[petsc-users] download zlib error
Mark Adams
mfadams at lbl.gov
Wed Jul 7 14:45:21 CDT 2021
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 <mfadams at lbl.gov> 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 <knepley at gmail.com> wrote:
>
>> On Wed, Jul 7, 2021 at 1:40 PM Mark Adams <mfadams at lbl.gov> wrote:
>>
>>>
>>>
>>> On Wed, Jul 7, 2021 at 1:26 PM Barry Smith <bsmith at petsc.dev> wrote:
>>>
>>>>
>>>> You will need to pass the -L arguments appropriately to zlib's
>>>> ./configure so it can link its shared library appropriately. That is, the
>>>> zlib configure requires the value obtained with
>>>> L'+os.environ['ROCM_PATH'],+'/lib -lhsa-runtime64',
>>>>
>>>
>>> It's not clear to me how to do that. I added the -L to my configure
>>> script. It is not clear to me how to modify Matt's command.
>>>
>>
>> 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 <mfadams at lbl.gov> wrote:
>>>>
>>>> Well, still getting these hsa errors:
>>>>
>>>> 13:07 jczhang/fix-kokkos-includes=
>>>> /gpfs/alpine/csc314/scratch/adams/petsc$ !136
>>>> cd
>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
>>>> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I${ROCM_PATH}/include"
>>>> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
>>>> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
>>>> Checking for shared library support...
>>>> Building shared library libz.so.1.2.11 with cc.
>>>> Checking for size_t... Yes.
>>>> Checking for off64_t... Yes.
>>>> Checking for fseeko... Yes.
>>>> Checking for strerror... No.
>>>> Checking for unistd.h... Yes.
>>>> Checking for stdarg.h... Yes.
>>>> Checking whether to use vs[n]printf() or s[n]printf()... using
>>>> vs[n]printf().
>>>> Checking for vsnprintf() in stdio.h... No.
>>>> WARNING: vsnprintf() not found, falling back to vsprintf(). zlib
>>>> can build but will be open to possible buffer-overflow security
>>>> vulnerabilities.
>>>> Checking for return value of vsprintf()... Yes.
>>>> Checking for attribute(visibility) support... Yes.
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o example.o
>>>> test/example.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o adler32.o adler32.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o crc32.o crc32.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o deflate.o deflate.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o infback.o infback.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inffast.o inffast.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inflate.o inflate.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o trees.o trees.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o zutil.o zutil.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o compress.o compress.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzread.o gzread.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o minigzip.o
>>>> test/minigzip.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/adler32.o adler32.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/crc32.o crc32.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/deflate.o deflate.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/infback.o infback.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/inffast.o inffast.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/inflate.o inflate.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/inftrees.o inftrees.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/trees.o trees.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/zutil.o zutil.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/compress.o compress.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/uncompr.o uncompr.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/gzclose.o gzclose.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/gzlib.o gzlib.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/gzread.o gzread.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>> -c -o objs/gzwrite.o gzwrite.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>>> example64.o test/example.c
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>>> minigzip64.o test/minigzip.c
>>>> ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o
>>>> inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o
>>>> gzwrite.o
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example example.o -L. libz.a
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
>>>> cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -fPIC
>>>> -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o
>>>> libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo
>>>> inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo
>>>> gzlib.lo gzread.lo gzwrite.lo -lc
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L.
>>>> libz.a
>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example64 example64.o -L.
>>>> libz.a
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>> [--no-allow-shlib-undefined]
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_amd_memory_pool_allocate
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>> [--no-allow-shlib-undefined]
>>>>
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_amd_agent_iterate_memory_pools
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_iterate_agents
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_signal_load_scacquire
>>>> [--no-allow-shlib-undefined]
>>>>
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_signal_load_scacquire
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_amd_memory_unlock
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_signal_destroy
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>> [--no-allow-shlib-undefined]
>>>>
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_amd_memory_pool_get_info
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_amd_memory_lock
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>
>>>> ld.lldld.lld: : error: error:
>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>> hsa_amd_memory_pool_free
>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_agents_allow_access
>>>> [--no-allow-shlib-undefined]
>>>>
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_agents_allow_access
>>>> [--no-allow-shlib-undefined]
>>>> clang-11: error: linker command failed with exit code 1 (use -v to see
>>>> invocation)
>>>> clang-11: error: linker command failed with exit code 1 (use -v to see
>>>> invocation)
>>>> gmake: *** [Makefile:289: example] Error 1
>>>> gmake: *** Waiting for unfinished jobs....
>>>> gmake: *** [Makefile:292: minigzip] Error 1
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>> [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>> [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_signal_load_scacquire
>>>> [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>> [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_agents_allow_access
>>>> [--no-allow-shlib-undefined]
>>>> clang-11: error: linker command failed with exit code 1 (use -v to see
>>>> invocation)
>>>> gmake: *** [Makefile:304: minigzip64] Error 1
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>> [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>> [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_signal_load_scacquire
>>>> [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>> [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>> undefined reference to hsa_amd_agents_allow_access
>>>> [--no-allow-shlib-undefined]
>>>> clang-11: error: linker command failed with exit code 1 (use -v to see
>>>> invocation)
>>>> gmake: *** [Makefile:301: example64] Error 1
>>>> rm -f libz.so libz.so.1
>>>> ln -s libz.so.1.2.11 libz.so
>>>> ln -s libz.so.1.2.11 libz.so.1
>>>>
>>>> On Wed, Jul 7, 2021 at 1:05 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>>
>>>>> Thanks, it was missing the /
>>>>>
>>>>> '--LDFLAGS=-L'+os.environ['ROCM_PATH'],+'/lib -lhsa-runtime64',
>>>>>
>>>>> On Wed, Jul 7, 2021 at 12:48 PM Matthew Knepley <knepley at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Did you look in /sw/spock/spack-envs/views/rocm-4.1.0lib ?
>>>>>>
>>>>>> Matt
>>>>>>
>>>>>> On Wed, Jul 7, 2021 at 12:29 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>
>>>>>>> Ok, I tried that but now I get this error.
>>>>>>>
>>>>>>> On Wed, Jul 7, 2021 at 12:13 PM Stefano Zampini <
>>>>>>> stefano.zampini at gmail.com> wrote:
>>>>>>>
>>>>>>>> There's an extra comma
>>>>>>>>
>>>>>>>> Il Mer 7 Lug 2021, 18:08 Mark Adams <mfadams at lbl.gov> ha scritto:
>>>>>>>>
>>>>>>>>> Humm, I get this error (I just copied your whole file into here):
>>>>>>>>>
>>>>>>>>> 12:06 jczhang/fix-kokkos-includes=
>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc$ ~/arch-spock-dbg-cray-kokkos.py
>>>>>>>>> Traceback (most recent call last):
>>>>>>>>> File "/ccs/home/adams/arch-spock-dbg-cray-kokkos.py", line 27,
>>>>>>>>> in <module>
>>>>>>>>> '--LDFLAGS=-L'+os.environ['ROCM_PATH'],+'lib -lhsa-runtime64',
>>>>>>>>> TypeError: bad operand type for unary +: 'str'
>>>>>>>>>
>>>>>>>>> On Wed, Jul 7, 2021 at 11:08 AM Stefano Zampini <
>>>>>>>>> stefano.zampini at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Mark
>>>>>>>>>>
>>>>>>>>>> On Spock, you can use
>>>>>>>>>> https://gitlab.com/petsc/petsc/-/blob/main/config/examples/arch-olcf-spock.py as
>>>>>>>>>> a template for your configuration. You need to add libraries as LDFLAGS to
>>>>>>>>>> resolve the hsa symbols
>>>>>>>>>>
>>>>>>>>>> On Jul 7, 2021, at 5:04 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> 08:30 jczhang/fix-kokkos-includes=
>>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc$ cd
>>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
>>>>>>>>>> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I${ROCM_PATH}/include"
>>>>>>>>>> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
>>>>>>>>>> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
>>>>>>>>>> Checking for shared library support...
>>>>>>>>>> Building shared library libz.so.1.2.11 with cc.
>>>>>>>>>> Checking for size_t... Yes.
>>>>>>>>>> Checking for off64_t... Yes.
>>>>>>>>>> Checking for fseeko... Yes.
>>>>>>>>>> Checking for strerror... No.
>>>>>>>>>> Checking for unistd.h... Yes.
>>>>>>>>>> Checking for stdarg.h... Yes.
>>>>>>>>>> Checking whether to use vs[n]printf() or s[n]printf()... using
>>>>>>>>>> vs[n]printf().
>>>>>>>>>> Checking for vsnprintf() in stdio.h... No.
>>>>>>>>>> WARNING: vsnprintf() not found, falling back to vsprintf(). zlib
>>>>>>>>>> can build but will be open to possible buffer-overflow security
>>>>>>>>>> vulnerabilities.
>>>>>>>>>> Checking for return value of vsprintf()... Yes.
>>>>>>>>>> Checking for attribute(visibility) support... Yes.
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o example.o
>>>>>>>>>> test/example.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o adler32.o adler32.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o crc32.o crc32.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o deflate.o deflate.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o infback.o infback.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inffast.o inffast.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inflate.o inflate.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o trees.o trees.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o zutil.o zutil.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o compress.o compress.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzread.o gzread.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o minigzip.o
>>>>>>>>>> test/minigzip.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/adler32.o adler32.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/crc32.o crc32.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/deflate.o deflate.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/infback.o infback.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/inffast.o inffast.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/inflate.o inflate.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/inftrees.o inftrees.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/trees.o trees.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/zutil.o zutil.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/compress.o compress.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/uncompr.o uncompr.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/gzclose.o gzclose.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/gzlib.o gzlib.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/gzread.o gzread.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>>> -c -o objs/gzwrite.o gzwrite.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>>>>>>>>> example64.o test/example.c
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>>>>>>>>> minigzip64.o test/minigzip.c
>>>>>>>>>> ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o
>>>>>>>>>> inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o
>>>>>>>>>> gzread.o gzwrite.o
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example example.o -L. libz.a
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
>>>>>>>>>> cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -fPIC
>>>>>>>>>> -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o
>>>>>>>>>> libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo
>>>>>>>>>> inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo
>>>>>>>>>> gzlib.lo gzread.lo gzwrite.lo -lc
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L.
>>>>>>>>>> libz.a
>>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example64 example64.o -L.
>>>>>>>>>> libz.a
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_allocate [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_agent_iterate_memory_pools [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_signal_load_scacquire [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_allocate
>>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>>>>>
>>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_agent_iterate_memory_pools
>>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>>>>>
>>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_iterate_agents
>>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>>>
>>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_signal_load_scacquire
>>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>>>>
>>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_unlock
>>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>>>>
>>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_signal_destroy
>>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>>>
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_get_info [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_agents_allow_access [--no-allow-shlib-undefined]
>>>>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v
>>>>>>>>>> to see invocation)
>>>>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v
>>>>>>>>>> to see invocation)
>>>>>>>>>> gmake: *** [Makefile:292: minigzip] Error 1
>>>>>>>>>> gmake: *** Waiting for unfinished jobs....
>>>>>>>>>> gmake: *** [Makefile:289: example] Error 1
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_allocate [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_agent_iterate_memory_pools [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_signal_load_scacquire [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_get_info [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_agents_allow_access [--no-allow-shlib-undefined]
>>>>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v
>>>>>>>>>> to see invocation)
>>>>>>>>>> gmake: *** [Makefile:304: minigzip64] Error 1
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_allocate [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_agent_iterate_memory_pools [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_signal_load_scacquire [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_get_info [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>>>> ld.lld: error:
>>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>>> hsa_amd_agents_allow_access [--no-allow-shlib-undefined]
>>>>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v
>>>>>>>>>> to see invocation)
>>>>>>>>>> gmake: *** [Makefile:301: example64] Error 1
>>>>>>>>>> rm -f libz.so libz.so.1
>>>>>>>>>> ln -s libz.so.1.2.11 libz.so
>>>>>>>>>> ln -s libz.so.1.2.11 libz.so.1
>>>>>>>>>> 11:03 2 jczhang/fix-kokkos-includes=
>>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11$
>>>>>>>>>>
>>>>>>>>>> On Wed, Jul 7, 2021 at 9:18 AM Matthew Knepley <knepley at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> It is hard to see the error. I suspect it is something crazy
>>>>>>>>>>> with the install. Can you run the build by hand?
>>>>>>>>>>>
>>>>>>>>>>> cd
>>>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
>>>>>>>>>>> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>>> -I${ROCM_PATH}/include"
>>>>>>>>>>> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
>>>>>>>>>>> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
>>>>>>>>>>>
>>>>>>>>>>> and see what happens, and what the error code is?
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Matt
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Jul 7, 2021 at 8:48 AM Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Also, this is in jczhang/fix-kokkos-includes
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Jul 7, 2021 at 8:46 AM Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Apparently the same error with
>>>>>>>>>>>>> --download-zlib=/yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Jul 6, 2021 at 11:53 PM Barry Smith <bsmith at petsc.dev>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> $ curl http://www.zlib.net/zlib-1.2.11.tar.gz >
>>>>>>>>>>>>>> zlib-1.2.11.tar.gz
>>>>>>>>>>>>>> % Total % Received % Xferd Average Speed Time Time
>>>>>>>>>>>>>> Time Current
>>>>>>>>>>>>>> Dload Upload Total
>>>>>>>>>>>>>> Spent Left Speed
>>>>>>>>>>>>>> 100 593k 100 593k 0 0 835k 0 --:--:--
>>>>>>>>>>>>>> --:--:-- --:--:-- 834k
>>>>>>>>>>>>>> ~/Src/petsc*
>>>>>>>>>>>>>> (barry/2021-07-03/demonstrate-network-parallel-build=)*
>>>>>>>>>>>>>> arch-demonstrate-network-parallel-build
>>>>>>>>>>>>>> $ tar -zxf zlib-1.2.11.tar.gz
>>>>>>>>>>>>>> ~/Src/petsc*
>>>>>>>>>>>>>> (barry/2021-07-03/demonstrate-network-parallel-build=)*
>>>>>>>>>>>>>> arch-demonstrate-network-parallel-build
>>>>>>>>>>>>>> $ ls zlib-1.2.11
>>>>>>>>>>>>>> CMakeLists.txt adler32.c deflate.c gzread.c
>>>>>>>>>>>>>> inflate.h os400 watcom zlib.h
>>>>>>>>>>>>>> ChangeLog amiga deflate.h gzwrite.c
>>>>>>>>>>>>>> inftrees.c qnx win32 zlib.map
>>>>>>>>>>>>>> FAQ compress.c doc infback.c
>>>>>>>>>>>>>> inftrees.h test zconf.h
>>>>>>>>>>>>>> zlib.pc.cmakein
>>>>>>>>>>>>>> INDEX configure examples inffast.c
>>>>>>>>>>>>>> make_vms.com treebuild.xml zconf.h.cmakein
>>>>>>>>>>>>>> zlib.pc.in
>>>>>>>>>>>>>> Makefile contrib gzclose.c inffast.h
>>>>>>>>>>>>>> msdos trees.c zconf.h.in zlib2ansi
>>>>>>>>>>>>>> Makefile.in crc32.c gzguts.h inffixed.h
>>>>>>>>>>>>>> nintendods trees.h zlib.3 zutil.c
>>>>>>>>>>>>>> README crc32.h gzlib.c inflate.c
>>>>>>>>>>>>>> old uncompr.c zlib.3.pdf zutil.h
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Jul 6, 2021, at 7:57 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tue, Jul 6, 2021 at 6:42 PM Barry Smith <bsmith at petsc.dev>
>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Mark,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> You can try what the configure error message should be
>>>>>>>>>>>>>>> suggesting (it is not clear if that is being printed to your screen or no).
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ERROR: Unable to download package ZLIB from:
>>>>>>>>>>>>>>> http://www.zlib.net/zlib-1.2.11.tar.gz
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> My browser can not open this and I could not see a download
>>>>>>>>>>>>>> button on this site.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Can you download this?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> * If URL specified manually - perhaps there is a typo?
>>>>>>>>>>>>>>> * If your network is disconnected - please reconnect and
>>>>>>>>>>>>>>> rerun ./configure
>>>>>>>>>>>>>>> * Or perhaps you have a firewall blocking the download
>>>>>>>>>>>>>>> * You can run with --with-packages-download-dir=/adirectory
>>>>>>>>>>>>>>> and ./configure will instruct you what packages to download manually
>>>>>>>>>>>>>>> * or you can download the above URL manually, to
>>>>>>>>>>>>>>> /yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>>>>>> and use the configure option:
>>>>>>>>>>>>>>> --download-zlib=/yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Barry
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> > On Jul 6, 2021, at 4:29 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>> > I am getting some sort of error in build zlib on Spock at
>>>>>>>>>>>>>>> ORNL.
>>>>>>>>>>>>>>> > Other libraries are downloaded and I am sure the network
>>>>>>>>>>>>>>> is fine.
>>>>>>>>>>>>>>> > Any ideas?
>>>>>>>>>>>>>>> > Thanks,
>>>>>>>>>>>>>>> > Mark
>>>>>>>>>>>>>>> > <configure.log>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> What most experimenters take for granted before they begin their
>>>>>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>>>>>> experiments lead.
>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>
>>>>>>>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>>>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>
>>>>>> --
>>>>>> What most experimenters take for granted before they begin their
>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>> experiments lead.
>>>>>> -- Norbert Wiener
>>>>>>
>>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>
>>>>> <configure.log>
>>>>
>>>>
>>>>
>>
>> --
>> 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/>
>>
>
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