[petsc-users] Compile petsc using intel mpi

Edoardo alinovi edoardo.alinovi at gmail.com
Thu Nov 29 07:07:00 CST 2018 

Ok, this makes sense, but the reason to use sudo was this one:

[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/>
>
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