[petsc-users] download zlib error
Mark Adams
mfadams at lbl.gov
Wed Jul 7 12:05:49 CDT 2021
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/>
>
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