[petsc-users] petsc+chombo

Discussion:

Juha Jaykka

2015-10-01 14:24:14 UTC

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

Barry Smith

2015-10-01 14:53:26 UTC

Permalink

We absolutely NEED configure.log to help you.

Barry

Post by Juha Jaykka
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-
/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

Satish Balay

2015-10-01 15:44:12 UTC

Permalink

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))

Post by Barry Smith
We absolutely NEED configure.log to help you.
Barry

Barry Smith

2015-10-01 18:39:34 UTC

Permalink

Post by Satish Balay
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.

Barry

Post by Satish Balay
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
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)
raise RuntimeError('Error running make on Chombo: '+str(e))

Post by Barry Smith
We absolutely NEED configure.log to help you.
Barry

Satish Balay

2015-10-01 18:46:02 UTC

Permalink

Post by Barry Smith

Post by Satish Balay
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

Post by Barry Smith
Barry

Post by Barry Smith
We absolutely NEED configure.log to help you.
Barry

Juha Jaykka

2015-10-02 09:38:56 UTC

Permalink

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

Post by Barry Smith
We absolutely NEED configure.log to help you.
Barry

Post by Juha Jaykka
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
/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

Barry Smith

2015-10-02 18:23:40 UTC

Permalink

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))

Post by Juha Jaykka
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

Post by Barry Smith
We absolutely NEED configure.log to help you.
Barry

Post by Juha Jaykka
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
/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

Juha Jäykkä

2015-10-02 21:03:55 UTC

Permalink

I'm sure that fixes it, but I would have hoped there is a proper way of just
configuring and making PETSc with --download-chombo. I.e. without patching
PETSc first. If there is no such way, I'm happy to apply the patch, but it is
really a last resort for 3.6; for > 3.6 it would of course be fine as it could
be released with the patch applied.

Cheers,
Juha

Post by 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
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,''),
raise RuntimeError('Error running make on Chombo: '+str(e))

Post by Barry Smith
We absolutely NEED configure.log to help you.
Barry

Post by Juha Jaykka
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
/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

--
-----------------------------------------------
| Juha Jäykkä, ***@iki.fi |
| http://koti.kapsi.fi/~juhaj/ |
-----------------------------------------------

Barry Smith

2015-10-02 21:14:02 UTC

Permalink

We have added it to our 3.6 repository so the next patch release will have the fix. It would be helpful for us to know that the patch worked for you since we have no way of testing it ourselves.

Barry

Post by Juha JÃ¤ykkÃ¤
I'm sure that fixes it, but I would have hoped there is a proper way of just
configuring and making PETSc with --download-chombo. I.e. without patching
PETSc first. If there is no such way, I'm happy to apply the patch, but it is
really a last resort for 3.6; for > 3.6 it would of course be fine as it could
be released with the patch applied.
Cheers,
Juha

Post by Barry Smith
We absolutely NEED configure.log to help you.
Barry

Post by Juha Jaykka
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
/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

--
-----------------------------------------------
| http://koti.kapsi.fi/~juhaj/ |
-----------------------------------------------

Satish Balay

2015-10-02 21:16:56 UTC

Permalink

I'm not sure why you think a patch is 'really a last resort for 3.6'

This is how issues get fixed - and then you have the fixes available
in the next patch release 3.6.2 etc. You can apply a patch [stored in
a patchfile] with the command:

patch -Np1 < patchfile

Or use git to obtain petsc - and use 'maint' for the 3.6 release - and
corresponding fixes. ttp://www.mcs.anl.gov/petsc/download/index.html

Or wait till petsc-3.6.2 gets released.

Satish

Post by Barry Smith
We absolutely NEED configure.log to help you.
Barry

Post by Juha Jaykka
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
/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