[petsc-users] How to configure PETSc with gcc-4.9
Justin Dong
jsd1 at rice.edu
Fri Apr 25 01:36:56 CDT 2014
Hi Satish,
Thanks, that installation worked and it's now compiling with gcc-4.9.
However, I'm still having the issue that OpenMP isn't working when I'm
using PETSc in the same code. I'm including this segment at the beginning
of my code:
int nthreads, tid;
#pragma omp parallel private(nthreads, tid)
{
/* Obtain thread number */
tid = omp_get_thread_num();
printf("Hello World from thread = %d\n", tid);
/* Only master thread does this */
if (tid == 0)
{
nthreads = omp_get_num_threads();
printf("Number of threads = %d\n", nthreads);
}
}
I have no problems getting this to run outside of PETSc, with typical
output as follows:
Hello World from thread = 0
Hello World from thread = 1
Hello World from thread = 3
Hello World from thread = 2
Number of threads = 4
But when I include that snippet of code in my larger PETSc code, all I get
is
Hello World from thread = 0
Number of threads = 1
My makefile is just
ALL:
include ${PETSC_DIR}/conf/variables
include ${PETSC_DIR}/conf/rules
include ${PETSC_DIR}/conf/test
main: main.o
-${CLINKER} -fopenmp -o main main.o ${PETSC_LIB}
${RM} -f main.o
I don't get any errors when compiling, as far as I can tell. This is the
output when compiling:
gcc-4.9 -o main.o -c -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
-Wno-unknown-pragmas -g3 -fno-inline -O0
-I/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/include
-I/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/arch-gcc/include
-I/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/include/mpiuni
-D__INSDIR__= main.c
gcc-4.9 -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress
-Wl,-commons,use_dylibs -Wl,-search_paths_first -fPIC -Wall
-Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -fno-inline
-O0 -fopenmp -o main main.o
-L/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/arch-gcc/lib
-L/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/arch-gcc/lib -lpetsc
-llapack -lblas -lpthread
-L/usr/local/lib/gcc/x86_64-apple-darwin13.1.0/4.9.0 -L/usr/local/lib -ldl
-lgfortran -lgfortran -lquadmath -lm -lm -lSystem -lgcc_ext.10.5 -ldl
/bin/rm -f -f main.o
On Fri, Apr 25, 2014 at 12:46 AM, Satish Balay <balay at mcs.anl.gov> wrote:
> if you are primarily intesrested in -fopenmp - and not mpi - just
> configure petsc with --with-mpi=0
>
> If you have currently working build with clang - and would
> like to just compile your code with gcc-4.9 - you can try:
>
> export MPICH_CC=gcc-4.9
> make [your-target]
>
> It might work. Or you might get link errors. [If you get
> errors - its best to rebuild PETSc with gcc-4.9]
>
> BTW: you can use a different PETSC_ARCH for each of your builds - so
> that they don't overwrite each other..
>
> ./configure PETSC_ARCH=arch-gcc --with-cc=gcc-4.9 --with-cxx=0 --with-mpi=0
>
> [on osx petsc can use VecLib so --download-f-blas-lapack shouldn't be
> needed]
>
> Satish
>
> On Fri, 25 Apr 2014, Justin Dong wrote:
>
> > I'll leave it running for a few hours and see what happens.
> >
> > In the meantime, is it possible to tell PETSc to compile a specific .c
> file
> > using gcc-4.9? Something along the lines of this:
> >
> > ALL:
> >
> > include ${PETSC_DIR}/conf/variables
> > include ${PETSC_DIR}/conf/rules
> > include ${PETSC_DIR}/conf/test
> >
> > main: main.o
> > gcc-4.9 -${CLINKER} -fopenmp -o main main.o ${PETSC_LIB}
> > ${RM} -f main.o
> >
> > The main reason I want to compile with gcc-4.9 is because I need to use
> > openmp for a simple parallel for loop. With the gcc compiler I have now
> > (clang), there's no support for openmp. I can get gcc-4.9 to work outside
> > of PETSc, but am not sure how to get it to work here if I want to do it
> for
> > a single example, or if that's even possible.
> >
> >
> > On Thu, Apr 24, 2014 at 10:03 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> >
> > >
> > > Leave it to run for several hours it could be that gcc-4.9 is just
> > > taking a very long time on mpich.
> > >
> > > Barry
> > >
> > > On Apr 24, 2014, at 8:35 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > >
> > > > On Thu, Apr 24, 2014 at 9:27 PM, Justin Dong <jsd1 at rice.edu> wrote:
> > > > Hi all,
> > > >
> > > > I'm trying to configure PETSc on Mac OS X with gcc-4.9. Currently,
> it's
> > > configured with gcc that comes with Xcode, but I want to use gcc-4.9
> that I
> > > installed myself. I try:
> > > >
> > > >
> > > > ./configure --with-cc=gcc-4.9 --with-fc=gfortran
> > > --download-f-blas-lapack --download-mpich
> > > >
> > > >
> > > >
> > > > But while configuring MPICH it gets stuck indefinitely. I've included
> > > the output below after I terminate the process. I don't have this
> issue if
> > > I just configure with cc=gcc. Any ideas what the problem is here?
> > > >
> > > > From the stack trace, its just taking a long time. If it overruns the
> > > timeout, it should just die. You can try
> > > > running using -useThreads=0 if you suspect the timeout is not
> working.
> > > >
> > > > Matt
> > > >
> > > > ^CTraceback (most recent call last):
> > > >
> > > > File "./configure", line 10, in <module>
> > > >
> > > > execfile(os.path.join(os.path.dirname(__file__), 'config',
> > > 'configure.py'))
> > > >
> > > > File "./config/configure.py", line 372, in <module>
> > > >
> > > > petsc_configure([])
> > > >
> > > > File "./config/configure.py", line 287, in petsc_configure
> > > >
> > > > framework.configure(out = sys.stdout)
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/framework.py",
> > > line 933, in configure
> > > >
> > > > child.configure()
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py",
> > > line 558, in configure
> > > >
> > > > self.executeTest(self.configureLibrary)
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/base.py",
> > > line 115, in executeTest
> > > >
> > > > ret = apply(test, args,kargs)
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/packages/MPI.py",
> > > line 748, in configureLibrary
> > > >
> > > > config.package.Package.configureLibrary(self)
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py",
> > > line 486, in configureLibrary
> > > >
> > > > for location, directory, lib, incl in self.generateGuesses():
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py",
> > > line 232, in generateGuesses
> > > >
> > > > d = self.checkDownload(1)
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/packages/MPI.py",
> > > line 351, in checkDownload
> > > >
> > > > return config.package.Package.checkDownload(self,
> requireDownload)
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py",
> > > line 340, in checkDownload
> > > >
> > > > return self.getInstallDir()
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/package.py",
> > > line 187, in getInstallDir
> > > >
> > > > return os.path.abspath(self.Install())
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/packages/MPI.py",
> > > line 366, in Install
> > > >
> > > > return self.InstallMPICH()
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/config/packages/MPI.py",
> > > line 544, in InstallMPICH
> > > >
> > > > output,err,ret = config.base.Configure.executeShellCommand('cd
> > > '+mpichDir+' && ./configure '+args, timeout=2000, log =
> self.framework.log)
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/script.py",
> > > line 254, in executeShellCommand
> > > >
> > > > (output, error, status) = runInShell(command, log, cwd)
> > > >
> > > > File
> > >
> "/Users/justindong/Classes/CAAMResearch/petsc-3.4.4/config/BuildSystem/script.py",
> > > line 243, in runInShell
> > > >
> > > > thread.join(timeout)
> > > >
> > > > File
> > >
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py",
> > > line 958, in join
> > > >
> > > > self.__block.wait(delay)
> > > >
> > > > File
> > >
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py",
> > > line 358, in wait
> > > >
> > > > _sleep(delay)
> > > >
> > > >
> > > > KeyboardInterrupt
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Sincerely,
> > > >
> > > > Justin
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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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