[petsc-users] download zlib error
Mark Adams
mfadams at lbl.gov
Wed Jul 7 12:18:56 CDT 2021
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/>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20210707/73d24553/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: configure.log
Type: application/octet-stream
Size: 1445691 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20210707/73d24553/attachment-0001.obj>
More information about the petsc-users
mailing list