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On Thu, Feb 29, 2024 at 4: 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)
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<div dir="ltr"><div dir="ltr">On Thu, Feb 29, 2024 at 4:22 PM Blondel, Sophie via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov">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 class="msg3926686841073134418">
<div style="font-size:1px;color:rgb(255,255,255);line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;display:none">
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
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I still get the same error when deactivating GPU-aware MPI.</div>
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<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
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):</div></div></div></blockquote><div><br></div><div>For this case, can you get a stack trace?</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 class="msg3926686841073134418"><div dir="ltr">
<p style="margin-top:0px;margin-bottom:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">0 TS dt 1e-12 time 0.</span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] [0]PETSC ERROR: </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] ------------------------------------------------------------------------</span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] [0]PETSC ERROR: </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] [0]PETSC ERROR: </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] Try option -start_in_debugger or -on_error_attach_debugger</span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] [0]PETSC ERROR: </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] or see
<a href="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$" id="m_3926686841073134418OWA55be8502-8d13-b445-887a-e3475b7e8ed4" rel="noopener noreferrer" style="margin-top:0px;margin-bottom:0px" target="_blank">
https://petsc.org/release/faq/#valgrind</a> and <a href="https://urldefense.us/v3/__https://urldefense.us/v2/url?u=https-3A__petsc.org_release_faq_&d=DwQGaQ&c=v4IIwRuZAmwupIjowmMWUmLasxPEgYsgNI-O7C4ViYc&r=SNsmM8pc4pmx4j-bqFq40w&m=1GLMwF9jewRd8MBil83VSwu-tVEn7Tkm_YfSAcgEMsZ9hDb2HvlnscmeqXsnzv5S&s=7e9oLVYLacda_1-8rSkzDEHL4Zy1BFnO4pnrfMNlgO4&e=__;!!G_uCfscf7eWS!bhpq7UF4Rq9PhMMRRb_zeSflUb9Cs5My48ggt02OxSWxoM4eIU_MDt3H6e2YnrxJizIsA21q76YdORVhI74qqyaL$" id="m_3926686841073134418OWA32fe1662-a183-8125-494e-edc4729a491b" rel="noopener noreferrer" style="margin-top:0px;margin-bottom:0px" target="_blank">
https://petsc.org/release/faq/</a></span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] [0]PETSC ERROR: </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] or try
<a href="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$" id="m_3926686841073134418OWAebfba962-cde8-2a72-2805-9166031fa676" rel="noopener noreferrer" style="margin-top:0px;margin-bottom:0px" target="_blank">
https://docs.nvidia.com/cuda/cuda-memcheck/index.html</a> on NVIDIA CUDA systems to find memory corruption errors</span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] [0]PETSC ERROR: </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] configure using --with-debugging=yes, recompile, link, and run </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] [0]PETSC ERROR: </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] to get more information on the crash.</span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] [0]PETSC ERROR: </span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">[ERROR] Run with -malloc_debug to check if memory corruption is causing the crash.</span></p>
<p style="margin:0px"><span style="font-family:Calibri,sans-serif;font-size:12pt;color:black">--------------------------------------------------------------------------</span></p>
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Best,</div>
<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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Sophie</div>
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<div id="m_3926686841073134418divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Blondel, Sophie via Xolotl-psi-development <<a href="mailto:xolotl-psi-development@lists.sourceforge.net" target="_blank">xolotl-psi-development@lists.sourceforge.net</a>><br>
<b>Sent:</b> Thursday, February 29, 2024 10:17<br>
<b>To:</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> [Xolotl-psi-development] PAMI error on Summit</font>
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Hi,</div>
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<br>
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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!ealcEfAPe2Mm8ybP__T3FwtT82O3mdXnxfl73KX3wF-_aFOo6hEarAdd0WryuSjgrwh3QbmG-_5WBWu6vKa3$" 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!ealcEfAPe2Mm8ybP__T3FwtT82O3mdXnxfl73KX3wF-_aFOo6hEarAdd0WryuSjgrwh3QbmG-_5WBWu6vKa3$" target="_blank">libc-2.28.so</a>(abort+0x164)[0x200005d53ff4]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864557] [ 3] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!ealcEfAPe2Mm8ybP__T3FwtT82O3mdXnxfl73KX3wF-_aFOo6hEarAdd0WryuSjgrwh3QbmG-_5WBWu6vKa3$" 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!ealcEfAPe2Mm8ybP__T3FwtT82O3mdXnxfl73KX3wF-_aFOo6hEarAdd0WryuSjgrwh3QbmG-_5WBWu6vKa3$" target="_blank">libc-2.28.so</a>(gsignal+0xd8)[0x200005d796f8]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [ 2] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!ealcEfAPe2Mm8ybP__T3FwtT82O3mdXnxfl73KX3wF-_aFOo6hEarAdd0WryuSjgrwh3QbmG-_5WBWu6vKa3$" 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!ealcEfAPe2Mm8ybP__T3FwtT82O3mdXnxfl73KX3wF-_aFOo6hEarAdd0WryuSjgrwh3QbmG-_5WBWu6vKa3$" target="_blank">libc-2.28.so</a>(+0x3d280)[0x200005d6d280]</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">[e28n07:864558] [ 4] /lib64/glibc-hwcaps/power9/<a href="https://urldefense.us/v3/__http://libc-2.28.so__;!!G_uCfscf7eWS!ealcEfAPe2Mm8ybP__T3FwtT82O3mdXnxfl73KX3wF-_aFOo6hEarAdd0WryuSjgrwh3QbmG-_5WBWu6vKa3$" target="_blank">libc-2.28.so</a>(__assert_fail+0x64)[0x200005d6d324]</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!bhpq7UF4Rq9PhMMRRb_zeSflUb9Cs5My48ggt02OxSWxoM4eIU_MDt3H6e2YnrxJizIsA21q76YdORVhI30Ylvr6$" target="_blank">https://petsc.org/release/manualpages/PetscSF/PetscSFBcastEnd/</a> so I wanted to check if you had seen this type of error before and if it could be related to how the code is compiled
or run. Let me know if I can provide any additional information.</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Best,</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Sophie<br>
</span></div>
</div>
</div>
</div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!ealcEfAPe2Mm8ybP__T3FwtT82O3mdXnxfl73KX3wF-_aFOo6hEarAdd0WryuSjgrwh3QbmG-_5WBVK8U12f$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>