On Wed, Jul 7, 2021 at 1:40 PM Mark Adams <mfadams@lbl.gov> wrote:

On Wed, Jul 7, 2021 at 1:26 PM Barry Smith <bsmith@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@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@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@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@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@gmail.com> wrote:

There's an extra comma

Il Mer 7 Lug 2021, 18:08 Mark Adams <mfadams@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@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@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@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@lbl.gov> wrote:

Also, this is in jczhang/fix-kokkos-includes

On Wed, Jul 7, 2021 at 8:46 AM Mark Adams <mfadams@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@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@lbl.gov> wrote:

On Tue, Jul 6, 2021 at 6:42 PM Barry Smith <bsmith@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@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/

--

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/

<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/