[petsc-users] p4est error

Sat Oct 20 19:44:16 CDT 2018

Thanks Satish.

I built this and it is working.

On Sat, Oct 20, 2018 at 5:39 PM Balay, Satish <balay at mcs.anl.gov> wrote:

> Pushed this change to branch balay/p4est-add-zlib-dep/maint [it works as
> desired on my laptop]
>
> Satish
>
> On Sat, 20 Oct 2018, Balay, Satish wrote:
>
> > I don't see an option for specifying zlib explicitly - so perhaps it can
> use it from LIBS?
> >
> > [untested patch]
> >
> > Satish
> >
> > --------
> >
> > diff --git a/config/BuildSystem/config/packages/p4est.py
> b/config/BuildSystem/config/packages/p4est.py
> > index 03d1e2fcb0..31d2307f2b 100644
> > --- a/config/BuildSystem/config/packages/p4est.py
> > +++ b/config/BuildSystem/config/packages/p4est.py
> > @@ -21,8 +21,9 @@ class Configure(config.package.GNUPackage):
> >    def setupDependencies(self, framework):
> >      config.package.GNUPackage.setupDependencies(self, framework)
> >      self.mpi        = framework.require('config.packages.MPI',self)
> > -    self.blasLapack =
> self.framework.require('config.packages.BlasLapack',self)
> > -    self.deps = [self.mpi,self.blasLapack]
> > +    self.blasLapack =
> framework.require('config.packages.BlasLapack',self)
> > +    self.zlib       = framework.require('config.packages.zlib',self)
> > +    self.deps = [self.mpi,self.blasLapack,self.zlib]
> >      return
> >
> >    def formGNUConfigureArgs(self):
> > @@ -30,7 +31,7 @@ class Configure(config.package.GNUPackage):
> >      if self.argDB['with-p4est-debugging']:
> >        args.append('--enable-debug')
> >      args.append('--enable-mpi')
> > -
> args.append('LIBS="'+self.libraries.toString(self.blasLapack.dlib)+'"')
> > +    args.append('LIBS="'+self.libraries.toString(self.dlib)+'"')
> >      return args
> >
> >    def updateGitDir(self):
> >
> >
> > On Sat, 20 Oct 2018, Smith, Barry F. wrote:
> >
> > >
> > >
> > > > On Oct 20, 2018, at 4:14 PM, Isaac, Tobin G <tisaac at cc.gatech.edu>
> wrote:
> > > >
> > > > I think adler32 is in zlib: p4est typically finds it in configure.
> Can you send along config.log from externalpackages/git.p4est?
> > >
> > >    Is there a way to pass the zlib information to ./configure? We
> should add that to p4est.py Reason: we don't like external packages making
> their own decisions, we want PETSc's configure making the decisions and
> passing the decisions down to the packages.
> > >
> > >     Barry
> > >
> > >    This is especially true for hairy machines that Mark likes to build
> on, where standard configure sometimes makes the wrong decision or cannot
> figure out something.
> > >
> > > >
> > > > On October 20, 2018 4:52:54 PM EDT, Mark Adams <mfadams at lbl.gov>
> wrote:
> > > >> I am getting this error. This was a clean build (nuked the arch
> > > >> directory).
> > > >>
> > > >> 13:50 nid12922 master= ~/petsc_install/petsc$ make
> > > >>
> PETSC_DIR=/global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel
> > > >> PETSC_ARCH="" test
> > > >> Running test examples to verify correct installation
> > > >> Using
> > > >>
> PETSC_DIR=/global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel
> > > >> and PETSC_ARCH=
> > > >> *******************Error detected during compile or
> > > >> link!*******************
> > > >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > >>
> /global/homes/m/madams/petsc_install/petsc/src/snes/examples/tutorials
> > > >> ex19
> > > >>
> *********************************************************************************
> > > >> cc -o ex19.o -c -g -fp-model fast
> > > >>
> -I/global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/include
> > > >> `pwd`/ex19.c
> > > >> cc -g -fp-model fast  -o ex19 ex19.o
> > > >>
> -L/global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib
> > > >>
> -Wl,-rpath,/global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib
> > > >>
> -L/global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib
> > > >> -lpetsc -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord
> > > >> -lscalapack -lfftw3_mpi -lfftw3 -lp4est -lsc -lflapack -lfblas
> > > >> -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lchaco -lparmetis
> > > >> -lmetis
> > > >> -lstdc++ -ldl
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libpetsc.a(dlimpl.o):
> > > >> In function `PetscDLOpen':
> > > >> /global/u2/m/madams/petsc_install/petsc/src/sys/dll/dlimpl.c:108:
> > > >> warning:
> > > >> Using 'dlopen' in statically linked applications requires at runtime
> > > >> the
> > > >> shared libraries from the glibc version used for linking
> > > >>
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:
> > > >> Warning: alignment 8 of symbol `ARCHITECTURE' in
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libchaco.a(user_params.o)
> > > >> is smaller than 32 in
> > > >> /opt/cray/pe/pmi/5.0.13/lib64/libpmi.a(_pmi_topology_discovery.o)
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libpetsc.a(send.o):
> > > >> In function `PetscOpenSocket':
> > > >>
> /global/u2/m/madams/petsc_install/petsc/src/sys/classes/viewer/impls/socket/send.c:108:
> > > >> warning: Using 'gethostbyname' in statically linked applications
> > > >> requires
> > > >> at runtime the shared libraries from the glibc version used for
> linking
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libp4est.a(src_libp4est_la-p4est.o):
> > > >> In function `p4est_checksum':
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/src/p4est.c:3228:
> > > >> undefined reference to `adler32'
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/src/p4est.c:3236:
> > > >> undefined reference to `adler32_combine'
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libp4est.a(src_libp4est_la-p4est_communication.o):
> > > >> In function `p4est_comm_checksum':
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/src/p4est_communication.c:903:
> > > >> undefined reference to `adler32_combine'
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libp4est.a(src_libp4est_la-p8est.o):
> > > >> In function `p8est_checksum':
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/src/p4est.c:3228:
> > > >> undefined reference to `adler32'
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/src/p4est.c:3236:
> > > >> undefined reference to `adler32_combine'
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libp4est.a(src_libp4est_la-p8est_communication.o):
> > > >> In function `p8est_comm_checksum':
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/src/p4est_communication.c:903:
> > > >> undefined reference to `adler32_combine'
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libsc.a(src_libsc_la-sc_containers.o):
> > > >> In function `sc_array_checksum':
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/sc/src/sc_containers.c:565:
> > > >> undefined reference to `adler32'
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/sc/src/sc_containers.c:571:
> > > >> undefined reference to `adler32'
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/libsc.a(src_libsc_la-sc_io.o):
> > > >> In function `sc_vtk_write_compressed':
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/sc/src/sc_io.c:492:
> > > >> undefined reference to `compress2'
> > > >>
> /global/u2/m/madams/petsc_install/petsc/arch-cori-haswell-opt-intel/externalpackages/git.p4est/sc/src/sc_io.c:507:
> > > >> undefined reference to `compress2'
> > > >>
> /global/homes/m/madams/petsc_install/petsc-cori-haswell-opt-intel/lib/petsc/conf/test:13:
> > > >> recipe for target 'ex19' failed
> > > >> gmake[3]: [ex19] Error 1 (ignored)
> > > >> true ex19
> > > >> rm ex19.o
> > >
> >
>
>
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