I do see this: 15:43 /sw/spock/spack-envs/views/rocm-4.1.0/lib$ nm libhsa-runtime64.so | grep -n hsa_signal_load_scacquir 349:0000000000074de0 T hsa_signal_load_scacquire 1491:000000000004bef0 t _ZN4rocr3HSA25hsa_signal_load_scacquireE12hsa_signal_s 15:43 /sw/spock/spack-envs/views/rocm-4.1.0/lib$
On Wed, Jul 7, 2021 at 3:45 PM Mark Adams <[email protected]> wrote: > No diffs. I added this: > > diff --git a/config/BuildSystem/config/packages/zlib.py > b/config/BuildSystem/config/packages/zlib.py > index fbf9bdf4a0..b76d362536 100644 > --- a/config/BuildSystem/config/packages/zlib.py > +++ b/config/BuildSystem/config/packages/zlib.py > @@ -25,6 +25,7 @@ class Configure(config.package.Package): > self.pushLanguage('C') > args.append('CC="'+self.getCompiler()+'"') > > args.append('CFLAGS="'+self.updatePackageCFlags(self.getCompilerFlags())+'"') > + args.append('LDFLAGS="'+self.getLinkerFlags()+'"') > args.append('prefix="'+self.installDir+'"') > self.popLanguage() > args=' '.join(args) > lines 1-12/12 (END) > > but it still fails. > > 15:20 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.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.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_allocate > [--no-allow-shlib-undefined] > > ld.lld: ld.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_agent_iterate_memory_pools [--no-allow-shlib-undefined]ld.lld > : ld.lld: error: 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] > /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) > 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 > > On Wed, Jul 7, 2021 at 2:03 PM Matthew Knepley <[email protected]> wrote: > >> On Wed, Jul 7, 2021 at 1:40 PM Mark Adams <[email protected]> wrote: >> >>> >>> >>> 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. >>> >> >> Can you try this? >> >> knepley/feature-orientation-rethink *$:/PETSc3/petsc/petsc-dev$ git diff >> config/BuildSystem/config/packages/zlib.py >> diff --git a/config/BuildSystem/config/packages/zlib.py >> b/config/BuildSystem/config/packages/zlib.py >> index fbf9bdf4a0a..b76d3625364 100644 >> --- a/config/BuildSystem/config/packages/zlib.py >> +++ b/config/BuildSystem/config/packages/zlib.py >> @@ -25,6 +25,7 @@ class Configure(config.package.Package): >> >> self.pushLanguage('C') >> args.append('CC="'+self.getCompiler()+'"') >> >> >> args.append('CFLAGS="'+self.updatePackageCFlags(self.getCompilerFlags())+'"') >> + args.append('LDFLAGS="'+self.getLinkerFlags()+'"') >> args.append('prefix="'+self.installDir+'"') >> self.popLanguage() >> args=' '.join(args) >> >> Matt >> >> >>> >>>> 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> >>>> >>>> >>>> >> >> -- >> 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/> >> >
