Re: [Xolotl-psi-development] PAMI error on Summit

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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://petsc.org/release/faq/#valgrind<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=> and https://petsc.org/release/faq/<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=>

[ERROR] [0]PETSC ERROR:

[ERROR] or try https://docs.nvidia.com/cuda/cuda-memcheck/index.html<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=> 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 <xol...@li...>
Sent: Thursday, February 29, 2024 10:17
To: xol...@li... <xol...@li...>; pet...@mc... <pet...@mc...>
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://petsc.org/release/manualpages/PetscSF/PetscSFBcastEnd/ 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