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',
> 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] > <mailto:[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] > <mailto:[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] > <mailto:[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] > <mailto:[email protected]>> wrote: > There's an extra comma > > Il Mer 7 Lug 2021, 18:08 Mark Adams <[email protected] > <mailto:[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] > <mailto:[email protected]>> wrote: > Mark > > On Spock, you can use > https://gitlab.com/petsc/petsc/-/blob/main/config/examples/arch-olcf-spock.py > <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] >> <mailto:[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] >> <mailto:[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] >> <mailto:[email protected]>> wrote: >> Also, this is in jczhang/fix-kokkos-includes >> >> On Wed, Jul 7, 2021 at 8:46 AM Mark Adams <[email protected] >> <mailto:[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] >> <mailto:[email protected]>> wrote: >> $ curl http://www.zlib.net/zlib-1.2.11.tar.gz >> <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 >> <http://make_vms.com/> treebuild.xml zconf.h.cmakein zlib.pc.in >> <http://zlib.pc.in/> >> Makefile contrib gzclose.c inffast.h msdos >> trees.c zconf.h.in <http://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] >>> <mailto:[email protected]>> wrote: >>> >>> >>> >>> On Tue, Jul 6, 2021 at 6:42 PM Barry Smith <[email protected] >>> <mailto:[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 >>> <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] >>> > <mailto:[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>
