[petsc-users] download zlib error
Mark Adams
mfadams at lbl.gov
Wed Jul 7 12:40:18 CDT 2021
On Wed, Jul 7, 2021 at 1:26 PM Barry Smith <bsmith at petsc.dev> wrote:
>
> You will need to pass the -L arguments appropriately to zlib's
> ./configure so it can link its shared library appropriately. That is, the
> zlib configure requires the value obtained with
> L'+os.environ['ROCM_PATH'],+'/lib -lhsa-runtime64',
>
It's not clear to me how to do that. I added the -L to my configure
script. It is not clear to me how to modify Matt's command.
> On Jul 7, 2021, at 12:18 PM, Mark Adams <mfadams at lbl.gov> wrote:
>
> Well, still getting these hsa errors:
>
> 13:07 jczhang/fix-kokkos-includes=
> /gpfs/alpine/csc314/scratch/adams/petsc$ !136
> cd
> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
> -I${ROCM_PATH}/include"
> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
> Checking for shared library support...
> Building shared library libz.so.1.2.11 with cc.
> Checking for size_t... Yes.
> Checking for off64_t... Yes.
> Checking for fseeko... Yes.
> Checking for strerror... No.
> Checking for unistd.h... Yes.
> Checking for stdarg.h... Yes.
> Checking whether to use vs[n]printf() or s[n]printf()... using
> vs[n]printf().
> Checking for vsnprintf() in stdio.h... No.
> WARNING: vsnprintf() not found, falling back to vsprintf(). zlib
> can build but will be open to possible buffer-overflow security
> vulnerabilities.
> Checking for return value of vsprintf()... Yes.
> Checking for attribute(visibility) support... Yes.
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o example.o
> test/example.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o adler32.o adler32.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o crc32.o crc32.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o deflate.o deflate.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o infback.o infback.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inffast.o inffast.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inflate.o inflate.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o trees.o trees.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o zutil.o zutil.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o compress.o compress.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzread.o gzread.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o minigzip.o
> test/minigzip.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/adler32.o adler32.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/crc32.o crc32.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/deflate.o deflate.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/infback.o infback.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/inffast.o inffast.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/inflate.o inflate.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/inftrees.o inftrees.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/trees.o trees.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/zutil.o zutil.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/compress.o compress.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/uncompr.o uncompr.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/gzclose.o gzclose.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/gzlib.o gzlib.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/gzread.o gzread.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
> -c -o objs/gzwrite.o gzwrite.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
> example64.o test/example.c
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
> minigzip64.o test/minigzip.c
> ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o
> inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o
> gzwrite.o
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example example.o -L. libz.a
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
> cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -fPIC
> -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o
> libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo
> inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo
> gzlib.lo gzread.lo gzwrite.lo -lc
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L.
> libz.a
> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example64 example64.o -L.
> libz.a
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_allocate
> [--no-allow-shlib-undefined]
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_amd_memory_pool_allocate
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_agent_iterate_memory_pools
> [--no-allow-shlib-undefined]
>
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_amd_agent_iterate_memory_pools
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_iterate_agents
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_signal_load_scacquire
> [--no-allow-shlib-undefined]
>
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_signal_load_scacquire
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_amd_memory_unlock
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_signal_destroy
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_get_info
> [--no-allow-shlib-undefined]
>
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_amd_memory_pool_get_info
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_amd_memory_lock
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>
> ld.lldld.lld: : error: error:
> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
> hsa_amd_memory_pool_free
> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_agents_allow_access
> [--no-allow-shlib-undefined]
>
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_agents_allow_access
> [--no-allow-shlib-undefined]
> clang-11: error: linker command failed with exit code 1 (use -v to see
> invocation)
> clang-11: error: linker command failed with exit code 1 (use -v to see
> invocation)
> gmake: *** [Makefile:289: example] Error 1
> gmake: *** Waiting for unfinished jobs....
> gmake: *** [Makefile:292: minigzip] Error 1
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_allocate
> [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_agent_iterate_memory_pools
> [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_signal_load_scacquire
> [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_get_info
> [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_agents_allow_access
> [--no-allow-shlib-undefined]
> clang-11: error: linker command failed with exit code 1 (use -v to see
> invocation)
> gmake: *** [Makefile:304: minigzip64] Error 1
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_allocate
> [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_agent_iterate_memory_pools
> [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_signal_load_scacquire
> [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_get_info
> [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
> undefined reference to hsa_amd_agents_allow_access
> [--no-allow-shlib-undefined]
> clang-11: error: linker command failed with exit code 1 (use -v to see
> invocation)
> gmake: *** [Makefile:301: example64] Error 1
> rm -f libz.so libz.so.1
> ln -s libz.so.1.2.11 libz.so
> ln -s libz.so.1.2.11 libz.so.1
>
> On Wed, Jul 7, 2021 at 1:05 PM Mark Adams <mfadams at lbl.gov> wrote:
>
>> Thanks, it was missing the /
>>
>> '--LDFLAGS=-L'+os.environ['ROCM_PATH'],+'/lib -lhsa-runtime64',
>>
>> On Wed, Jul 7, 2021 at 12:48 PM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> Did you look in /sw/spock/spack-envs/views/rocm-4.1.0lib ?
>>>
>>> Matt
>>>
>>> On Wed, Jul 7, 2021 at 12:29 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>
>>>> Ok, I tried that but now I get this error.
>>>>
>>>> On Wed, Jul 7, 2021 at 12:13 PM Stefano Zampini <
>>>> stefano.zampini at gmail.com> wrote:
>>>>
>>>>> There's an extra comma
>>>>>
>>>>> Il Mer 7 Lug 2021, 18:08 Mark Adams <mfadams at lbl.gov> ha scritto:
>>>>>
>>>>>> Humm, I get this error (I just copied your whole file into here):
>>>>>>
>>>>>> 12:06 jczhang/fix-kokkos-includes=
>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc$ ~/arch-spock-dbg-cray-kokkos.py
>>>>>> Traceback (most recent call last):
>>>>>> File "/ccs/home/adams/arch-spock-dbg-cray-kokkos.py", line 27, in
>>>>>> <module>
>>>>>> '--LDFLAGS=-L'+os.environ['ROCM_PATH'],+'lib -lhsa-runtime64',
>>>>>> TypeError: bad operand type for unary +: 'str'
>>>>>>
>>>>>> On Wed, Jul 7, 2021 at 11:08 AM Stefano Zampini <
>>>>>> stefano.zampini at gmail.com> wrote:
>>>>>>
>>>>>>> Mark
>>>>>>>
>>>>>>> On Spock, you can use
>>>>>>> https://gitlab.com/petsc/petsc/-/blob/main/config/examples/arch-olcf-spock.py as
>>>>>>> a template for your configuration. You need to add libraries as LDFLAGS to
>>>>>>> resolve the hsa symbols
>>>>>>>
>>>>>>> On Jul 7, 2021, at 5:04 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> 08:30 jczhang/fix-kokkos-includes=
>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc$ cd
>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
>>>>>>> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I${ROCM_PATH}/include"
>>>>>>> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
>>>>>>> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
>>>>>>> Checking for shared library support...
>>>>>>> Building shared library libz.so.1.2.11 with cc.
>>>>>>> Checking for size_t... Yes.
>>>>>>> Checking for off64_t... Yes.
>>>>>>> Checking for fseeko... Yes.
>>>>>>> Checking for strerror... No.
>>>>>>> Checking for unistd.h... Yes.
>>>>>>> Checking for stdarg.h... Yes.
>>>>>>> Checking whether to use vs[n]printf() or s[n]printf()... using
>>>>>>> vs[n]printf().
>>>>>>> Checking for vsnprintf() in stdio.h... No.
>>>>>>> WARNING: vsnprintf() not found, falling back to vsprintf(). zlib
>>>>>>> can build but will be open to possible buffer-overflow security
>>>>>>> vulnerabilities.
>>>>>>> Checking for return value of vsprintf()... Yes.
>>>>>>> Checking for attribute(visibility) support... Yes.
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o example.o
>>>>>>> test/example.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o adler32.o adler32.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o crc32.o crc32.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o deflate.o deflate.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o infback.o infback.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inffast.o inffast.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inflate.o inflate.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o trees.o trees.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o zutil.o zutil.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o compress.o compress.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzread.o gzread.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o minigzip.o
>>>>>>> test/minigzip.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/adler32.o adler32.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/crc32.o crc32.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/deflate.o deflate.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/infback.o infback.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/inffast.o inffast.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/inflate.o inflate.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/inftrees.o inftrees.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/trees.o trees.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/zutil.o zutil.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/compress.o compress.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/uncompr.o uncompr.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/gzclose.o gzclose.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/gzlib.o gzlib.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/gzread.o gzread.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>> -c -o objs/gzwrite.o gzwrite.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>>>>>> example64.o test/example.c
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>>>>>> minigzip64.o test/minigzip.c
>>>>>>> ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o
>>>>>>> inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o
>>>>>>> gzread.o gzwrite.o
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example example.o -L. libz.a
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
>>>>>>> cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -fPIC
>>>>>>> -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o
>>>>>>> libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo
>>>>>>> inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo
>>>>>>> gzlib.lo gzread.lo gzwrite.lo -lc
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L.
>>>>>>> libz.a
>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example64 example64.o -L.
>>>>>>> libz.a
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_signal_load_scacquire
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lldld.lld: : error: error:
>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>> hsa_amd_memory_pool_allocate
>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>>
>>>>>>> ld.lldld.lld: : error: error:
>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>> hsa_amd_agent_iterate_memory_pools
>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>>
>>>>>>> ld.lldld.lld: : error: error:
>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>> hsa_iterate_agents
>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>
>>>>>>> ld.lldld.lld: : error: error:
>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>> hsa_signal_load_scacquire
>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>
>>>>>>> ld.lldld.lld: : error: error:
>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>> hsa_amd_memory_unlock
>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>
>>>>>>> ld.lldld.lld: : error: error:
>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>> hsa_signal_destroy
>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v to
>>>>>>> see invocation)
>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v to
>>>>>>> see invocation)
>>>>>>> gmake: *** [Makefile:292: minigzip] Error 1
>>>>>>> gmake: *** Waiting for unfinished jobs....
>>>>>>> gmake: *** [Makefile:289: example] Error 1
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_signal_load_scacquire
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v to
>>>>>>> see invocation)
>>>>>>> gmake: *** [Makefile:304: minigzip64] Error 1
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_signal_load_scacquire
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>> [--no-allow-shlib-undefined]
>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v to
>>>>>>> see invocation)
>>>>>>> gmake: *** [Makefile:301: example64] Error 1
>>>>>>> rm -f libz.so libz.so.1
>>>>>>> ln -s libz.so.1.2.11 libz.so
>>>>>>> ln -s libz.so.1.2.11 libz.so.1
>>>>>>> 11:03 2 jczhang/fix-kokkos-includes=
>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11$
>>>>>>>
>>>>>>> On Wed, Jul 7, 2021 at 9:18 AM Matthew Knepley <knepley at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> It is hard to see the error. I suspect it is something crazy with
>>>>>>>> the install. Can you run the build by hand?
>>>>>>>>
>>>>>>>> cd
>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
>>>>>>>> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>> -I${ROCM_PATH}/include"
>>>>>>>> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
>>>>>>>> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
>>>>>>>>
>>>>>>>> and see what happens, and what the error code is?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Matt
>>>>>>>>
>>>>>>>> On Wed, Jul 7, 2021 at 8:48 AM Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>>
>>>>>>>>> Also, this is in jczhang/fix-kokkos-includes
>>>>>>>>>
>>>>>>>>> On Wed, Jul 7, 2021 at 8:46 AM Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>>>
>>>>>>>>>> Apparently the same error with
>>>>>>>>>> --download-zlib=/yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>
>>>>>>>>>> On Tue, Jul 6, 2021 at 11:53 PM Barry Smith <bsmith at petsc.dev>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> $ curl http://www.zlib.net/zlib-1.2.11.tar.gz >
>>>>>>>>>>> zlib-1.2.11.tar.gz
>>>>>>>>>>> % Total % Received % Xferd Average Speed Time Time
>>>>>>>>>>> Time Current
>>>>>>>>>>> Dload Upload Total Spent
>>>>>>>>>>> Left Speed
>>>>>>>>>>> 100 593k 100 593k 0 0 835k 0 --:--:-- --:--:--
>>>>>>>>>>> --:--:-- 834k
>>>>>>>>>>> ~/Src/petsc*
>>>>>>>>>>> (barry/2021-07-03/demonstrate-network-parallel-build=)*
>>>>>>>>>>> arch-demonstrate-network-parallel-build
>>>>>>>>>>> $ tar -zxf zlib-1.2.11.tar.gz
>>>>>>>>>>> ~/Src/petsc*
>>>>>>>>>>> (barry/2021-07-03/demonstrate-network-parallel-build=)*
>>>>>>>>>>> arch-demonstrate-network-parallel-build
>>>>>>>>>>> $ ls zlib-1.2.11
>>>>>>>>>>> CMakeLists.txt adler32.c deflate.c gzread.c
>>>>>>>>>>> inflate.h os400 watcom zlib.h
>>>>>>>>>>> ChangeLog amiga deflate.h gzwrite.c
>>>>>>>>>>> inftrees.c qnx win32 zlib.map
>>>>>>>>>>> FAQ compress.c doc infback.c
>>>>>>>>>>> inftrees.h test zconf.h zlib.pc.cmakein
>>>>>>>>>>> INDEX configure examples inffast.c
>>>>>>>>>>> make_vms.com treebuild.xml zconf.h.cmakein zlib.pc.in
>>>>>>>>>>> Makefile contrib gzclose.c inffast.h
>>>>>>>>>>> msdos trees.c zconf.h.in zlib2ansi
>>>>>>>>>>> Makefile.in crc32.c gzguts.h inffixed.h
>>>>>>>>>>> nintendods trees.h zlib.3 zutil.c
>>>>>>>>>>> README crc32.h gzlib.c inflate.c
>>>>>>>>>>> old uncompr.c zlib.3.pdf zutil.h
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Jul 6, 2021, at 7:57 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Jul 6, 2021 at 6:42 PM Barry Smith <bsmith at petsc.dev>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Mark,
>>>>>>>>>>>>
>>>>>>>>>>>> You can try what the configure error message should be
>>>>>>>>>>>> suggesting (it is not clear if that is being printed to your screen or no).
>>>>>>>>>>>>
>>>>>>>>>>>> ERROR: Unable to download package ZLIB from:
>>>>>>>>>>>> http://www.zlib.net/zlib-1.2.11.tar.gz
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> My browser can not open this and I could not see a download
>>>>>>>>>>> button on this site.
>>>>>>>>>>>
>>>>>>>>>>> Can you download this?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> * If URL specified manually - perhaps there is a typo?
>>>>>>>>>>>> * If your network is disconnected - please reconnect and rerun
>>>>>>>>>>>> ./configure
>>>>>>>>>>>> * Or perhaps you have a firewall blocking the download
>>>>>>>>>>>> * You can run with --with-packages-download-dir=/adirectory and
>>>>>>>>>>>> ./configure will instruct you what packages to download manually
>>>>>>>>>>>> * or you can download the above URL manually, to
>>>>>>>>>>>> /yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>>> and use the configure option:
>>>>>>>>>>>> --download-zlib=/yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>>>
>>>>>>>>>>>> Barry
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> > On Jul 6, 2021, at 4:29 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>> >
>>>>>>>>>>>> > I am getting some sort of error in build zlib on Spock at
>>>>>>>>>>>> ORNL.
>>>>>>>>>>>> > Other libraries are downloaded and I am sure the network is
>>>>>>>>>>>> fine.
>>>>>>>>>>>> > Any ideas?
>>>>>>>>>>>> > Thanks,
>>>>>>>>>>>> > Mark
>>>>>>>>>>>> > <configure.log>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> What most experimenters take for granted before they begin their
>>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>>> experiments lead.
>>>>>>>> -- Norbert Wiener
>>>>>>>>
>>>>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>> <configure.log>
>
>
>
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