On Wed, Jul 7, 2021 at 1:26 PM Barry Smith <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> >> 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 <[email protected]> wrote: >>> >>>> Ok, I tried that but now I get this error. >>>> >>>> On Wed, Jul 7, 2021 at 12:13 PM Stefano Zampini < >>>> [email protected]> wrote: >>>> >>>>> 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/> >>>>>>>> >>>>>>> >>>>>>> >>> >>> -- >>> 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> > > >
