[petsc-users] download zlib error
Matthew Knepley
knepley at gmail.com
Wed Jul 7 11:47:51 CDT 2021
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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