 'a')
>
> ------
>
> Edoardo Alinovi, Ph.D.
>
> DICCA, Scuola Politecnica,
> Universita' degli Studi di Genova,
> 1, via Montallegro,
> 16145 Genova, Italy
>
>
> Il giorno gio 29 nov 2018 alle ore 14:10 Matthew Knepley <
> knepley at gmail.com> ha scritto:
>
>> On Thu, Nov 29, 2018 at 4:23 AM Edoardo alinovi <
>> edoardo.alinovi at gmail.com> wrote:
>>
>>> Hello guys,
>>>
>>> thank you very much for you suggestions and sorry for getting back you
>>> late. Unfortunately, actually my attempts to compile with intel are not
>>> successful.
>>>
>>> Here my command:
>>>
>>
>> Do NOT sudo the configure. This is really dangerous, and as you see
>> 'root' has a different path than you do. Run configure normally
>> and make, and only use 'sudo' for 'make install'.
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> sudo ./configure --prefix=/home/edo/software/petsc-3.10.2
>>> PETSC_ARCH=arch-intel-opt --with-cc=mpiicc --with-cxx=mpiiccp
>>> --with-fc=mpiifort FOPTFLAGS='-O3' COPTFLAGS='-O3' CXXOPTFLAGS='-O3'
>>> --with-blas-lapack-dir=/home/edo/intel/mkl/lib/intel64/ --with-debugging=no
>>> --download-fblaslapack=1 --download-superlu_dist --download-mumps
>>> --download-hypre --download-metis --download-parmetis
>>>
>>> The log file states that:
>>>
>>> ------------------ LOG ------------------
>>>
>>> TEST checkCCompiler from
>>> config.setCompilers(/home/edo/software/petsc_intel/config/BuildSystem/config/setCompilers.py:587)
>>> TESTING: checkCCompiler from
>>> config.setCompilers(config/BuildSystem/config/setCompilers.py:587)
>>> Locate a functional C compiler
>>> Checking for program /usr/sbin/mpiicc...not found
>>> Checking for program /usr/bin/mpiicc...not found
>>> Checking for program /sbin/mpiicc...not found
>>> Checking for program /bin/mpiicc...not found
>>> Checking for program
>>> /home/edo/software/petsc_intel/lib/petsc/bin/win32fe/mpiicc...not found
>>>
>>> *******************************************************************************
>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log
>>> for details):
>>>
>>> -------------------------------------------------------------------------------
>>> C compiler you provided with -with-cc=mpiicc does not work.
>>>
>>> ------------------------------------
>>>
>>> It seems that petsc is not able to find mpiicc. However, the path to
>>> intel is well defined in my .bashrc and I can easily compile a test file
>>> with those compiler.
>>>
>>> if I put the full path in --with-cc= ... then I get:
>>>
>>> ------------------ LOG ------------------
>>>
>>> TEST checkCCompiler from
>>> config.setCompilers(/home/edo/software/petsc_intel/config/BuildSystem/config/setCompilers.py:587)
>>> TESTING: checkCCompiler from
>>> config.setCompilers(config/BuildSystem/config/setCompilers.py:587)
>>> Locate a functional C compiler
>>> Checking for program
>>> /home/edo/intel/compilers_and_libraries_2019/linux/mpi/intel64/bin/mpiicc...found
>>> Defined make macro "CC" to
>>> "/home/edo/intel/compilers_and_libraries_2019/linux/mpi/intel64/bin/mpiicc"
>>> Pushing language C
>>> All intermediate test results are stored in
>>> /tmp/petsc-ZLGfap
>>> All intermediate test results are stored in
>>> /tmp/petsc-ZLGfap/config.setCompilers
>>> Executing:
>>> /home/edo/intel/compilers_and_libraries_2019/linux/mpi/intel64/bin/mpiicc
>>> -c -o /tmp/petsc-ZLGfap/config.setCompilers/conftest.o
>>> -I/tmp/petsc-ZLGfap/config.setCompilers
>>> /tmp/petsc-ZLGfap/config.setCompilers/conftest.c
>>> Possible ERROR while running compiler: exit code 32512
>>> stderr:
>>> /home/edo/intel/compilers_and_libraries_2019/linux/mpi/intel64/bin/mpiicc:
>>> line 557: icc: command not found
>>> Source:
>>> #include "confdefs.h"
>>> #include "conffix.h"
>>>
>>> int main() {
>>> ;
>>> return 0;
>>> }
>>> Popping language C
>>> Error testing C compiler: Cannot compile C with
>>> /home/edo/intel/compilers_and_libraries_2019/linux/mpi/intel64/bin/mpiicc.
>>> Deleting "CC"
>>>
>>> ------------------------------------
>>>
>>> Do you see any error in my setup?
>>>
>>> Thank you very much!
>>>
>>> ------
>>>
>>> Edoardo Alinovi, Ph.D.
>>>
>>> DICCA, Scuola Politecnica,
>>> Universita' degli Studi di Genova,
>>> 1, via Montallegro,
>>> 16145 Genova, Italy
>>>
>>>
>>> Il giorno mar 27 nov 2018 alle ore 17:16 Matthew Knepley <
>>> knepley at gmail.com> ha scritto:
>>>
>>>> On Tue, Nov 27, 2018 at 6:25 AM Edoardo alinovi via petsc-users <
>>>> petsc-users at mcs.anl.gov> wrote:
>>>>
>>>>> Dear users,
>>>>>
>>>>> I have installed intel parallel studio on my workstation and thus I
>>>>> would like to take advantage of intel compiler.
>>>>>
>>>>> Before messing up my installation, have you got some guidelines to
>>>>> survive at this attempt? I have found here in the mailing list the
>>>>> following instructions:
>>>>>
>>>>> --with-cc=icc --with-fc=ifort --with-mpi-include=/path-to-intel
>>>>> --with-mpi-lib=/path-to-intel
>>>>>
>>>>
>>>> Yes, this looks right.
>>>>
>>>>
>>>>> Are they correct?
>>>>>
>>>>> Also I have an already existing and clean installation of petsc using
>>>>> openmpi. I would like to retain this installtion since it is working very
>>>>> well and switching between the two somehow. Any tips on this?
>>>>>
>>>>
>>>> When you do the Intel configuration, use a different name like
>>>> --PETSC_ARCH=arch-intelps-opt
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> I will never stop to say thank you for your precious support!
>>>>>
>>>>> Edoardo
>>>>>
>>>>> ------
>>>>>
>>>>> Edoardo Alinovi, Ph.D.
>>>>>
>>>>> DICCA, Scuola Politecnica,
>>>>> Universita' degli Studi di Genova,
>>>>> 1, via Montallegro,
>>>>> 16145 Genova, Italy
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>> https://www.cse.buffalo.edu/~knepley/
>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>
>>>
>>
>> --
>> 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
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>
--
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
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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