[petsc-users] petsc+chombo

[Barry Smith]

  I think Satish already told you the fix. Please let us know if it does not work.

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

------
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 Oct 2, 2015, at 4:38 AM, Juha Jaykka <juhaj at iki.fi> wrote:
> 
> Dear Barry,
> 
> Please find the configure.log at http://www.iki.fi/~juhaj/configure.log.
> 
> On a more general level, I wonder if the chombo-petsc interoperability is 
> documented anywhere? I grepped through the examples and came up blank.
> 
> Cheers,
> Juha
> 
> On Thursday 01 Oct 2015 09:53:26 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.m
>>> pif90.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