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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">I have a few more remarks about this question (I have been in contact with Marcus about this):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:10.0pt;font-family:"Courier New""><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:10.0pt;font-family:"Courier New"">the idea of the jobscript is that SLURM does not do any binding and leaves binding up to<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> mpirun.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> - this works fine on the first node, where SLURM does not bind the processes (so mpirun can do this)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> - on the second node SLURM uses (faulty) core binding (all processes are bound round-robin to the hyperthreads
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""> of the first core). Intel’s mpirun respects the cpuset and as a result the processes are bound incorrectly.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">This looks like a SLURM issue to me. SLURM version 19.05.5 is used.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">A workaround is to use I_MPI_PIN_RESPECT_CPUSET=no.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">John<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">Hi everyone,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">I am facing a bit of a weird issue with CPU bindings and mpirun:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">My jobscript:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">#SBATCH -N 20<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">#SBATCH --tasks-per-node=40<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">#SBATCH -p medium40<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">#SBATCH -t 30
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">#SBATCH -o out/%J.out<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">#SBATCH -e out/%J.err<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">#SBATCH --reservation=root_98<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">module load impi/2019.4 2>&1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">export I_MPI_DEBUG=6<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">export SLURM_CPU_BIND=none<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">. /sw/comm/impi/compilers_and_libraries_2019.4.243/linux/mpi/intel64/bin/mpivars.sh realease<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">BENCH=/sw/comm/impi/compilers_and_libraries_2019.4.243/linux/mpi/intel64/bin/IMB-MPI1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">mpirun -np 800 $BENCH -npmin 800 -iter 50 -time 120 -msglog 16:18 -include Allreduce Bcast Barrier Exchange Gather PingPing PingPong Reduce Scatter Allgather
Alltoall Reduce_scatter<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">My output is as follows:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[...]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[0] MPI startup(): 37 154426 gcn1311 {37,77}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[0] MPI startup(): 38 154427 gcn1311 {38,78}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[0] MPI startup(): 39 154428 gcn1311 {39,79}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[0] MPI startup(): 40 161061 gcn1312 {0}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[0] MPI startup(): 41 161062 gcn1312 {40}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[0] MPI startup(): 42 161063 gcn1312 {0}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[0] MPI startup(): 43 161064 gcn1312 {40}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[0] MPI startup(): 44 161065 gcn1312 {0}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">[...]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">On 8 out of 20 nodes I got the wrong pinning. In the slurmd logs I found<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">that on nodes, where the pinning was correct, manual binding was<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">communicated correctly:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""> lllp_distribution jobid [2065227] manual binding: none<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">On those, where it did not work, not so much:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""> lllp_distribution jobid [2065227] default auto binding: cores, dist 1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">So, for some reason, slurm told some task to use CPU bindings and for<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">some, the cpu binding was (correctly) disabled.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">Any ideas what could cause this?<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">Best,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Courier New"">Marcus<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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