There's an extra comma Il Mer 7 Lug 2021, 18:08 Mark Adams <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote: >>> >>>> Also, this is in jczhang/fix-kokkos-includes >>>> >>>> On Wed, Jul 7, 2021 at 8:46 AM Mark Adams <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote: >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Jul 6, 2021 at 6:42 PM Barry Smith <[email protected]> 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 <[email protected]> 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/> >>> >> >>
