[petsc-users] p4est error

[Mark Adams]

There is something going on with zlib. When I get on a compute node I get a
message that zlib (and cmake) module is not found. But I add it manually
and I see it, but still get the same error.

I nuked p4est and am testing Satish's fix. I'll send the log file if it is
not working.

Thanks,

On Sat, Oct 20, 2018 at 5:14 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?
>
> 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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