[petsc-users] p4est error

[Smith, Barry F.]

> 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