[petsc-dev] [petsc-maint] problem installing petsc 3.4

[Satish Balay]

>>>
[Errno 13] Permission denied: '/share/apps/petsc-petsc-7cd361a5361c/linux-gnu-debug/externalpackages/sowing-1.1.16f/sowing'  File "./config/configure.py", line 272, in petsc_configure
<<<

Perahps some files were modified as root.

Please delete them - and retry the first option. If it fails - send us logs.

sudo rm -rf /share/apps/petsc-petsc-7cd361a5361c/linux-gnu-debug

Satish



On Wed, 16 Apr 2014, Borazjani, Iman wrote:

> Guys,
> 
> I tested with all the options but in all the configure crashes:
> ./configure PETSC_ARCH=linux-gnu-debug
> --with-mpi-dir=/share/apps/openmpi-1.5.1-open64/
> --with-blas-lapack-dir=/share/apps/acml4.4.0/open64/open64_64
> --download-hypre=1 --with-debugging=1
> --prefix=/opt/software/petsc/3.5.0-ompi-1.5.1-open64-debug
> --with-shared-libraries=0
> 
> ./configure PETSC_ARCH=linux-gnu-debug
> --with-mpi-dir=/share/apps/openmpi-1.5.1-open64/
> --with-blas-lapack-dir=/share/apps/acml4.4.0/open64/open64_64
> --download-hypre=1 --with-debugging=1
> --prefix=/opt/software/petsc/3.5.0-ompi-1.5.1-open64-debug
> --with-shared-libraries=1 --with-clib-autodetect=0
> --with-fortranlib-autodetect=0 LIBS='-lfortran -lmv -lffio'
> --with-cxx-autodetect=0
> 
> ./configure PETSC_ARCH=linux-gnu-debug
> --with-mpi-dir=/share/apps/openmpi-1.5.1-open64/
> --with-blas-lapack-dir=/share/apps/acml4.4.0/open64/open64_64
> --download-hypre=1 --with-debugging=1
> --prefix=/opt/software/petsc/3.5.0-ompi-1.5.1-open64-debug
> --with-shared-libraries=1 --with-clib-autodetect=0
> --with-fortranlib-autodetect=0 LIBS='-lfortran -lmv -lffio'
> 
> Iman
> 
> On 4/16/2014 2:07 PM, Jed Brown wrote:
> > Satish Balay <balay at mcs.anl.gov> writes:
> >
> > > On Wed, 16 Apr 2014, Jed Brown wrote:
> > >
> > > > "Borazjani, Iman" <iman at buffalo.edu> writes:
> > > >
> > > > > Hi Jed,
> > > > >
> > > > > I tried both ways and still get a compiler error, but this time I
> > > > > think
> > > > > it is the -g option:
> > > > >     CLINKER
> > > > > /share/apps/petsc-petsc-7cd361a5361c/linux-gnu-debug/lib/libpetsc.so.3.04.4
> > > > > /usr/bin/ld:
> > > > > /share/apps/open64/lib/gcc-lib/x86_64-open64-linux/4.2.4/libopen64rt.a(cacheinfo.o):
> > > > > relocation R_X86_64_32S against `a local symbol' can not be used when
> > > > > making a shared object; recompile with -fPIC
> > > > > /share/apps/open64/lib/gcc-lib/x86_64-open64-linux/4.2.4/libopen64rt.a:
> > > > > could not read symbols: Bad value
> > > > Looks like this compiler claims to be able to link with shared
> > > > libraries, but in fact cannot (since no shared version of libopen64rt.a
> > > > is available).  Configure --with-shared-libraries=0 to get a static
> > > > build of PETSc.
> > > There was a discussion about this on petsc-maint a couple of years ago
> > > with a reference to
> > >
> > > http://devgurus.amd.com/thread/159277
> > >
> > > i.e the compiler links to libopen64rt_shared.a when -shared options is
> > > specified.
> > >
> > > But we detect the compiler libraries libraries without using '-shared'
> > >
> > >
> > > Workarround discussed at that time:
> > >
> > > --with-shared-libraries=1 --with-clib-autodetect=0
> > > --with-fortranlib-autodetect=0 LIBS='-lfortran -lmv -lffio'
> > >
> > > [but we mignt need --with-cxx-autodetect=0 aswell [with -lstdc++ in LIBS]
> > Would we have more or less failures if we used the Fortran linker and
> > passed -lstdc++ when needed (with no other autodetect)?  I hate
> > second-guessing the compilers.
> >
> > > > This is something we should be able to detect in our configure tests.
> > > >
> 
>