[petsc-users] p4est error

Sat Oct 20 16:39:22 CDT 2018

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
> > 
> 