[petsc-users] petsc+chombo

[Satish Balay]

On Thu, 1 Oct 2015, Barry Smith wrote:

> 
> > On Oct 1, 2015, at 10:44 AM, Satish Balay <balay at mcs.anl.gov> wrote:
> > 
> > Hm - we usually try to avoiding creating binaries in externalpackages
> > [if not needed] - esp the examples/tests.
> > 
> > So perhaps chombo shoul have the following change.
> 
>  Satish,
> 
>   Looks good to me, push if it works for you.

pushed to maint [and merged to master]

Satish

> 
>    Barry
> 
> > 
> > Satish
> > 
> > ------
> > diff --git a/config/BuildSystem/config/packages/Chombo.py b/config/BuildSystem/config/packages/Chombo.py
> > index effbca6..7a13b0a 100644
> > --- a/config/BuildSystem/config/packages/Chombo.py
> > +++ b/config/BuildSystem/config/packages/Chombo.py
> > @@ -110,7 +110,7 @@ class Configure(config.package.Package):
> >           raise RuntimeError('Error running make on Chombo: config value not found')
> >         config_value=poutput.split('=')[1]
> >         self.logPrint('Chombo installed using config=%s\n'%config_value)
> > -        output,err,ret = config.package.Package.executeShellCommand('cd '+os.path.join(self.packageDir,'lib') +' && make clean && make all', timeout=2500, log = self.log)
> > +        output,err,ret = config.package.Package.executeShellCommand('cd '+os.path.join(self.packageDir,'lib') +' && make clean && make lib', timeout=2500, log = self.log)
> >         output,err,ret = config.package.Package.executeShellCommand('cd '+self.packageDir+self.installSudo+'&& cp -f lib/lib*.'+self.setCompilers.AR_LIB_SUFFIX+' '+os.path.join(self.installDir,self.libdir,'')+' &&  '+self.installSudo+'cp -f lib/include/*.H '+os.path.join(self.installDir,self.includedir,''), timeout=2500, log = self.log)
> >       except RuntimeError, e:
> >         raise RuntimeError('Error running make on Chombo: '+str(e))
> > 
> > On Thu, 1 Oct 2015, Barry Smith wrote:
> > 
> >> 
> >>  We absolutely NEED configure.log to help you.
> >> 
> >>  Barry
> >> 
> >>> On Oct 1, 2015, at 9:24 AM, Juha Jaykka <juhaj at iki.fi> wrote:
> >>> 
> >>> Hi list,
> >>> 
> >>> I'm trying to compile PETSc 3.6 with --download-chombo, but keep failing. It 
> >>> seems to me the chombo build system is not told to link in libgfortran.so, but 
> >>> no matter how I try to convince PETSc to add that, it won't. How should this 
> >>> be used, please?
> >>> 
> >>> The full configure line is
> >>> 
> >>> ./configure --prefix=/home/juhaj/progs+3.6/petsc --with-shared-libraries --
> >>> with-debugging=0 \
> >>>         --useThreads 0 --with-clanguage=C++ --with-c-support \
> >>>         --with-fortran-interfaces=1 \
> >>>         --with-mpi=1 --with-mpi-shared=1 \
> >>> 	  --with-blas-lapack-include=/usr/include/openblas --with-blas-
> >>> lib=/usr/lib/openblas-base/libblas.so --with-lapack-lib=/usr/lib/openblas-
> >>> base/liblapack.so \
> >>>         --with-scalapack=1 --with-scalapack-include=/usr/include \
> >>>         --with-scalapack-lib=/usr/lib/libscalapack-openmpi.so \
> >>>         --with-mumps=0 \
> >>> 	  --with-suitesparse=0 \
> >>>         --with-spooles=1 --with-spooles-include=/usr/include/spooles \
> >>>         --with-spooles-lib=/usr/lib/libspooles.so \
> >>>         --with-hypre=1 --with-hypre-include=/usr/include --with-hypre-
> >>> lib=/usr/lib/libHYPRE_IJ_mv-2.8.0b.so \
> >>>         --with-fftw=1 --with-fftw-include=/usr/include \
> >>>         --with-fftw-lib=[/usr/lib/x86_64-linux-
> >>> gnu/libfftw3.so,/usr/lib/x86_64-linux-gnu/libfftw3_mpi.so] \
> >>>         --with-hdf5=1 --with-hdf5-include=/usr/include/hdf5/openmpi --with-
> >>> hdf5-lib=/usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so \
> >>> 	  --CXX_LINKER_FLAGS="-Wl,--no-as-needed -lgfortran" --LDFLAGS="-
> >>> lgfortran -g" --LIBS="-lgfortran" \
> >>> 	  --with-clean=1 --with-memalign=64 --with-log=0 --with-valgrind=1 \
> >>> 	  --with-afterimage=1 --with-afterimage-
> >>> include=/usr/include/libAfterImage --with-afterimage-lib=/usr/lib/x86_64-
> >>> linux-gnu/libAfterImage.so \
> >>> 	  --with-boost=1 \
> >>> 	  --with-netcdf=1 --with-netcdf-include=/usr/include/ --with-netcdf-
> >>> lib=/usr/lib/libnetcdf.so \
> >>> 	  --with-triangle=0 \
> >>> 	  --with-numpy=1 \
> >>> 	  --with-hwloc=1  --with-external-packages-
> >>> dir=/home/juhaj/progs+3.6/automatic-downloads \
> >>> 	  --with-parmetis=0 --with-metis=0 \
> >>> 	  --with-tetgen=0 \
> >>> 	  --with-scalar-type=real --with-pic=1 --with-gnu-compilers=1 --with-
> >>> openmp=1 \
> >>> 	  --with-64-bit-indices \
> >>> 	  --download-chombo
> >>> 
> >>> and the final error in configure is
> >>> 
> >>> /bin/csh -f -c "mpicxx -g          
> >>> o/2d.Linux.64.mpicxx.mpif90.DEBUG/testFourthOrderFillPatch.o   -
> >>> L/home/juhaj/progs+3.6/automatic-downloads/arch-linux2-cxx-
> >>> opt/Chombo/lib/test/AMRTimeDependent/../.. -
> >>> lamrtimedependent2d.Linux.64.mpicxx.mpif90.DEBUG -
> >>> lamrtools2d.Linux.64.mpicxx.mpif90.DEBUG -
> >>> lboxtools2d.Linux.64.mpicxx.mpif90.DEBUG -
> >>> lbasetools2d.Linux.64.mpicxx.mpif90.DEBUG  -Wl,-rpath,/usr/lib/x86_64-linux-
> >>> gnu -L/usr/lib/x86_64-linux-gnu -lhdf5_openmpi     -Wl,-
> >>> rpath,/usr/lib/openblas-base -L/usr/lib/openblas-base -llapack -Wl,-
> >>> rpath,/usr/lib/openblas-base -L/usr/lib/openblas-base -lblas  -o 
> >>> testFourthOrderFillPatch2d.Linux.64.mpicxx.mpif90.DEBUG.ex |&  awk -f 
> >>> /home/juhaj/progs+3.6/automatic-downloads/arch-linux2-cxx-
> >>> opt/Chombo/lib/test/AMRTimeDependent/../../mk/tempnam.awk"
> >>> /usr/bin/ld: /home/juhaj/progs+3.6/automatic-downloads/arch-linux2-cxx-
> >>> opt/Chombo/lib/test/AMRTimeDependent/../../libamrtools2d.Linux.64.mpicxx.mpif90.DEBUG.a(CFLeastSquares.o): 
> >>> undefined reference to symbol '_gfortran_transfer_integer_write@@GFORTRAN_1.4'
> >>> /usr/lib/x86_64-linux-gnu/libgfortran.so.3: error adding symbols: DSO missing 
> >>> from command line
> >>> collect2: error: ld returned 1 exit status
> >>> 
> >>> 
> >>> 
> >>> Cheers,
> >>> Juha
> >> 
> >> 
> > 
> 
>