Hi, Sophie, I tried various modules and compilers on Summit and failed to find one that works with gpu aware mpi. The one that could build petsc and kokkos was "module load cuda/11.7.1 gcc/9.3.0-compiler_only spectrum-mpi essl netlib-lapack". But it only worked with "-use_gpu_aware_mpi 0". Without it, I saw code crashes. From what I can see, the gpu-aware mpi on Summit is an unusable and unmaintained state.
--Junchao Zhang On Fri, Mar 1, 2024 at 3:58 PM Junchao Zhang <junchao.zh...@gmail.com> wrote: > It is weird, with > jsrun --smpiargs "-gpu" -n 6 -a 1 -c 1 -g 1 /gpfs/alpine2/mat267/proj- > shared/dependencies/petsc-kokkos/src/ksp/ksp/tutorials/bench_kspsolve > -mat_type aijkokkos -use_gpu_aware_mpi 1 > > petsc tried to test if the MPI is gpu aware (by doing an MPI_Allreduce on > device buffers). It tried and found it was not, so it threw out the > complaint in the error message. > > From > https://urldefense.us/v3/__https://docs.olcf.ornl.gov/systems/summit_user_guide.html*cuda-aware-mpi__;Iw!!G_uCfscf7eWS!cq445CXteimKBMZKF1HQqgEFTwREIrbMMm5Cn-sCV3wDm2A3tixBsge_FLfW-3YKRxtbYWK9D29cMq338kMstbOGRUZc$ > , > I think your flags were right. > > I just got my Summit account reactivated today. I will give it a try. > > --Junchao Zhang > > > On Fri, Mar 1, 2024 at 3:32 PM Blondel, Sophie <sblon...@utk.edu> wrote: > >> I have been using --smpiargs "-gpu". >> >> I tried the benchmark with "jsrun --smpiargs "-gpu" -n 6 -a 1 -c 1 -g 1 >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos/src/ksp/ksp/tutorials/bench_kspsolve >> -mat_type aijkokkos -use_gpu_aware_mpi 0" and it seems to work: >> Fri Mar 1 16:27:14 EST 2024 >> =========================================== >> Test: KSP performance - Poisson >> Input matrix: 27-pt finite difference stencil >> -n 100 >> DoFs = 1000000 >> Number of nonzeros = 26463592 >> >> Step1 - creating Vecs and Mat... >> Step2 - running KSPSolve()... >> Step3 - calculating error norm... >> >> Error norm: 5.591e-02 >> KSP iters: 63 >> KSPSolve: 3.16646 seconds >> FOM: 3.158e+05 DoFs/sec >> =========================================== >> >> ------------------------------------------------------------ >> Sender: LSF System <lsfadmin@batch3> >> Subject: Job 3322694: <xolotlTest> in cluster <summit> Done >> >> Job <xolotlTest> was submitted from host <login2> by user <bqo> in >> cluster <summit> at Fri Mar 1 16:26:58 2024 >> Job was executed on host(s) <1*batch3>, in queue <debug>, as user <bqo> >> in cluster <summit> at Fri Mar 1 16:27:00 2024 >> <42*a35n05> >> </ccs/home/bqo> was used as the home directory. >> </gpfs/alpine2/mat267/scratch/bqo/test> was used as the working directory. >> Started at Fri Mar 1 16:27:00 2024 >> Terminated at Fri Mar 1 16:27:26 2024 >> Results reported at Fri Mar 1 16:27:26 2024 >> >> The output (if any) is above this job summary. >> >> >> If I switch to "jsrun --smpiargs "-gpu" -n 6 -a 1 -c 1 -g 1 >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos/src/ksp/ksp/tutorials/bench_kspsolve >> -mat_type aijkokkos -use_gpu_aware_mpi 1" it complains: >> Fri Mar 1 16:25:02 EST 2024 >> =========================================== >> Test: KSP performance - Poisson >> Input matrix: 27-pt finite difference stencil >> -n 100 >> DoFs = 1000000 >> Number of nonzeros = 26463592 >> >> Step1 - creating Vecs and Mat... >> [5]PETSC ERROR: PETSc is configured with GPU support, but your MPI is not >> GPU-aware. For better performance, please use a GPU-aware MPI. >> [5]PETSC ERROR: If you do not care, add option -use_gpu_aware_mpi 0. To >> not see the message again, add the option to your .petscrc, OR add it to >> the env var PETSC_OPTIONS. >> [5]PETSC ERROR: If you do care, for IBM Spectrum MPI on OLCF Summit, you >> may need jsrun --smpiargs=-gpu. >> [5]PETSC ERROR: For Open MPI, you need to configure it --with-cuda ( >> https://urldefense.us/v3/__https://www.open-mpi.org/faq/?category=buildcuda__;!!G_uCfscf7eWS!cq445CXteimKBMZKF1HQqgEFTwREIrbMMm5Cn-sCV3wDm2A3tixBsge_FLfW-3YKRxtbYWK9D29cMq338kMstegRM8hj$ >> ) >> [5]PETSC ERROR: For MVAPICH2-GDR, you need to set MV2_USE_CUDA=1 ( >> https://urldefense.us/v3/__http://mvapich.cse.ohio-state.edu/userguide/gdr/__;!!G_uCfscf7eWS!cq445CXteimKBMZKF1HQqgEFTwREIrbMMm5Cn-sCV3wDm2A3tixBsge_FLfW-3YKRxtbYWK9D29cMq338kMstf6tc3Lv$ >> ) >> [5]PETSC ERROR: For Cray-MPICH, you need to set >> MPICH_GPU_SUPPORT_ENABLED=1 (man mpi to see manual of cray-mpich) >> -------------------------------------------------------------------------- >> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >> with errorcode 76. >> >> Best, >> >> Sophie >> ------------------------------ >> *From:* Junchao Zhang <junchao.zh...@gmail.com> >> *Sent:* Thursday, February 29, 2024 17:09 >> *To:* Blondel, Sophie <sblon...@utk.edu> >> *Cc:* xolotl-psi-developm...@lists.sourceforge.net < >> xolotl-psi-developm...@lists.sourceforge.net>; petsc-users@mcs.anl.gov < >> petsc-users@mcs.anl.gov> >> *Subject:* Re: [petsc-users] PAMI error on Summit >> >> You don't often get email from junchao.zh...@gmail.com. Learn why this >> is important >> <https://urldefense.us/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!G_uCfscf7eWS!cq445CXteimKBMZKF1HQqgEFTwREIrbMMm5Cn-sCV3wDm2A3tixBsge_FLfW-3YKRxtbYWK9D29cMq338kMstYnzecTK$ >> > >> Could you try a petsc example to see if the environment is good? >> For example, >> >> cd src/ksp/ksp/tutorials >> make bench_kspsolve >> mpirun -n 6 ./bench_kspsolve -mat_type aijkokkos -use_gpu_aware_mpi {0 >> or 1} >> >> BTW, I remember to use gpu-aware mpi on Summit, one needs to pass >> --smpiargs "-gpu" to jsrun >> >> --Junchao Zhang >> >> >> On Thu, Feb 29, 2024 at 3:22 PM Blondel, Sophie via petsc-users < >> petsc-users@mcs.anl.gov> wrote: >> >> I still get the same error when deactivating GPU-aware MPI. I also tried >> unloading spectrum MPI and using openMPI instead (recompiling everything) >> and I get a segfault in PETSc in that case (still using GPU-aware MPI I >> think, at least not explicitly >> ZjQcmQRYFpfptBannerStart >> This Message Is From an External Sender >> This message came from outside your organization. >> >> ZjQcmQRYFpfptBannerEnd >> I still get the same error when deactivating GPU-aware MPI. >> >> I also tried unloading spectrum MPI and using openMPI instead >> (recompiling everything) and I get a segfault in PETSc in that case (still >> using GPU-aware MPI I think, at least not explicitly turning it off): >> >> 0 TS dt 1e-12 time 0. >> >> [ERROR] [0]PETSC ERROR: >> >> [ERROR] >> ------------------------------------------------------------------------ >> >> [ERROR] [0]PETSC ERROR: >> >> [ERROR] Caught signal number 11 SEGV: Segmentation Violation, probably >> memory access out of range >> >> [ERROR] [0]PETSC ERROR: >> >> [ERROR] Try option -start_in_debugger or -on_error_attach_debugger >> >> [ERROR] [0]PETSC ERROR: >> >> [ERROR] or see >> https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!cq445CXteimKBMZKF1HQqgEFTwREIrbMMm5Cn-sCV3wDm2A3tixBsge_FLfW-3YKRxtbYWK9D29cMq338kMstTXwhErY$ >> >> <https://urldefense.us/v3/__https://urldefense.us/v2/url?u=https-3A__petsc.org_release_faq_-23valgrind&d=DwQGaQ&c=v4IIwRuZAmwupIjowmMWUmLasxPEgYsgNI-O7C4ViYc&r=SNsmM8pc4pmx4j-bqFq40w&m=1GLMwF9jewRd8MBil83VSwu-tVEn7Tkm_YfSAcgEMsZ9hDb2HvlnscmeqXsnzv5S&s=Loebf9sk4dgXGOOKPK3IHxp-C5SjGtr7Svr49LwaM4E&e=__;!!G_uCfscf7eWS!bhpq7UF4Rq9PhMMRRb_zeSflUb9Cs5My48ggt02OxSWxoM4eIU_MDt3H6e2YnrxJizIsA21q76YdORVhI0jsXekj$> >> and >> https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!cq445CXteimKBMZKF1HQqgEFTwREIrbMMm5Cn-sCV3wDm2A3tixBsge_FLfW-3YKRxtbYWK9D29cMq338kMstcIOR87Y$ >> >> <https://urldefense.us/v3/__https://urldefense.us/v2/url?u=https-3A__petsc.org_release_faq_&d=DwQGaQ&c=v4IIwRuZAmwupIjowmMWUmLasxPEgYsgNI-O7C4ViYc&r=SNsmM8pc4pmx4j-bqFq40w&m=1GLMwF9jewRd8MBil83VSwu-tVEn7Tkm_YfSAcgEMsZ9hDb2HvlnscmeqXsnzv5S&s=7e9oLVYLacda_1-8rSkzDEHL4Zy1BFnO4pnrfMNlgO4&e=__;!!G_uCfscf7eWS!bhpq7UF4Rq9PhMMRRb_zeSflUb9Cs5My48ggt02OxSWxoM4eIU_MDt3H6e2YnrxJizIsA21q76YdORVhI74qqyaL$> >> >> [ERROR] [0]PETSC ERROR: >> >> [ERROR] or try >> https://urldefense.us/v3/__https://docs.nvidia.com/cuda/cuda-memcheck/index.html__;!!G_uCfscf7eWS!cq445CXteimKBMZKF1HQqgEFTwREIrbMMm5Cn-sCV3wDm2A3tixBsge_FLfW-3YKRxtbYWK9D29cMq338kMstUmD8idW$ >> >> <https://urldefense.us/v3/__https://urldefense.us/v2/url?u=https-3A__docs.nvidia.com_cuda_cuda-2Dmemcheck_index.html&d=DwQGaQ&c=v4IIwRuZAmwupIjowmMWUmLasxPEgYsgNI-O7C4ViYc&r=SNsmM8pc4pmx4j-bqFq40w&m=1GLMwF9jewRd8MBil83VSwu-tVEn7Tkm_YfSAcgEMsZ9hDb2HvlnscmeqXsnzv5S&s=2gHentsiEM2njpPim4k40mYA96k7v_ivjI3erSECebM&e=__;!!G_uCfscf7eWS!bhpq7UF4Rq9PhMMRRb_zeSflUb9Cs5My48ggt02OxSWxoM4eIU_MDt3H6e2YnrxJizIsA21q76YdORVhI3YGCBJ5$> >> on >> NVIDIA CUDA systems to find memory corruption errors >> >> [ERROR] [0]PETSC ERROR: >> >> [ERROR] configure using --with-debugging=yes, recompile, link, and run >> >> [ERROR] [0]PETSC ERROR: >> >> [ERROR] to get more information on the crash. >> >> [ERROR] [0]PETSC ERROR: >> >> [ERROR] Run with -malloc_debug to check if memory corruption is causing >> the crash. >> >> -------------------------------------------------------------------------- >> >> Best, >> >> Sophie >> ------------------------------ >> *From:* Blondel, Sophie via Xolotl-psi-development < >> xolotl-psi-developm...@lists.sourceforge.net> >> *Sent:* Thursday, February 29, 2024 10:17 >> *To:* xolotl-psi-developm...@lists.sourceforge.net < >> xolotl-psi-developm...@lists.sourceforge.net>; petsc-users@mcs.anl.gov < >> petsc-users@mcs.anl.gov> >> *Subject:* [Xolotl-psi-development] PAMI error on Summit >> >> Hi, >> >> I am using PETSc build with the Kokkos CUDA backend on Summit but when I >> run my code with multiple MPI tasks I get the following error: >> 0 TS dt 1e-12 time 0. >> errno 14 pid 864558 >> xolotl: >> /__SMPI_build_dir__________________________/ibmsrc/pami/ibm-pami/buildtools/pami_build_port/../pami/components/devices/shmem/shaddr/CMAShaddr.h:164: >> size_t PAMI::Dev >> ice::Shmem::CMAShaddr::read_impl(PAMI::Memregion*, size_t, >> PAMI::Memregion*, size_t, size_t, bool*): Assertion `cbytes > 0' failed. >> errno 14 pid 864557 >> xolotl: >> /__SMPI_build_dir__________________________/ibmsrc/pami/ibm-pami/buildtools/pami_build_port/../pami/components/devices/shmem/shaddr/CMAShaddr.h:164: >> size_t PAMI::Dev >> ice::Shmem::CMAShaddr::read_impl(PAMI::Memregion*, size_t, >> PAMI::Memregion*, size_t, size_t, bool*): Assertion `cbytes > 0' failed. >> [e28n07:864557] *** Process received signal *** >> [e28n07:864557] Signal: Aborted (6) >> [e28n07:864557] Signal code: (-6) >> [e28n07:864557] [ 0] >> linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000604d8] >> [e28n07:864557] [ 1] /lib64/glibc-hwcaps/power9/libc-2.28.so >> (gsignal+0xd8)[0x200005d796f8] >> [e28n07:864557] [ 2] /lib64/glibc-hwcaps/power9/libc-2.28.so >> (abort+0x164)[0x200005d53ff4] >> [e28n07:864557] [ 3] /lib64/glibc-hwcaps/power9/libc-2.28.so >> (+0x3d280)[0x200005d6d280] >> [e28n07:864557] [ 4] [e28n07:864558] *** Process received signal *** >> [e28n07:864558] Signal: Aborted (6) >> [e28n07:864558] Signal code: (-6) >> [e28n07:864558] [ 0] >> linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000604d8] >> [e28n07:864558] [ 1] /lib64/glibc-hwcaps/power9/libc-2.28.so >> (gsignal+0xd8)[0x200005d796f8] >> [e28n07:864558] [ 2] /lib64/glibc-hwcaps/power9/libc-2.28.so >> (abort+0x164)[0x200005d53ff4] >> [e28n07:864558] [ 3] /lib64/glibc-hwcaps/power9/libc-2.28.so >> (+0x3d280)[0x200005d6d280] >> [e28n07:864558] [ 4] /lib64/glibc-hwcaps/power9/libc-2.28.so >> (__assert_fail+0x64)[0x200005d6d324] >> [e28n07:864557] [ 5] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> >> (_ZN4PAMI8Protocol3Get7GetRdmaINS_6Device5Shmem8DmaModelINS3_11ShmemDeviceINS_4Fifo8WrapFifoINS7_10FifoPacketILj64ELj4096EEENS_7Counter15IndirectBoundedINS_6Atomic12NativeAt >> >> omicEEELj256EEENSB_8IndirectINSB_6NativeEEENS4_9CMAShaddrELj256ELj512EEELb0EEESL_E6simpleEP18pami_rget_simple_t+0x1d8)[0x20007f3971d8] >> [e28n07:864557] [ 6] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> >> (_ZN4PAMI8Protocol3Get13CompositeRGetINS1_4RGetES3_E6simpleEP18pami_rget_simple_t+0x40)[0x20007f2ecc10] >> [e28n07:864557] [ 7] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> (_ZN4PAMI7Context9rget_implEP18pami_rget_simple_t+0x28c)[0x20007f31a78c] >> [e28n07:864557] [ 8] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> (PAMI_Rget+0x18)[0x20007f2d94a8] >> [e28n07:864557] [ 9] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/spectrum_mpi/mca_pml_p >> ami.so(process_rndv_msg+0x46c)[0x2000a80159ac] >> [e28n07:864557] [10] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/spectrum_mpi/mca_pml_p >> ami.so(pml_pami_recv_rndv_cb+0x2bc)[0x2000a801670c] >> [e28n07:864557] [11] /lib64/glibc-hwcaps/power9/libc-2.28.so >> (__assert_fail+0x64)[0x200005d6d324] >> [e28n07:864558] [ 5] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> >> (_ZN4PAMI8Protocol3Get7GetRdmaINS_6Device5Shmem8DmaModelINS3_11ShmemDeviceINS_4Fifo8WrapFifoINS7_10FifoPacketILj64ELj4096EEENS_7Counter15IndirectBoundedINS_6Atomic12NativeAt >> >> omicEEELj256EEENSB_8IndirectINSB_6NativeEEENS4_9CMAShaddrELj256ELj512EEELb0EEESL_E6simpleEP18pami_rget_simple_t+0x1d8)[0x20007f3971d8] >> [e28n07:864558] [ 6] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> >> (_ZN4PAMI8Protocol3Get13CompositeRGetINS1_4RGetES3_E6simpleEP18pami_rget_simple_t+0x40)[0x20007f2ecc10] >> [e28n07:864558] [ 7] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> (_ZN4PAMI7Context9rget_implEP18pami_rget_simple_t+0x28c)[0x20007f31a78c] >> [e28n07:864558] [ 8] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> (PAMI_Rget+0x18)[0x20007f2d94a8] >> [e28n07:864558] [ 9] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/spectrum_mpi/mca_pml_p >> ami.so(process_rndv_msg+0x46c)[0x2000a80159ac] >> [e28n07:864558] [10] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/spectrum_mpi/mca_pml_p >> ami.so(pml_pami_recv_rndv_cb+0x2bc)[0x2000a801670c] >> [e28n07:864558] [11] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> >> (_ZN4PAMI8Protocol4Send11EagerSimpleINS_6Device5Shmem11PacketModelINS3_11ShmemDeviceINS_4Fifo8WrapFifoINS7_10FifoPacketILj64ELj4096EEENS_7Counter15IndirectBoundedINS_6Atomic >> >> 12NativeAtomicEEELj256EEENSB_8IndirectINSB_6NativeEEENS4_9CMAShaddrELj256ELj512EEEEELNS1_15configuration_tE5EE15dispatch_packedEPvSP_mSP_SP_+0x4c)[0x20007f2e30ac] >> [e28n07:864557] [12] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> (PAMI_Context_advancev+0x6b0)[0x20007f2da540] >> [e28n07:864557] [13] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/spectrum_mpi/mca_pml_p >> ami.so(mca_pml_pami_progress+0x34)[0x2000a80073e4] >> [e28n07:864557] [14] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/libopen-pal.so.3(opal_ >> progress+0x6c)[0x20003d60640c] >> [e28n07:864557] [15] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/libmpi_ibm.so.3(ompi_r >> equest_default_wait_all+0x144)[0x2000034c4b04] >> [e28n07:864557] [16] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/libmpi_ibm.so.3(PMPI_W >> aitall+0x10c)[0x20000352790c] >> [e28n07:864557] [17] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> >> (_ZN4PAMI8Protocol4Send11EagerSimpleINS_6Device5Shmem11PacketModelINS3_11ShmemDeviceINS_4Fifo8WrapFifoINS7_10FifoPacketILj64ELj4096EEENS_7Counter15IndirectBoundedINS_6Atomic >> >> 12NativeAtomicEEELj256EEENSB_8IndirectINSB_6NativeEEENS4_9CMAShaddrELj256ELj512EEEEELNS1_15configuration_tE5EE15dispatch_packedEPvSP_mSP_SP_+0x4c)[0x20007f2e30ac] >> [e28n07:864558] [12] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/pami_port/libpami.so.3 >> (PAMI_Context_advancev+0x6b0)[0x20007f2da540] >> [e28n07:864558] [13] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/spectrum_mpi/mca_pml_p >> ami.so(mca_pml_pami_progress+0x34)[0x2000a80073e4] >> [e28n07:864558] [14] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/libopen-pal.so.3(opal_ >> progress+0x6c)[0x20003d60640c] >> [e28n07:864558] [15] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/libmpi_ibm.so.3(ompi_r >> equest_default_wait_all+0x144)[0x2000034c4b04] >> [e28n07:864558] [16] >> /sw/summit/spack-envs/summit-plus/opt/gcc-12.1.0/spectrum-mpi-10.4.0.6-20230210-db5xakaaqowbhp3nqwebpxrdbwtm4knu/container/../lib/libmpi_ibm.so.3(PMPI_W >> aitall+0x10c)[0x20000352790c] >> [e28n07:864558] [17] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x3ca7b0)[0x2000004ea7b0] >> [e28n07:864557] [18] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x3ca7b0)[0x2000004ea7b0] >> [e28n07:864558] [18] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x3c5e68)[0x2000004e5e68] >> [e28n07:864557] [19] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x3c5e68)[0x2000004e5e68] >> [e28n07:864558] [19] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(PetscSFBcastEnd+0x74)[0x2000004c9214] >> [e28n07:864557] [20] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(PetscSFBcastEnd+0x74)[0x2000004c9214] >> [e28n07:864558] [20] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x3b4cb0)[0x2000004d4cb0] >> [e28n07:864557] [21] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x3b4cb0)[0x2000004d4cb0] >> [e28n07:864558] [21] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(VecScatterEnd+0x178)[0x2000004dd038] >> [e28n07:864558] [22] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(VecScatterEnd+0x178)[0x2000004dd038] >> [e28n07:864557] [22] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x1112be0)[0x200001232be0] >> [e28n07:864558] [23] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x1112be0)[0x200001232be0] >> [e28n07:864557] [23] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(DMGlobalToLocalEnd+0x470)[0x200000e9b0f0] >> [e28n07:864557] [24] >> /gpfs/alpine2/mat267/proj-shared/code/xolotl-stable-cuda/xolotl/solver/libxolotlSolver.so(_ZN6xolotl6solver11PetscSolver11rhsFunctionEP5_p_TSdP6_p_VecS5 >> _+0xc4)[0x200005f710d4] >> [e28n07:864557] [25] >> /gpfs/alpine2/mat267/proj-shared/code/xolotl-stable-cuda/xolotl/solver/libxolotlSolver.so(_ZN6xolotl6solver11RHSFunctionEP5_p_TSdP6_p_VecS4_Pv+0x2c)[0x2 >> 00005f7130c] >> [e28n07:864557] [26] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(DMGlobalToLocalEnd+0x470)[0x200000e9b0f0] >> [e28n07:864558] [24] >> /gpfs/alpine2/mat267/proj-shared/code/xolotl-stable-cuda/xolotl/solver/libxolotlSolver.so(_ZN6xolotl6solver11PetscSolver11rhsFunctionEP5_p_TSdP6_p_VecS5 >> _+0xc4)[0x200005f710d4] >> [e28n07:864558] [25] >> /gpfs/alpine2/mat267/proj-shared/code/xolotl-stable-cuda/xolotl/solver/libxolotlSolver.so(_ZN6xolotl6solver11RHSFunctionEP5_p_TSdP6_p_VecS4_Pv+0x2c)[0x2 >> 00005f7130c] >> [e28n07:864558] [26] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSComputeRHSFunction+0x1bc)[0x2000017621dc] >> [e28n07:864557] [27] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSComputeRHSFunction+0x1bc)[0x2000017621dc] >> [e28n07:864558] [27] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSComputeIFunction+0x418)[0x200001763ad8] >> [e28n07:864557] [28] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSComputeIFunction+0x418)[0x200001763ad8] >> [e28n07:864558] [28] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x16f2ef0)[0x200001812ef0] >> [e28n07:864557] [29] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x16f2ef0)[0x200001812ef0] >> [e28n07:864558] [29] >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSStep+0x228)[0x200001768088] >> [e28n07:864557] *** End of error message *** >> >> /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSStep+0x228)[0x200001768088] >> [e28n07:864558] *** End of error message *** >> >> It seems to be pointing to >> https://urldefense.us/v3/__https://petsc.org/release/manualpages/PetscSF/PetscSFBcastEnd/__;!!G_uCfscf7eWS!cq445CXteimKBMZKF1HQqgEFTwREIrbMMm5Cn-sCV3wDm2A3tixBsge_FLfW-3YKRxtbYWK9D29cMq338kMste-N8hvu$ >> >> <https://urldefense.us/v3/__https://petsc.org/release/manualpages/PetscSF/PetscSFBcastEnd/__;!!G_uCfscf7eWS!bhpq7UF4Rq9PhMMRRb_zeSflUb9Cs5My48ggt02OxSWxoM4eIU_MDt3H6e2YnrxJizIsA21q76YdORVhI30Ylvr6$> >> so I wanted to check if you had seen this type of error before and if it >> could be related to how the code is compiled or run. Let me know if I can >> provide any additional information. >> >> Best, >> >> Sophie >> >>
