[petsc-users] Modifying built files for use with Japan's K computer
TAY wee-beng
zonexo at gmail.com
Sun Apr 24 21:31:46 CDT 2016
On 25/4/2016 2:52 AM, Matthew Knepley wrote:
> On Sun, Apr 24, 2016 at 10:12 AM, Wee-beng TAY <zonexo at gmail.com
> <mailto:zonexo at gmail.com>> wrote:
>
> Hi Matt,
>
> I have attached the page which explains what to modify to use
> PETSc with the K computer.
>
> These changes are now in knepley/feature-configure-kcomputer, so you
>
> cd $PETSC_DIR
> git fetch
> git checkout knepley/feature-configure-kcomputer
> <follow configure instructions from your email>
Hi,
I got the warning and error:
" --LD_SHARED="" --LDDFLAGS="" --with-openmp=1 --with-mpiexec=mpiexec
--known-endian=big --with-shared-libraries=0
--with-blas-lapack-lib="-SSL2" --with-scalapack-lib="-SCALAPACK"
--prefix=/home/hp150306/t00196/lib/petsc-3.6.4_rel
--with-fortran-interfaces=1 --download-hypre=1 --with-debugging=0
--with-batch=1
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
===============================================================================
*****WARNING: PETSC_DIR appears to be a Git clone - but git is not found
in PATH********
===============================================================================
TESTING: checkCCompiler from
config.setCompilers(config/BuildSystem/config/setCompilers.py:553)
Exception AttributeError: AttributeError("Popen3 instance has no
attribute 'pid'",) in <bound method Popen3.__del__ of <popen2.Popen3
instance at 0x107bbf38>> ignored
*******************************************************************************
UNABLE to EXECUTE BINARIES for ./configure
-------------------------------------------------------------------------------
[Errno 12] Cannot allocate memory
*******************************************************************************
Any other solution?
Thanks!
>
> Thanks,
>
> Matt
>
> Thanks
>
>
>
> On 24/4/2016 10:52 PM, Matthew Knepley wrote:
>> On Sun, Apr 24, 2016 at 4:14 AM, Wee-beng TAY <zonexo at gmail.com
>> <mailto:zonexo at gmail.com>> wrote:
>>
>> Hi,
>>
>> I was recently given access to Japan's K computer. I'm trying
>> to compile PETSc on their sys, which uses Fujitsu's compiler.
>> There's a help file but it's in Japanese. I guess I need to
>> change some options to make PETSc compile with Fujitsu's
>> compiler.
>>
>> It looks like they want us to include some different options for
>> the build. If you send what you want,
>> I will make a branch for you to try out.
>>
>> Thanks,
>>
>> Matt
>>
>> Part of the help is below. So how should I use the diff or
>> some other command to do the correction? I tried to run:
>>
>> diff -u petsc-3.6.4/config/BuildSystem/config/package.py.org
>> <http://package.py.org>
>> petsc-3.6.4/config/BuildSystem/config/package.py
>>
>> but got the err:
>>
>> diff: petsc-3.6.4/config/BuildSystem/config/package.py.org
>> <http://package.py.org>: No such file or directory
>>
>> Please advice. Thanks.
>>
>>
>> /|$ diff -u
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/|//|package|//|.py.org
>> <http://py.org>
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/|//|package|//|.py|/
>> /|---
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/|//|package|//|.py.org
>> <http://py.org>
>> |//|2015|//|-|//|12|//|-|//|04|////|14|//|:|//|06|//|:|//|42.000000000|////|+|//|0900|/
>> /|+++
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/|//|package|//|.py
>> |//|2016|//|-|//|01|//|-|//|22|////|11|//|:|//|09|//|:|//|37.000000000|////|+|//|0900|/
>> /|@@ -|//|174|//|,|//|7|////|+|//|174|//|,|//|7|////|@@|/
>> /||//|return|////|''|/
>> //
>> /||//|def getSharedFlag(self,cflags):|/
>> /|- |//|for|////|flag in
>> [|//|'-PIC'|//|,|//|'-fPIC'|//|,|//|'-KPIC'|//|,|//|'-qpic'|//|]:|/
>> /|+ |//|for|////|flag in
>> [|//|'-KPIC'|//|,|//|'-fPIC'|//|,|//|'-PIC'|//|,|//|'-qpic'|//|]:|/
>> /||//|if|////|cflags.find(flag)
>> >=|//|0|//|:|//|return|////|flag|/
>> /||//|return|////|''|/
>> /||/
>> /|$ diff -u
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/setCompilers.py.org
>> <http://setCompilers.py.org>
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/setCompilers.py|/
>> /|---
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/setCompilers.py.org
>> <http://setCompilers.py.org>
>> |//|2015|//|-|//|07|//|-|//|23|////|00|//|:|//|22|//|:|//|46.000000000|////|+|//|0900|/
>> /|+++
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/setCompilers.py
>> |//|2016|//|-|//|01|//|-|//|22|////|11|//|:|//|10|//|:|//|05.000000000|////|+|//|0900|/
>> /|@@ -|//|1017|//|,|//|7|////|+|//|1017|//|,|//|7|////|@@|/
>> /||//|self.pushLanguage(language)|/
>> /||//|#different compilers are sensitive to the order of
>> testing these flags. So separete out GCC test.|/
>> /||//|if|////|config.setCompilers.Configure.isGNU(self.getCompiler()):
>> testFlags = [|//|'-fPIC'|//|]|/
>> /|- |//|else|//|: testFlags =
>> [|//|'-PIC'|//|,|//|'-fPIC'|//|,|//|'-KPIC'|//|,|//|'-qpic'|//|]|/
>> /|+ |//|else|//|: testFlags =
>> [|//|'-KPIC'|//|,|//|'-fPIC'|//|,|//|'-PIC'|//|,|//|'-qpic'|//|]|/
>> /||//|for|////|testFlag in testFlags:|/
>> /||//|try|//|:|/
>> /||//|self.logPrint(|//|'Trying '|//|+language+|//|' compiler
>> flag '|//|+testFlag)|/
>> /|$ diff -u
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/packages/openmp.py.org
>> <http://openmp.py.org>
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/packages/openmp.py|/
>> /|---
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/packages/openmp.py.org
>> <http://openmp.py.org>
>> |//|2016|//|-|//|01|//|-|//|25|////|15|//|:|//|42|//|:|//|23.000000000|//|+|//|0900|/
>> /|+++
>> petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/packages/openmp.py
>> |//|2016|//|-|//|01|//|-|//|22|////|17|//|:|//|13|//|:|//|52.000000000|////|+|//|0900|/
>> /|@@ -|//|19|//|,|//|7|////|+|//|19|//|,|//|8|////|@@|/
>> /||//|self.found =|//|0|/
>> /||//|self.setCompilers.pushLanguage(|//|'C'|//|)|/
>> /||//|#|/
>> /|- |//|for|////|flag in [|//|"-fopenmp"|//|, # Gnu|/
>> /|+ |//|for|////|flag in [|//|"-Kopenmp"|//|, # Fujitsu|/
>> /|+ |//|"-fopenmp"|//|, # Gnu|/
>> /||//|"-qsmp=omp"|//|,# IBM XL C/C++|/
>> /||//|"-h omp"|//|, # Cray. Must come after XL because XL
>> interprets|//|this|////|option as meaning|//|"-soname omp"|/
>> /||//|"-mp"|//|, # Portland Group|/
>> //
>> /|$ diff -u
>> ./petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/compilers.py.org
>> <http://compilers.py.org>
>> ./petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/compilers.py|/
>> /|---
>> ./petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/compilers.py.org
>> <http://compilers.py.org>
>> |//|2015|//|-|//|06|//|-|//|10|////|06|//|:|//|24|//|:|//|49.000000000|////|+|//|0900|/
>> /|+++
>> ./petsc-|//|3.6|//|.|//|3|//|/config/BuildSystem/config/compilers.py
>> |//|2016|//|-|//|02|//|-|//|19|////|11|//|:|//|56|//|:|//|12.000000000|////|+|//|0900|/
>> /|@@ -|//|164|//|,|//|7|////|+|//|164|//|,|//|7|////|@@|/
>> /||//|def checkCLibraries(self):|/
>> /||//|''|//|'Determines the libraries needed to link with
>> C'|//|''|/
>> /||//|oldFlags = self.setCompilers.LDFLAGS|/
>> /|- self.setCompilers.LDFLAGS +=|//|' -v'|/
>> /|+ self.setCompilers.LDFLAGS +=|//|' -###'|/
>> /||//|self.pushLanguage(|//|'C'|//|)|/
>> /||//|(output, returnCode) =
>> self.outputLink(|//|''|//|,|//|''|//|)|/
>> /||//|self.setCompilers.LDFLAGS = oldFlags|/
>> /|@@ -|//|413|//|,|//|7|////|+|//|413|//|,|//|7|////|@@|/
>> /||//|def checkCxxLibraries(self):|/
>> /||//|''|//|'Determines the libraries needed to link with
>> C++'|//|''|/
>> /||//|oldFlags = self.setCompilers.LDFLAGS|/
>> /|- self.setCompilers.LDFLAGS +=|//|' -v'|/
>> /|+ self.setCompilers.LDFLAGS +=|//|' -###'|/
>> /||//|self.pushLanguage(|//|'Cxx'|//|)|/
>> /||//|(output, returnCode) =
>> self.outputLink(|//|''|//|,|//|''|//|)|/
>> /||//|self.setCompilers.LDFLAGS = oldFlags|/
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> 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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