[petsc-users] download zlib error
Matthew Knepley
knepley at gmail.com
Wed Jul 7 16:49:42 CDT 2021
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.
>
It is hard to understand how that was added. You can see that 'CC',
'CFLAGS', and 'prefix' are present on the line below, but 'LDFLAGS' is not.
That is difficult to reconcile.
Thanks,
Matt
> 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/>
>>
>
--
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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