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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Bruce,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks for the details. Since you already instructed `sbatch` with `-N 2 -n 6` I thought you could simply run with `srun`, i.e. without further `-n`? I believe hydra also reads environment so you could also
try `mpiexec` without `-n`. Did you also try `-N 1` and `-N 6`?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">-- <br>
Hui Zhou<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">"Palmer, Bruce J" <Bruce.Palmer@pnnl.gov><br>
<b>Date: </b>Thursday, May 7, 2020 at 11:16 AM<br>
<b>To: </b>"Zhou, Hui" <zhouh@anl.gov>, "discuss@mpich.org" <discuss@mpich.org><br>
<b>Subject: </b>Re: [mpich-discuss] MPICH configure<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Hui,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Sorry for the late reply, I keep getting pulled off on other projects. I’m actually running a test suite most of the time, so the job scripts look like</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">#!/bin/csh</span><o:p></o:p></p>
<p class="p1"><span class="s1">#SBATCH -t 02:30:00</span><o:p></o:p></p>
<p class="p1"><span class="s1">#SBATCH -A XGA</span><o:p></o:p></p>
<p class="p1"><span class="s1">#SBATCH -p short,slurm,gpu</span><o:p></o:p></p>
<p class="p1"><span class="s1">#SBATCH -N 2</span><o:p></o:p></p>
<p class="p1"><span class="s1">#SBATCH -n 6</span><o:p></o:p></p>
<p class="p1"><span class="s1">#SBATCH -o ./test.out</span><o:p></o:p></p>
<p class="p1"><span class="s1">#SBATCH -e ./test.err</span><o:p></o:p></p>
<p class="p2"> <o:p></o:p></p>
<p class="p1"><span class="s1">source /etc/profile.d/modules.csh</span><o:p></o:p></p>
<p class="p2"> <o:p></o:p></p>
<p class="p1"><span class="s1">source ~/set_mpich</span><o:p></o:p></p>
<p class="p1"><span class="s1">env | grep PATH</span><o:p></o:p></p>
<p class="p1"><span class="s1">module list</span><o:p></o:p></p>
<p class="p2"> <o:p></o:p></p>
<p class="p1"><span class="s1">#make check-ga MPIEXEC="mpirun -n 6 "</span><o:p></o:p></p>
<p class="p1"><span class="s1">make check-ga MPIEXEC="srun -n 6 "</span><o:p></o:p></p>
<p class="p1"><span class="s1"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">I’ve tried using mpirun, srun and mpiexec in the MPIEXEC variable. If I run a test standalone, then the job submission script is</span><o:p></o:p></p>
<p class="p1"><span class="s1"> </span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#5230E1">#!/bin/csh</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#5230E1">#SBATCH -t 02:30:00</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#5230E1">#SBATCH -A XGA</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#5230E1">#SBATCH -p short,slurm,gpu</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#5230E1">#SBATCH -N 2</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#5230E1">#SBATCH -n 6</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#5230E1">#SBATCH -o ./test.out</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#5230E1">#SBATCH -e ./test.err</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#AFAD24">source</span><span style="font-size:8.5pt;font-family:Menlo;color:black"> /etc/profile.d/modules.csh</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:#AFAD24">source</span><span style="font-size:8.5pt;font-family:Menlo;color:black"> ~/set_mpich</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black">env | grep
</span><span style="font-size:8.5pt;font-family:Menlo;color:#D53BD3">PATH</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black">module list</span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black">srun -n
</span><span style="font-size:8.5pt;font-family:Menlo;color:#C33720">6</span><span style="font-size:8.5pt;font-family:Menlo;color:black"> test.x
</span><span style="font-size:8.5pt;font-family:Menlo;color:#AFAD24">></span><span style="font-size:8.5pt;font-family:Menlo;color:black"> test.out</span><o:p></o:p></p>
<p class="p1"> <o:p></o:p></p>
<p class="p1">Again, I’ve tried running with mpirun, srun, and mpiexec. The environment in the set_mpich file is<o:p></o:p></p>
<p class="p1"> <o:p></o:p></p>
<p class="p1"><span class="s1">module purge</span><o:p></o:p></p>
<p class="p1"><span class="s1">module load gcc/5.2.0</span><o:p></o:p></p>
<p class="p1"><span class="s1">module load python/2.7.8</span><o:p></o:p></p>
<p class="p1"><span class="s1">module load cmake/3.8.2</span><o:p></o:p></p>
<p class="p1"><span class="s1">module load git</span><o:p></o:p></p>
<p class="p1"><span class="s1">module load mkl</span><o:p></o:p></p>
<p class="p1"><span class="s1">setenv CC gcc</span><o:p></o:p></p>
<p class="p1"><span class="s1">setenv CFLAGS "-pthread"</span><o:p></o:p></p>
<p class="p1"><span class="s1">setenv CXX g++</span><o:p></o:p></p>
<p class="p1"><span class="s1">setenv CXXFLAGS "-pthread"</span><o:p></o:p></p>
<p class="p1"><span class="s1">setenv FC gfortran</span><o:p></o:p></p>
<p class="p1"><span class="s1">setenv FCFLAGS "-pthread"</span><o:p></o:p></p>
<p class="p1"><span class="s1">unsetenv F90</span><o:p></o:p></p>
<p class="p1"><span class="s1">unsetenv F90FLAGS</span><o:p></o:p></p>
<p class="p2"> <o:p></o:p></p>
<p class="p1"><span class="s1">setenv PATH /people/d3g293/mpich/mpich-3.3.2/install/bin:${PATH}</span><o:p></o:p></p>
<p class="p1"><span class="s1">setenv MANPATH /people/d3g293/mpich/mpich-3.3.2/install/share/man:${MANPATH}</span><o:p></o:p></p>
<p class="p1"><span class="s1">setenv LD_LIBRARY_PATH /people/d3g293/mpich/mpich-3.3.2/install/lib:${LD_LIBRARY_PATH}</span><o:p></o:p></p>
<p class="p1"> <o:p></o:p></p>
<p class="p1">Bruce<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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