[petsc-users] download zlib error
Matthew Knepley
knepley at gmail.com
Wed Jul 7 13:02:55 CDT 2021
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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