Mark,  I can reproduce this error with PrgEnv-cray, i.e., using the Cray compiler (clang-11).  Previously I used PrgEnv-gnu, which did not have this error.  

Probably it is a problem of Spock.  But I am not sure.

--Junchao Zhang

On Sat, Jul 17, 2021 at 10:17 AM Mark Adams <mfadams@lbl.gov> wrote:

And I can run a fortran test, with warnings, but C tests fail:

11:15 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc$ make PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc PETSC_ARCH=arch-spock-opt-cray-kokkos -f gmakefile test search='ts_utils_dmplexlandau_tutorials-ex1f90_0'
Using MAKEFLAGS: -- search=ts_utils_dmplexlandau_tutorials-ex1f90_0 PETSC_ARCH=arch-spock-opt-cray-kokkos PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc
          FC arch-spock-opt-cray-kokkos/tests/ts/utils/dmplexlandau/tutorials/ex1f90.o
     FLINKER arch-spock-opt-cray-kokkos/tests/ts/utils/dmplexlandau/tutorials/ex1f90
/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: warning: alignment 128 of symbol `$host_init$$runtime_init_for_iso_c_binding$iso_c_binding_' in /opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in arch-spock-opt-cray-kokkos/tests/ts/utils/dmplexlandau/tutorials/ex1f90.o
/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: warning: alignment 64 of symbol `$data_init$iso_c_binding_' in /opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in arch-spock-opt-cray-kokkos/tests/ts/utils/dmplexlandau/tutorials/ex1f90.o
        TEST arch-spock-opt-cray-kokkos/tests/counts/ts_utils_dmplexlandau_tutorials-ex1f90_0.counts
 ok ts_utils_dmplexlandau_tutorials-ex1f90_0
 ok diff-ts_utils_dmplexlandau_tutorials-ex1f90_0

On Sat, Jul 17, 2021 at 10:53 AM Mark Adams <mfadams@lbl.gov> wrote:

HUmm, I can not reproduce this.

10:49 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc$ make PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc PETSC_ARCH=arch-spock-dbg-kokkos check
Running check examples to verify correct installation
Using PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc and PETSC_ARCH=arch-spock-dbg-kokkos
gmake[3]: [/gpfs/alpine/csc314/scratch/adams/petsc/lib/petsc/conf/rules:301: ex19.PETSc] Error 2 (ignored)
*******************Error detected during compile or link!*******************
See http://www.mcs.anl.gov/petsc/documentation/faq.html
/gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials ex19
*********************************************************************************
cc -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lamdhip64 -lhsa-runtime64  -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -Qunused-arguments -fvisibility=hidden -g -O0  -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -Qunused-arguments -fvisibility=hidden -g -O0 -I/sw/spock/spack-envs/views/rocm-4.1.0/include   -I/gpfs/alpine/csc314/scratch/adams/petsc/include -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include  -I/sw/spock/spack-envs/views/rocm-4.1.0/include    ex19.c  -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/gcc/8.1.0/snos/lib64 -L/opt/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -L/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -Wl,-rpath,/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -L/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -L/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lsci_cray_mpi -lsci_cray -lmpifort_cray -lmpi_cray -lmpi_gtl_hsa -lxpmem -ldsmml -lpgas-shmem -lquadmath -lcrayacc_amdgpu -lopenacc -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64 -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -o ex19
ld.lld: error: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_start.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined]
ld.lld: error: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_size.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined]
ld.lld: error: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_cache.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined]
clang-11: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[4]: *** [<builtin>: ex19] Error 1
gmake[3]: [/gpfs/alpine/csc314/scratch/adams/petsc/lib/petsc/conf/rules:301: ex3k.PETSc] Error 2 (ignored)
*******************Error detected during compile or link!*******************
See http://www.mcs.anl.gov/petsc/documentation/faq.html
/gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials ex3k
*********************************************************************************
hipcc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O0 -std=c++14  -I/gpfs/alpine/csc314/scratch/adams/petsc/include -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include  -I/sw/spock/spack-envs/views/rocm-4.1.0/include    -I/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/include -I/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/include -I/opt/cray/pe/pmi/6.0.10/include -I/opt/cray/pe/dsmml/0.1.4/dsmml//include -I/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/include  -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml//lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib/pkgconfig/../ -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,--as-needed,-lsci_cray_mpi,--no-as-needed -Wl,--as-needed,-lsci_cray,--no-as-needed -Wl,--as-needed,-lmpi_cray,--no-as-needed -Wl,--as-needed,-ldsmml,--no-as-needed -Wl,--as-needed,-lpgas-shmem,--no-as-needed  -lpmi -ldl -lmpi_gtl_hsa -lxpmem -lquadmath -lmodules -lfi -lcraymath -lf -lu -lcsup  ex3k.kokkos.cxx  -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/gcc/8.1.0/snos/lib64 -L/opt/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -L/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -Wl,-rpath,/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -L/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -L/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lsci_cray_mpi -lsci_cray -lmpifort_cray -lmpi_cray -lmpi_gtl_hsa -lxpmem -ldsmml -lpgas-shmem -lquadmath -lcrayacc_amdgpu -lopenacc -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64 -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -o ex3k
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to `.omp_offloading.img_size.cray_amdgcn-amd-amdhsa'
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to `.omp_offloading.img_start.cray_amdgcn-amd-amdhsa'
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to `.omp_offloading.img_cache.cray_amdgcn-amd-amdhsa'
clang-12: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[4]: *** [/gpfs/alpine/csc314/scratch/adams/petsc/lib/petsc/conf/test:26: ex3k] Error 1
gmake[3]: [makefile:102: runex3k_kokkos] Error 2 (ignored)
1,25c1,4
< atol=1e-50, rtol=1e-08, stol=1e-08, maxit=50, maxf=10000
< Vec Object: Exact Solution 2 MPI processes
<   type: mpikokkos
< Process [0]
< 0.
< 0.015625
< 0.125
< Process [1]
< 0.421875
< 1.
< Vec Object: Forcing function 2 MPI processes
<   type: mpikokkos
< Process [0]
< 1e-72
< 1.50024
< 3.01563
< Process [1]
< 4.67798
< 7.
<   0 SNES Function norm 5.414682427127e+00
<   1 SNES Function norm 2.952582418265e-01
<   2 SNES Function norm 4.502293658739e-04
<   3 SNES Function norm 1.389665806646e-09
< Number of SNES iterations = 3
< Norm of error 1.49752e-10 Iterations 3
---
> slurmstepd: error: execve(): /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials/./ex3k: No such file or directory
> slurmstepd: error: execve(): /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials/./ex3k: No such file or directory
> srun: error: spock01: tasks 0-1: Exited with exit code 2
> srun: launch/slurm: _step_signal: Terminating StepId=272979.0
/gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials
Possible problem with ex3k running with kokkos-kernels, diffs above
=========================================
*******************Error detected during compile or link!*******************
See http://www.mcs.anl.gov/petsc/documentation/faq.html
/gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials ex5f
*********************************************************
ftn -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lamdhip64 -lhsa-runtime64  -fPIC -g -O0   -fPIC -g -O0    -I/gpfs/alpine/csc314/scratch/adams/petsc/include -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include     ex5f.F90  -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/gcc/8.1.0/snos/lib64 -L/opt/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -L/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -Wl,-rpath,/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -L/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -L/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lsci_cray_mpi -lsci_cray -lmpifort_cray -lmpi_cray -lmpi_gtl_hsa -lxpmem -ldsmml -lpgas-shmem -lquadmath -lcrayacc_amdgpu -lopenacc -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64 -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -o ex5f
/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: warning: alignment 128 of symbol `$host_init$$runtime_init_for_iso_c_binding$iso_c_binding_' in /opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in /tmp/pe_30429/ex5f_1.o
/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: warning: alignment 64 of symbol `$data_init$iso_c_binding_' in /opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in /tmp/pe_30429/ex5f_1.o
Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
Completed test examples
10:49 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc$ ll

On Fri, Jul 16, 2021 at 11:28 PM Junchao Zhang <junchao.zhang@gmail.com> wrote:

Mark, I configured with Fortran binding enabled with main + MR !4175

'--with-mpiexec=srun',

'--with-shared-libraries=1',

'--with-cc=cc',

'--with-cxx=CC',

'--with-fc=ftn',

'--with-fortran-bindings',

'--with-hip',

'--with-hipc=hipcc',

'--with-debugging',

'--CPPFLAGS=-I${ROCM_PATH}/include',

'--CXXPPFLAGS=-I${ROCM_PATH}/include',

'--CC_LINKER_FLAGS=-L${ROCM_PATH}/lib -lamdhip64 -lhsa-runtime64',

'--CXX_LINKER_FLAGS=-L${ROCM_PATH}/lib -lamdhip64 -lhsa-runtime64',

'--FC_LINKER_FLAGS=-L${ROCM_PATH}/lib -lamdhip64 -lhsa-runtime64',

'--COPTFLAGS=-g -O0',

'--CXXOPTFLAGS=-g -O0',

'--FOPTFLAGS=-g -O0',

'--download-kokkos',

'--download-kokkos-kernels',

'--download-kokkos-commit=3.4.01',

'--download-kokkos-kernels-commit=3.4.01',

'--with-kokkos-hip-arch=VEGA908',

and 'make check' ran smoothly on a compute node

$ make check

Running check examples to verify correct installation

Using PETSC_DIR=/ccs/home/jczhang/petsc and PETSC_ARCH=arch-spock-cray-kokkos-dbg

C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process

C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes

C/C++ example src/snes/tutorials/ex3k run successfully with kokkos-kernels

Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process

Completed test examples

--Junchao Zhang

On Fri, Jul 16, 2021 at 6:04 PM Mark Adams <mfadams@lbl.gov> wrote:

And I find that this error, on non-Kokkos C tests, is fixed by turning the fortran bindings off:

ld.lld: error: /gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_start.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined]
ld.lld: error: /gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_size.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined]
ld.lld: error: /gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_cache.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined]

On Fri, Jul 16, 2021 at 3:53 PM Mark Adams <mfadams@lbl.gov> wrote:

Not complex. THis has some overlap with my problem w/o Kokkos.

On Fri, Jul 16, 2021 at 12:54 PM Junchao Zhang <junchao.zhang@gmail.com> wrote:

Do you use complex? post your configure.log. 

--Junchao Zhang

On Fri, Jul 16, 2021 at 9:47 AM Mark Adams <mfadams@lbl.gov> wrote:

The simple Kokkos example is failing for me on Spock.

Any ideas?

Thanks,

10:44 main *= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ make PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc PETSC_ARCH=arch-spock-opt-cray-kokkos ex3k
MPICH_CXX="hipcc" OMPI_CXX="hipcc" CC -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lhsa-runtime64 -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lamdhip64 -lhsa-runtime64  -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O2   -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O3 -std=c++14  -I/gpfs/alpine/csc314/scratch/adams/petsc/include -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/include -I/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include  -I/sw/spock/spack-envs/views/rocm-4.1.0/include    ex3k.kokkos.cxx  -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/lib -Wl,-rpath,/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib -L/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/gcc/8.1.0/snos/lib64 -L/opt/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -L/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -Wl,-rpath,/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -L/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -L/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lsci_cray_mpi -lsci_cray -lmpifort_cray -lmpi_cray -lmpi_gtl_hsa -lxpmem -ldsmml -lpgas-shmem -lquadmath -lcrayacc_amdgpu -lopenacc -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64 -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -o ex3k
In file included from ex3k.kokkos.cxx:3:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscdmda_kokkos.hpp:4:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec_kokkos.hpp:14:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec.h:9:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsys.h:42:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsystypes.h:255:
In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Complex.hpp:47:
In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Atomic.hpp:212:
/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Atomic_Exchange.hpp:259:11: error: no member named 'lock_address_host_space' in namespace 'Kokkos::Impl::Kokkos::Impl'; did you mean simply 'lock_address_host_space'?
  while (!Impl::lock_address_host_space((void*)dest))
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          lock_address_host_space
/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_HostSpace.hpp:83:6: note: 'lock_address_host_space' declared here
bool lock_address_host_space(void* ptr);
     ^
In file included from ex3k.kokkos.cxx:3:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscdmda_kokkos.hpp:4:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec_kokkos.hpp:14:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec.h:9:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsys.h:42:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsystypes.h:255:
In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Complex.hpp:47:
In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Atomic.hpp:212:
/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Atomic_Exchange.hpp:261:3: error: no member named 'memory_fence' in namespace 'Kokkos::Impl::Kokkos'; did you mean simply 'memory_fence'?
  Kokkos::memory_fence();
  ^~~~~~~~~~~~~~~~~~~~
  memory_fence
/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Memory_Fence.hpp:53:6: note: 'memory_fence' declared here
void memory_fence() {
     ^
In file included from ex3k.kokkos.cxx:3:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscdmda_kokkos.hpp:4:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec_kokkos.hpp:14:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec.h:9:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsys.h:42:
In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsystypes.h:255:
In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Complex.hpp:47:
In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Atomic.hpp:212:
/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Atomic_Exchange.hpp:277:3: error: no member named 'memory_fence' in namespace 'Kokkos::Impl::Kokkos'; did you mean simply 'memory_fence'?
  Kokkos::memory_fence();
  ^~~~~~~~~~~~~~~~~~~~
  memory_fence
/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Memory_Fence.hpp:53:6: note: 'memory_fence' declared here
void memory_fence() {
     ^