<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Mon, Sep 1, 2014 at 3:22 AM, Åsmund Ervik <span dir="ltr"><<a href="mailto:asmund.ervik@ntnu.no" target="_blank">asmund.ervik@ntnu.no</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
When I try to configure PETSc with HDF5 by using "--download-hdf5", I<br>
get a very long error message from PETSc compiling HDF5 (see attached<br>
error-down-hdf5.tar.gz) which boils down to<br>
<br>
h5tools_str.c: In function 'h5tools_str_indent':<br>
h5tools_str.c:635:1: error: expected expression before '/' token<br>
<br>
This happens both with PETSc 3.5.1 and 3.4.5. It appears this was an<br>
error in HDF5 version 1.8.10, cf.<br>
<a href="https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777" target="_blank">https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777</a><br>
<br>
<br>
Subsequently I installed HDF5 v. 1.8.12 using my OS package manager and<br>
then tried to configure with "--with-hdf5<br>
--with-hdf5-dir=/path/to/system/hdf5" using PETSc 3.5.1. This time both<br>
configure and make were successful, but "make test" fails with loads of<br>
undefined references to PETSc HDF5 stuff (see below). configure.log and<br>
make.log attached also for this case (error-with-hdf5.tar.gz)<br></blockquote><div><br></div><div>It did not build src/sys/classes/viewer/impls/hdf5/, clearly from the log. However, it</div><div>should have. We have been trying to understand why Make behaves in a bad way</div>
<div>after configuration failure. It should go away with make clean and another make.</div><div><br></div><div>Jed, here is another case of this make bug.</div><div><br></div><div>   Thanks,</div><div><br></div><div>      Matt</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
If you need any more info, just ask :)<br>
<br>
Regards,<br>
Åsmund<br>
<br>
<br>
Using PETSC_DIR=/opt/petsc/optim_gfortran and PETSC_ARCH=linux<br>
*******************Error detected during compile or link!*******************<br>
See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a><br>
/opt/petsc/optim_gfortran/src/snes/examples/tutorials ex19<br>
*********************************************************************************<br>
/opt/petsc/optim_gfortran/linux/bin/mpicc -o ex19.o -c -fPIC -Wall<br>
-Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O3<br>
-march=native   -I/opt/petsc/optim_gfortran/include<br>
-I/opt/petsc/optim_gfortran/linux/include -I/usr/include    `pwd`/ex19.c<br>
/opt/petsc/optim_gfortran/linux/bin/mpicc -fPIC -Wall -Wwrite-strings<br>
-Wno-strict-aliasing -Wno-unknown-pragmas -O3 -march=native  -o ex19<br>
ex19.o -Wl,-rpath,/opt/petsc/optim_gfortran/linux/lib<br>
-L/opt/petsc/optim_gfortran/linux/lib  -lpetsc<br>
-Wl,-rpath,/opt/petsc/optim_gfortran/linux/lib -lHYPRE<br>
-Wl,-rpath,/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.0<br>
-L/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.0 -lmpichcxx -lstdc++<br>
-lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lX11 -lpthread -lssl<br>
-lcrypto -Wl,-rpath,/usr/lib -L/usr/lib -lhdf5_hl -lhdf5 -lm -lmpichf90<br>
-lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpichcxx -lstdc++ -ldl<br>
-lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5GetFileId'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5PushGroup'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5PopGroup'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerCreate_HDF5'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5ReadAttribute'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5WriteAttribute'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5SetTimestep'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PETSC_VIEWER_HDF5_'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5HasAttribute'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5GetTimestep'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5GetGroup'<br>
collect2: error: ld returned 1 exit status<br>
makefile:108: recipe for target 'ex19' failed<br>
make[3]: [ex19] Error 1 (ignored)<br>
/usr/bin/rm -f ex19.o<br>
*******************Error detected during compile or link!*******************<br>
See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a><br>
/opt/petsc/optim_gfortran/src/snes/examples/tutorials ex5f<br>
*********************************************************<br>
/opt/petsc/optim_gfortran/linux/bin/mpif90 -c  -fPIC  -Wall<br>
-Wno-unused-variable -ffree-line-length-0 -Wno-unused-dummy-argument -O3<br>
-march=native -fno-protect-parens -fstack-arrays<br>
-I/opt/petsc/optim_gfortran/include<br>
-I/opt/petsc/optim_gfortran/linux/include -I/usr/include    -o ex5f.o ex5f.F<br>
/opt/petsc/optim_gfortran/linux/bin/mpif90 -fPIC  -Wall<br>
-Wno-unused-variable -ffree-line-length-0 -Wno-unused-dummy-argument -O3<br>
-march=native -fno-protect-parens -fstack-arrays  -o ex5f ex5f.o<br>
-Wl,-rpath,/opt/petsc/optim_gfortran/linux/lib<br>
-L/opt/petsc/optim_gfortran/linux/lib  -lpetsc<br>
-Wl,-rpath,/opt/petsc/optim_gfortran/linux/lib -lHYPRE<br>
-Wl,-rpath,/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.0<br>
-L/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.0 -lmpichcxx -lstdc++<br>
-lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lX11 -lpthread -lssl<br>
-lcrypto -Wl,-rpath,/usr/lib -L/usr/lib -lhdf5_hl -lhdf5 -lm -lmpichf90<br>
-lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpichcxx -lstdc++ -ldl<br>
-lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5GetFileId'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5PushGroup'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5PopGroup'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerCreate_HDF5'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5ReadAttribute'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5WriteAttribute'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5SetTimestep'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PETSC_VIEWER_HDF5_'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5HasAttribute'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5GetTimestep'<br>
/opt/petsc/optim_gfortran/linux/lib/libpetsc.so: undefined reference to<br>
`PetscViewerHDF5GetGroup'<br>
collect2: error: ld returned 1 exit status<br>
makefile:50: recipe for target 'ex5f' failed<br>
<br>
<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div>