[petsc-users] download zlib error
Mark Adams
mfadams at lbl.gov
Wed Jul 7 14:45:06 CDT 2021
No diffs. I added this:
diff --git a/config/BuildSystem/config/packages/zlib.py
b/config/BuildSystem/config/packages/zlib.py
index fbf9bdf4a0..b76d362536 100644
--- a/config/BuildSystem/config/packages/zlib.py
+++ b/config/BuildSystem/config/packages/zlib.py
@@ -25,6 +25,7 @@ class Configure(config.package.Package):
self.pushLanguage('C')
args.append('CC="'+self.getCompiler()+'"')
args.append('CFLAGS="'+self.updatePackageCFlags(self.getCompilerFlags())+'"')
+ args.append('LDFLAGS="'+self.getLinkerFlags()+'"')
args.append('prefix="'+self.installDir+'"')
self.popLanguage()
args=' '.join(args)
lines 1-12/12 (END)
but it still fails.
15:20 jczhang/fix-kokkos-includes *=
/gpfs/alpine/csc314/scratch/adams/petsc$ cd
/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
&& CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
-I${ROCM_PATH}/include"
prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
Checking for shared library support...
Building shared library libz.so.1.2.11 with cc.
Checking for size_t... Yes.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... No.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using
vs[n]printf().
Checking for vsnprintf() in stdio.h... No.
WARNING: vsnprintf() not found, falling back to vsprintf(). zlib
can build but will be open to possible buffer-overflow security
vulnerabilities.
Checking for return value of vsprintf()... Yes.
Checking for attribute(visibility) support... Yes.
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o example.o
test/example.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o adler32.o adler32.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o crc32.o crc32.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o deflate.o deflate.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o infback.o infback.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inffast.o inffast.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inflate.o inflate.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o trees.o trees.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o zutil.o zutil.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o compress.o compress.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzread.o gzread.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o minigzip.o
test/minigzip.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/adler32.o adler32.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/crc32.o crc32.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/deflate.o deflate.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/infback.o infback.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/inffast.o inffast.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/inflate.o inflate.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/inftrees.o inftrees.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/trees.o trees.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/zutil.o zutil.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/compress.o compress.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/uncompr.o uncompr.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/gzclose.o gzclose.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/gzlib.o gzlib.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/gzread.o gzread.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
-c -o objs/gzwrite.o gzwrite.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
example64.o test/example.c
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
minigzip64.o test/minigzip.c
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o
inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o
gzwrite.o
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example example.o -L. libz.a
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -fPIC
-fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
-D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o
libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo
inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo
gzlib.lo gzread.lo gzwrite.lo -lc
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L.
libz.a
cc -fPIC -fstack-protector -Qunused-arguments -g -O0
-I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
-DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example64 example64.o -L.
libz.a
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_allocate
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_agent_iterate_memory_pools
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_signal_load_scacquire
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_get_info
[--no-allow-shlib-undefined]
ld.lldld.lld: : error: error:
/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
hsa_amd_memory_lock
[--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_allocate
[--no-allow-shlib-undefined]
ld.lld: ld.lld: error: error:
/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
hsa_amd_agent_iterate_memory_pools [--no-allow-shlib-undefined]ld.lld
: ld.lld: error: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_agents_allow_access
[--no-allow-shlib-undefined]
/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
hsa_iterate_agents [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_signal_load_scacquire
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_get_info
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_agents_allow_access
[--no-allow-shlib-undefined]
clang-11: error: linker command failed with exit code 1 (use -v to see
invocation)
clang-11: error: linker command failed with exit code 1 (use -v to see
invocation)
gmake: *** [Makefile:292: minigzip] Error 1
gmake: *** Waiting for unfinished jobs....
gmake: *** [Makefile:289: example] Error 1
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_allocate
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_agent_iterate_memory_pools
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_signal_load_scacquire
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_get_info
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_agents_allow_access
[--no-allow-shlib-undefined]
clang-11: error: linker command failed with exit code 1 (use -v to see
invocation)
gmake: *** [Makefile:304: minigzip64] Error 1
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_allocate
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_agent_iterate_memory_pools
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_signal_load_scacquire
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_get_info
[--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
undefined reference to hsa_amd_agents_allow_access
[--no-allow-shlib-undefined]
clang-11: error: linker command failed with exit code 1 (use -v to see
invocation)
gmake: *** [Makefile:301: example64] Error 1
rm -f libz.so libz.so.1
ln -s libz.so.1.2.11 libz.so
On Wed, Jul 7, 2021 at 2:03 PM Matthew Knepley <knepley at gmail.com> wrote:
> On Wed, Jul 7, 2021 at 1:40 PM Mark Adams <mfadams at lbl.gov> wrote:
>
>>
>>
>> On Wed, Jul 7, 2021 at 1:26 PM Barry Smith <bsmith at petsc.dev> wrote:
>>
>>>
>>> You will need to pass the -L arguments appropriately to zlib's
>>> ./configure so it can link its shared library appropriately. That is, the
>>> zlib configure requires the value obtained with
>>> L'+os.environ['ROCM_PATH'],+'/lib -lhsa-runtime64',
>>>
>>
>> It's not clear to me how to do that. I added the -L to my configure
>> script. It is not clear to me how to modify Matt's command.
>>
>
> Can you try this?
>
> knepley/feature-orientation-rethink *$:/PETSc3/petsc/petsc-dev$ git diff
> config/BuildSystem/config/packages/zlib.py
> diff --git a/config/BuildSystem/config/packages/zlib.py
> b/config/BuildSystem/config/packages/zlib.py
> index fbf9bdf4a0a..b76d3625364 100644
> --- a/config/BuildSystem/config/packages/zlib.py
> +++ b/config/BuildSystem/config/packages/zlib.py
> @@ -25,6 +25,7 @@ class Configure(config.package.Package):
>
> self.pushLanguage('C')
> args.append('CC="'+self.getCompiler()+'"')
>
> args.append('CFLAGS="'+self.updatePackageCFlags(self.getCompilerFlags())+'"')
> + args.append('LDFLAGS="'+self.getLinkerFlags()+'"')
> args.append('prefix="'+self.installDir+'"')
> self.popLanguage()
> args=' '.join(args)
>
> Matt
>
>
>>
>>> On Jul 7, 2021, at 12:18 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>
>>> Well, still getting these hsa errors:
>>>
>>> 13:07 jczhang/fix-kokkos-includes=
>>> /gpfs/alpine/csc314/scratch/adams/petsc$ !136
>>> cd
>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
>>> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I${ROCM_PATH}/include"
>>> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
>>> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
>>> Checking for shared library support...
>>> Building shared library libz.so.1.2.11 with cc.
>>> Checking for size_t... Yes.
>>> Checking for off64_t... Yes.
>>> Checking for fseeko... Yes.
>>> Checking for strerror... No.
>>> Checking for unistd.h... Yes.
>>> Checking for stdarg.h... Yes.
>>> Checking whether to use vs[n]printf() or s[n]printf()... using
>>> vs[n]printf().
>>> Checking for vsnprintf() in stdio.h... No.
>>> WARNING: vsnprintf() not found, falling back to vsprintf(). zlib
>>> can build but will be open to possible buffer-overflow security
>>> vulnerabilities.
>>> Checking for return value of vsprintf()... Yes.
>>> Checking for attribute(visibility) support... Yes.
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o example.o
>>> test/example.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o adler32.o adler32.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o crc32.o crc32.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o deflate.o deflate.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o infback.o infback.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inffast.o inffast.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inflate.o inflate.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o trees.o trees.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o zutil.o zutil.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o compress.o compress.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzread.o gzread.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o minigzip.o
>>> test/minigzip.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/adler32.o adler32.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/crc32.o crc32.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/deflate.o deflate.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/infback.o infback.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/inffast.o inffast.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/inflate.o inflate.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/inftrees.o inftrees.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/trees.o trees.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/zutil.o zutil.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/compress.o compress.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/uncompr.o uncompr.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/gzclose.o gzclose.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/gzlib.o gzlib.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/gzread.o gzread.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>> -c -o objs/gzwrite.o gzwrite.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>> example64.o test/example.c
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>> minigzip64.o test/minigzip.c
>>> ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o
>>> inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o
>>> gzwrite.o
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example example.o -L. libz.a
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
>>> cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -fPIC
>>> -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o
>>> libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo
>>> inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo
>>> gzlib.lo gzread.lo gzwrite.lo -lc
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L.
>>> libz.a
>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example64 example64.o -L.
>>> libz.a
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_allocate
>>> [--no-allow-shlib-undefined]
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_amd_memory_pool_allocate
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>> [--no-allow-shlib-undefined]
>>>
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_amd_agent_iterate_memory_pools
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_iterate_agents
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_signal_load_scacquire
>>> [--no-allow-shlib-undefined]
>>>
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_signal_load_scacquire
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_amd_memory_unlock
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_signal_destroy
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_get_info
>>> [--no-allow-shlib-undefined]
>>>
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_amd_memory_pool_get_info
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_amd_memory_lock
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>
>>> ld.lldld.lld: : error: error:
>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>> hsa_amd_memory_pool_free
>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_agents_allow_access
>>> [--no-allow-shlib-undefined]
>>>
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_agents_allow_access
>>> [--no-allow-shlib-undefined]
>>> clang-11: error: linker command failed with exit code 1 (use -v to see
>>> invocation)
>>> clang-11: error: linker command failed with exit code 1 (use -v to see
>>> invocation)
>>> gmake: *** [Makefile:289: example] Error 1
>>> gmake: *** Waiting for unfinished jobs....
>>> gmake: *** [Makefile:292: minigzip] Error 1
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_allocate
>>> [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>> [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_signal_load_scacquire
>>> [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_get_info
>>> [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_agents_allow_access
>>> [--no-allow-shlib-undefined]
>>> clang-11: error: linker command failed with exit code 1 (use -v to see
>>> invocation)
>>> gmake: *** [Makefile:304: minigzip64] Error 1
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_allocate
>>> [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>> [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_signal_load_scacquire
>>> [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_get_info
>>> [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>> undefined reference to hsa_amd_agents_allow_access
>>> [--no-allow-shlib-undefined]
>>> clang-11: error: linker command failed with exit code 1 (use -v to see
>>> invocation)
>>> gmake: *** [Makefile:301: example64] Error 1
>>> rm -f libz.so libz.so.1
>>> ln -s libz.so.1.2.11 libz.so
>>> ln -s libz.so.1.2.11 libz.so.1
>>>
>>> On Wed, Jul 7, 2021 at 1:05 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>
>>>> Thanks, it was missing the /
>>>>
>>>> '--LDFLAGS=-L'+os.environ['ROCM_PATH'],+'/lib -lhsa-runtime64',
>>>>
>>>> On Wed, Jul 7, 2021 at 12:48 PM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> Did you look in /sw/spock/spack-envs/views/rocm-4.1.0lib ?
>>>>>
>>>>> Matt
>>>>>
>>>>> On Wed, Jul 7, 2021 at 12:29 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>>>
>>>>>> Ok, I tried that but now I get this error.
>>>>>>
>>>>>> On Wed, Jul 7, 2021 at 12:13 PM Stefano Zampini <
>>>>>> stefano.zampini at gmail.com> wrote:
>>>>>>
>>>>>>> There's an extra comma
>>>>>>>
>>>>>>> Il Mer 7 Lug 2021, 18:08 Mark Adams <mfadams at lbl.gov> ha scritto:
>>>>>>>
>>>>>>>> Humm, I get this error (I just copied your whole file into here):
>>>>>>>>
>>>>>>>> 12:06 jczhang/fix-kokkos-includes=
>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc$ ~/arch-spock-dbg-cray-kokkos.py
>>>>>>>> Traceback (most recent call last):
>>>>>>>> File "/ccs/home/adams/arch-spock-dbg-cray-kokkos.py", line 27, in
>>>>>>>> <module>
>>>>>>>> '--LDFLAGS=-L'+os.environ['ROCM_PATH'],+'lib -lhsa-runtime64',
>>>>>>>> TypeError: bad operand type for unary +: 'str'
>>>>>>>>
>>>>>>>> On Wed, Jul 7, 2021 at 11:08 AM Stefano Zampini <
>>>>>>>> stefano.zampini at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Mark
>>>>>>>>>
>>>>>>>>> On Spock, you can use
>>>>>>>>> https://gitlab.com/petsc/petsc/-/blob/main/config/examples/arch-olcf-spock.py as
>>>>>>>>> a template for your configuration. You need to add libraries as LDFLAGS to
>>>>>>>>> resolve the hsa symbols
>>>>>>>>>
>>>>>>>>> On Jul 7, 2021, at 5:04 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> 08:30 jczhang/fix-kokkos-includes=
>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc$ cd
>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
>>>>>>>>> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I${ROCM_PATH}/include"
>>>>>>>>> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
>>>>>>>>> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
>>>>>>>>> Checking for shared library support...
>>>>>>>>> Building shared library libz.so.1.2.11 with cc.
>>>>>>>>> Checking for size_t... Yes.
>>>>>>>>> Checking for off64_t... Yes.
>>>>>>>>> Checking for fseeko... Yes.
>>>>>>>>> Checking for strerror... No.
>>>>>>>>> Checking for unistd.h... Yes.
>>>>>>>>> Checking for stdarg.h... Yes.
>>>>>>>>> Checking whether to use vs[n]printf() or s[n]printf()... using
>>>>>>>>> vs[n]printf().
>>>>>>>>> Checking for vsnprintf() in stdio.h... No.
>>>>>>>>> WARNING: vsnprintf() not found, falling back to vsprintf(). zlib
>>>>>>>>> can build but will be open to possible buffer-overflow security
>>>>>>>>> vulnerabilities.
>>>>>>>>> Checking for return value of vsprintf()... Yes.
>>>>>>>>> Checking for attribute(visibility) support... Yes.
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o example.o
>>>>>>>>> test/example.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o adler32.o adler32.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o crc32.o crc32.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o deflate.o deflate.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o infback.o infback.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inffast.o inffast.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inflate.o inflate.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o trees.o trees.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o zutil.o zutil.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o compress.o compress.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzread.o gzread.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -c -o minigzip.o
>>>>>>>>> test/minigzip.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/adler32.o adler32.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/crc32.o crc32.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/deflate.o deflate.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/infback.o infback.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/inffast.o inffast.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/inflate.o inflate.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/inftrees.o inftrees.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/trees.o trees.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/zutil.o zutil.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/compress.o compress.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/uncompr.o uncompr.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/gzclose.o gzclose.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/gzlib.o gzlib.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/gzread.o gzread.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -DPIC
>>>>>>>>> -c -o objs/gzwrite.o gzwrite.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>>>>>>>> example64.o test/example.c
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o
>>>>>>>>> minigzip64.o test/minigzip.c
>>>>>>>>> ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o
>>>>>>>>> inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o
>>>>>>>>> gzread.o gzwrite.o
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example example.o -L. libz.a
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
>>>>>>>>> cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -fPIC
>>>>>>>>> -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -fPIC
>>>>>>>>> -D_LARGEFILE64_SOURCE=1 -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o
>>>>>>>>> libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo
>>>>>>>>> inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo
>>>>>>>>> gzlib.lo gzread.lo gzwrite.lo -lc
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L.
>>>>>>>>> libz.a
>>>>>>>>> cc -fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>> -I/sw/spock/spack-envs/views/rocm-4.1.0/include -D_LARGEFILE64_SOURCE=1
>>>>>>>>> -DNO_STRERROR -DNO_vsnprintf -DHAVE_HIDDEN -o example64 example64.o -L.
>>>>>>>>> libz.a
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_signal_load_scacquire
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>> hsa_amd_memory_pool_allocate
>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>>>>
>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>> hsa_amd_agent_iterate_memory_pools
>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>>>>
>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>> hsa_iterate_agents
>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>>
>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>> hsa_signal_load_scacquire
>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>>>
>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>> hsa_amd_memory_unlock
>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>>>
>>>>>>>>> ld.lldld.lld: : error: error:
>>>>>>>>> /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so: undefined reference to
>>>>>>>>> hsa_signal_destroy
>>>>>>>>> [--no-allow-shlib-undefined]/opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>>
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v to
>>>>>>>>> see invocation)
>>>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v to
>>>>>>>>> see invocation)
>>>>>>>>> gmake: *** [Makefile:292: minigzip] Error 1
>>>>>>>>> gmake: *** Waiting for unfinished jobs....
>>>>>>>>> gmake: *** [Makefile:289: example] Error 1
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_signal_load_scacquire
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v to
>>>>>>>>> see invocation)
>>>>>>>>> gmake: *** [Makefile:304: minigzip64] Error 1
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_allocate
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_agent_iterate_memory_pools
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_iterate_agents [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_signal_load_scacquire
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_unlock [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_signal_destroy [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_get_info
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_lock [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_memory_pool_free [--no-allow-shlib-undefined]
>>>>>>>>> ld.lld: error: /opt/cray/pe/mpich/8.1.4/gtl/lib/libmpi_gtl_hsa.so:
>>>>>>>>> undefined reference to hsa_amd_agents_allow_access
>>>>>>>>> [--no-allow-shlib-undefined]
>>>>>>>>> clang-11: error: linker command failed with exit code 1 (use -v to
>>>>>>>>> see invocation)
>>>>>>>>> gmake: *** [Makefile:301: example64] Error 1
>>>>>>>>> rm -f libz.so libz.so.1
>>>>>>>>> ln -s libz.so.1.2.11 libz.so
>>>>>>>>> ln -s libz.so.1.2.11 libz.so.1
>>>>>>>>> 11:03 2 jczhang/fix-kokkos-includes=
>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11$
>>>>>>>>>
>>>>>>>>> On Wed, Jul 7, 2021 at 9:18 AM Matthew Knepley <knepley at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> It is hard to see the error. I suspect it is something crazy with
>>>>>>>>>> the install. Can you run the build by hand?
>>>>>>>>>>
>>>>>>>>>> cd
>>>>>>>>>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/externalpackages/zlib-1.2.11
>>>>>>>>>> && CC="cc" CFLAGS="-fPIC -fstack-protector -Qunused-arguments -g -O0
>>>>>>>>>> -I${ROCM_PATH}/include"
>>>>>>>>>> prefix="/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos"
>>>>>>>>>> ./configure && /usr/bin/gmake -j8 -l307.2 && /usr/bin/gmake install
>>>>>>>>>>
>>>>>>>>>> and see what happens, and what the error code is?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Matt
>>>>>>>>>>
>>>>>>>>>> On Wed, Jul 7, 2021 at 8:48 AM Mark Adams <mfadams at lbl.gov>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Also, this is in jczhang/fix-kokkos-includes
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Jul 7, 2021 at 8:46 AM Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Apparently the same error with
>>>>>>>>>>>> --download-zlib=/yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Jul 6, 2021 at 11:53 PM Barry Smith <bsmith at petsc.dev>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> $ curl http://www.zlib.net/zlib-1.2.11.tar.gz >
>>>>>>>>>>>>> zlib-1.2.11.tar.gz
>>>>>>>>>>>>> % Total % Received % Xferd Average Speed Time Time
>>>>>>>>>>>>> Time Current
>>>>>>>>>>>>> Dload Upload Total
>>>>>>>>>>>>> Spent Left Speed
>>>>>>>>>>>>> 100 593k 100 593k 0 0 835k 0 --:--:--
>>>>>>>>>>>>> --:--:-- --:--:-- 834k
>>>>>>>>>>>>> ~/Src/petsc*
>>>>>>>>>>>>> (barry/2021-07-03/demonstrate-network-parallel-build=)*
>>>>>>>>>>>>> arch-demonstrate-network-parallel-build
>>>>>>>>>>>>> $ tar -zxf zlib-1.2.11.tar.gz
>>>>>>>>>>>>> ~/Src/petsc*
>>>>>>>>>>>>> (barry/2021-07-03/demonstrate-network-parallel-build=)*
>>>>>>>>>>>>> arch-demonstrate-network-parallel-build
>>>>>>>>>>>>> $ ls zlib-1.2.11
>>>>>>>>>>>>> CMakeLists.txt adler32.c deflate.c gzread.c
>>>>>>>>>>>>> inflate.h os400 watcom zlib.h
>>>>>>>>>>>>> ChangeLog amiga deflate.h gzwrite.c
>>>>>>>>>>>>> inftrees.c qnx win32 zlib.map
>>>>>>>>>>>>> FAQ compress.c doc infback.c
>>>>>>>>>>>>> inftrees.h test zconf.h
>>>>>>>>>>>>> zlib.pc.cmakein
>>>>>>>>>>>>> INDEX configure examples inffast.c
>>>>>>>>>>>>> make_vms.com treebuild.xml zconf.h.cmakein zlib.pc.in
>>>>>>>>>>>>> Makefile contrib gzclose.c inffast.h
>>>>>>>>>>>>> msdos trees.c zconf.h.in zlib2ansi
>>>>>>>>>>>>> Makefile.in crc32.c gzguts.h inffixed.h
>>>>>>>>>>>>> nintendods trees.h zlib.3 zutil.c
>>>>>>>>>>>>> README crc32.h gzlib.c inflate.c
>>>>>>>>>>>>> old uncompr.c zlib.3.pdf zutil.h
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Jul 6, 2021, at 7:57 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Jul 6, 2021 at 6:42 PM Barry Smith <bsmith at petsc.dev>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Mark,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> You can try what the configure error message should be
>>>>>>>>>>>>>> suggesting (it is not clear if that is being printed to your screen or no).
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ERROR: Unable to download package ZLIB from:
>>>>>>>>>>>>>> http://www.zlib.net/zlib-1.2.11.tar.gz
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> My browser can not open this and I could not see a download
>>>>>>>>>>>>> button on this site.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Can you download this?
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * If URL specified manually - perhaps there is a typo?
>>>>>>>>>>>>>> * If your network is disconnected - please reconnect and
>>>>>>>>>>>>>> rerun ./configure
>>>>>>>>>>>>>> * Or perhaps you have a firewall blocking the download
>>>>>>>>>>>>>> * You can run with --with-packages-download-dir=/adirectory
>>>>>>>>>>>>>> and ./configure will instruct you what packages to download manually
>>>>>>>>>>>>>> * or you can download the above URL manually, to
>>>>>>>>>>>>>> /yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>>>>> and use the configure option:
>>>>>>>>>>>>>> --download-zlib=/yourselectedlocation/zlib-1.2.11.tar.gz
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Barry
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> > On Jul 6, 2021, at 4:29 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > I am getting some sort of error in build zlib on Spock at
>>>>>>>>>>>>>> ORNL.
>>>>>>>>>>>>>> > Other libraries are downloaded and I am sure the network is
>>>>>>>>>>>>>> fine.
>>>>>>>>>>>>>> > Any ideas?
>>>>>>>>>>>>>> > Thanks,
>>>>>>>>>>>>>> > Mark
>>>>>>>>>>>>>> > <configure.log>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> What most experimenters take for granted before they begin their
>>>>>>>>>> experiments is infinitely more interesting than any results to which their
>>>>>>>>>> experiments lead.
>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>
>>>>>>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>
>>>>> --
>>>>> What most experimenters take for granted before they begin their
>>>>> experiments is infinitely more interesting than any results to which their
>>>>> experiments lead.
>>>>> -- Norbert Wiener
>>>>>
>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>
>>>> <configure.log>
>>>
>>>
>>>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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