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Yes, it is a runtime option. No need to reconfigure petsc. Just add "-use_gpu_aware_mpi 0" to your test's command line. --Junchao Zhang On Thu, Feb 29, 2024 at 10: 07 AM Matthew Knepley <knepley@ gmail. com> wrote: On Thu, Feb
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<div dir="ltr"><div>Yes, it is a runtime option. No need to reconfigure petsc. Just add "-use_gpu_aware_mpi 0" to your test's command line. </div><div><br></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">--Junchao Zhang</div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 29, 2024 at 10:07 AM Matthew Knepley <<a href="mailto:knepley@gmail.com">knepley@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">On Thu, Feb 29, 2024 at 11:03 AM Blondel, Sophie via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>
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Thank you Junchao, Yes, I am using gpu-aware MPI. Is "-use_gpu_aware_mpi 0" a runtime option or a compile option? Best, Sophie From: Junchao Zhang <junchao. zhang@ gmail. com> Sent: Thursday, February 29, 2024 10: 50 To: Blondel,
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Thank you Junchao,</div>
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Yes, I am using gpu-aware MPI.</div>
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<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Is "-use_gpu_aware_mpi 0" a runtime option or a compile option?</span></div></div></div></blockquote><div><br></div><div>That is a configure option, so</div><div><br></div><div> cd $PETSC_DIR</div><div> ./${PETSC_ARCH}/lib./petsc/conf/reconfigure-${PETSC_ARCH}.py -use-gpu_aware_mpi 0</div><div> make all</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div dir="ltr">
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Best,</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
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<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Sophie<br>
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<div id="m_-4934386083206862621m_2646287569393159098divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Junchao Zhang <<a href="mailto:junchao.zhang@gmail.com" target="_blank">junchao.zhang@gmail.com</a>><br>
<b>Sent:</b> Thursday, February 29, 2024 10:50<br>
<b>To:</b> Blondel, Sophie <<a href="mailto:sblondel@utk.edu" target="_blank">sblondel@utk.edu</a>><br>
<b>Cc:</b> <a href="mailto:xolotl-psi-development@lists.sourceforge.net" target="_blank">xolotl-psi-development@lists.sourceforge.net</a> <<a href="mailto:xolotl-psi-development@lists.sourceforge.net" target="_blank">xolotl-psi-development@lists.sourceforge.net</a>>; <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br>
<b>Subject:</b> Re: [petsc-users] PAMI error on Summit</font>
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<div dir="ltr">Hi Sophie,<br>
PetscSFBcastEnd() was calling MPI_Waitall() to finish the communication in DMGlobalToLocal.
<div> I guess you used gpu-aware MPI. The error you saw might be due to it. You can try without it with a petsc option -use_gpu_aware_mpi 0</div>
<div> But we generally recommend gpu-aware mpi. You can try on other GPU machines to see if it is just an IBM Spectrum MPI problem. <br>
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Thanks.<br clear="all">
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<div dir="ltr">--Junchao Zhang</div>
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<div dir="ltr">On Thu, Feb 29, 2024 at 9:17 AM Blondel, Sophie via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
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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:
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Hi,</div>
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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:</div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">0 TS dt 1e-12 time 0.</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">errno 14 pid 864558</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">xolotl: /__SMPI_build_dir__________________________/ibmsrc/pami/ibm-pami/buildtools/pami_build_port/../pami/components/devices/shmem/shaddr/CMAShaddr.h:164: size_t
PAMI::Dev</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">ice::Shmem::CMAShaddr::read_impl(PAMI::Memregion*, size_t, PAMI::Memregion*, size_t, size_t, bool*): Assertion `cbytes > 0' failed.</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">errno 14 pid 864557</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">xolotl: /__SMPI_build_dir__________________________/ibmsrc/pami/ibm-pami/buildtools/pami_build_port/../pami/components/devices/shmem/shaddr/CMAShaddr.h:164: size_t
PAMI::Dev</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">ice::Shmem::CMAShaddr::read_impl(PAMI::Memregion*, size_t, PAMI::Memregion*, size_t, size_t, bool*): Assertion `cbytes > 0' failed.</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] *** Process received signal ***</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] Signal: Aborted (6)</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] Signal code: (-6)</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [ 0] linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000604d8]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [ 1] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!facODjKBT4NdUpQRG3bRO5aufX56SW84P_ciaPKeSHjRxArfCGndt8hUfkRcvfjlBIbRbEra5PwQNlA6YlO8YWjh$" target="_blank">libc-2.28.so</a>(gsignal+0xd8)[0x200005d796f8]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [ 2] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!facODjKBT4NdUpQRG3bRO5aufX56SW84P_ciaPKeSHjRxArfCGndt8hUfkRcvfjlBIbRbEra5PwQNlA6YlO8YWjh$" target="_blank">libc-2.28.so</a>(abort+0x164)[0x200005d53ff4]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [ 3] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!facODjKBT4NdUpQRG3bRO5aufX56SW84P_ciaPKeSHjRxArfCGndt8hUfkRcvfjlBIbRbEra5PwQNlA6YlO8YWjh$" target="_blank">libc-2.28.so</a>(+0x3d280)[0x200005d6d280]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [ 4] [e28n07:864558] *** Process received signal ***</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] Signal: Aborted (6)</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] Signal code: (-6)</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [ 0] linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000604d8]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [ 1] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!facODjKBT4NdUpQRG3bRO5aufX56SW84P_ciaPKeSHjRxArfCGndt8hUfkRcvfjlBIbRbEra5PwQNlA6YlO8YWjh$" target="_blank">libc-2.28.so</a>(gsignal+0xd8)[0x200005d796f8]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [ 2] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!facODjKBT4NdUpQRG3bRO5aufX56SW84P_ciaPKeSHjRxArfCGndt8hUfkRcvfjlBIbRbEra5PwQNlA6YlO8YWjh$" target="_blank">libc-2.28.so</a>(abort+0x164)[0x200005d53ff4]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [ 3] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!facODjKBT4NdUpQRG3bRO5aufX56SW84P_ciaPKeSHjRxArfCGndt8hUfkRcvfjlBIbRbEra5PwQNlA6YlO8YWjh$" target="_blank">libc-2.28.so</a>(+0x3d280)[0x200005d6d280]</span></div>
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<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">_+0xc4)[0x200005f710d4]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [25] /gpfs/alpine2/mat267/proj-shared/code/xolotl-stable-cuda/xolotl/solver/libxolotlSolver.so(_ZN6xolotl6solver11RHSFunctionEP5_p_TSdP6_p_VecS4_Pv+0x2c)[0x2</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">00005f7130c]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [26] /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(DMGlobalToLocalEnd+0x470)[0x200000e9b0f0]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [24] /gpfs/alpine2/mat267/proj-shared/code/xolotl-stable-cuda/xolotl/solver/libxolotlSolver.so(_ZN6xolotl6solver11PetscSolver11rhsFunctionEP5_p_TSdP6_p_VecS5</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">_+0xc4)[0x200005f710d4]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [25] /gpfs/alpine2/mat267/proj-shared/code/xolotl-stable-cuda/xolotl/solver/libxolotlSolver.so(_ZN6xolotl6solver11RHSFunctionEP5_p_TSdP6_p_VecS4_Pv+0x2c)[0x2</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">00005f7130c]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [26] /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSComputeRHSFunction+0x1bc)[0x2000017621dc]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [27] /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSComputeRHSFunction+0x1bc)[0x2000017621dc]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [27] /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSComputeIFunction+0x418)[0x200001763ad8]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [28] /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSComputeIFunction+0x418)[0x200001763ad8]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [28] /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x16f2ef0)[0x200001812ef0]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [29] /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(+0x16f2ef0)[0x200001812ef0]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [29] /gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSStep+0x228)[0x200001768088]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] *** End of error message ***</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">/gpfs/alpine2/mat267/proj-shared/dependencies/petsc-kokkos-cuda/lib/libpetsc.so.3.020(TSStep+0x228)[0x200001768088]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] *** End of error message ***</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">It seems to be pointing to
<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/PetscSF/PetscSFBcastEnd/__;!!G_uCfscf7eWS!Y8h5WLnoArdfhK2_UDmISOEiqxAN9gBUzvWniKOoMwtA9cGjg8w9sYX6V8aIgfzL8Uhea5ppiRbuTGr1jZ_R2DOV$" target="_blank">
https://petsc.org/release/manualpages/PetscSF/PetscSFBcastEnd/</a> 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.</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Best,</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Sophie<br>
</span></div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ZBO5bwscjJ9rJaoZv-Rx4CHgZHLOKndY6BSOrpa0uSogfb1Q3a-75DvLGvvLl-szrEPZmpzcGqj8L_YdatnKcAGYRafK$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
</blockquote></div>