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<p>Ideally, all the #PBS directives should go into your
SubmitScript. However, that's not your problem.</p>
<p>I am wondering whether your mpirun and configured mpi match. This
could give you the error you see.</p>
<p>Cactus configures mpi based on which mpic++ (or mpicc) is in your
path at the time of configuration. Did you do the same module load
before compiling as you do for running? (module load
/home2/mallick/ET/Cactus/openmpi-x86_64)<br>
<br>
Note, some builds of MPI now use the PMI interface and don't have
an actual mpirun command. Please make sure this isn't what's going
on here.
</p>
<p>Curiosity question: Is your batch queue system Torque, or are you
using the PBS interface to slurm?</p>
<p>--Steve<br>
</p>
<div class="moz-cite-prefix">On 8/12/2021 9:44 AM, Shamim Haque
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAHrQTHV2yqpj4qRxzmnY2O62pNm3=N9S0Xa9T6AfdRnZ5xQT1Q@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div class="gmail_default" style="color:#000000">For that, I
write a separate jobscript and submit it in the queue. That
jobscript looks like this:</div>
<div class="gmail_default" style="color:#000000"><br>
</div>
<div class="gmail_default" style=""><i style=""><font
color="#a64d79">#!/bin/bash<br>
#PBS -N nsns2<br>
#PBS -j oe<br>
#PBS -V<br>
#PBS -v TEMP=/scratch1<br>
#PBS -o job_nsns2.out<br>
#PBS -e job_nsns2.err<br>
#PBS -l select=2:ncpus=16<br>
#PBS -l walltime=24:10:00<br>
#PBS -q p-queue<br>
export OMP_NUM_THREADS=1<br>
cd /home2/mallick/ET/Cactus<br>
CPUS=`cat $PBS_NODEFILE | wc -l`<br>
DATE=`date +%c`<br>
echo Job started at $DATE<br>
module load /home2/mallick/ET/Cactus/openmpi-x86_64</font></i></div>
<div class="gmail_default" style=""><i style=""><font
color="#a64d79"><br>
/home2/mallick/ET/Cactus/simfactory/bin/sim whoami<br>
<br>
</font></i></div>
<div class="gmail_default" style=""><i style=""><font
color="#a64d79">time mpirun
/home2/mallick/ET/Cactus/simfactory/bin/sim create-submit
nsns30 --basedir=/home2/mallick/simulations --procs=32
--ppn=16 --num-threads=1 --num-smt=1 --ppn-used=16
--parfile
/home2/mallick/ET/Cactus/parfile/nsns_vlr_mass_diff.par
--walltime=24:00:00<br>
DATE=`date +%c`<br>
echo Job finished at $DATE</font></i></div>
<div class="gmail_default" style=""><span
style="color:rgb(102,102,102)"><br>
</span></div>
<div class="gmail_default" style=""><font color="#000000">Regards</font></div>
<div class="gmail_default" style=""><span
style="color:rgb(102,102,102)">Shamim Haque</span></div>
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr"><font color="#666666">Junior Research
Fellow (JRF)<br>
</font>
<div><font color="#666666">Department of Physics</font></div>
<div><font color="#666666">IISER Bhopal</font></div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
<div hspace="streak-pt-mark" style="max-height:1px"><img alt=""
style="width:0px;max-height:0px;overflow:hidden"
src="https://mailfoogae.appspot.com/t?sender=ac2hhbWltc0BpaXNlcmIuYWMuaW4%3D&type=zerocontent&guid=e910e754-16d4-48d2-ad25-d4cca28e9b71"
moz-do-not-send="true"><font size="1" color="#ffffff">ᐧ</font></div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Aug 12, 2021 at 7:52
PM Steven R. Brandt <<a href="mailto:sbrandt@cct.lsu.edu"
moz-do-not-send="true">sbrandt@cct.lsu.edu</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>
<p>Something I'm not understanding. You want to run on 2
nodes, but you don't seem to be using a batch queue
system... so how does MPI know which two nodes to use?
Does this machine have slurm installed?<br>
</p>
<p>--Steve<br>
</p>
<div>On 8/12/2021 12:28 AM, Shamim Haque wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default" style="color:rgb(0,0,0)">Hi Steven,</div>
<div class="gmail_default" style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default" style="color:rgb(0,0,0)">I
used the generic Submitscript, no change in that. The
Runscript is as follows:</div>
<div class="gmail_default" style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"><i><font color="#a64d79">echo
"Preparing:"<br>
set -x # Output commands<br>
set -e # Abort on errors<br>
cd @RUNDIR@-active<br>
echo "Checking:"<br>
pwd<br>
hostname<br>
date<br>
echo "Environment:"<br>
module load
/home2/mallick/ET/Cactus/openmpi-x86_64<br>
export CACTUS_NUM_PROCS=@NUM_PROCS@<br>
export CACTUS_NUM_THREADS=@NUM_THREADS@<br>
export GMON_OUT_PREFIX=gmon.out<br>
export OMP_NUM_THREADS=@NUM_THREADS@<br>
env | sort > SIMFACTORY/ENVIRONMENT<br>
echo "Starting:"<br>
export CACTUS_STARTTIME=$(date +%s)<br>
mpirun -np @NUM_PROCS@ @EXECUTABLE@ -L 3 @PARFILE@<br>
</font></i></div>
<div class="gmail_default"><i><font color="#a64d79">echo
"Stopping:"<br>
date<br>
echo "Done."<br>
</font></i></div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr"><font color="#666666"><br>
</font></div>
<div><span class="gmail_default"
style="color:rgb(0,0,0)">I have
attached these files here as well.
All the output/error files are
attached in my previous mail. </span></div>
<div><font color="#666666"><span
class="gmail_default"
style="color:rgb(0,0,0)"><br>
</span></font></div>
<div><font color="#666666"><span
class="gmail_default"
style="color:rgb(0,0,0)">Regards</span></font></div>
<div dir="ltr"><font color="#666666">Shamim
Haque</font></div>
<div dir="ltr"><font color="#666666">Junior
Research Fellow (JRF)<br>
</font>
<div><font color="#666666">Department
of Physics</font></div>
<div><font color="#666666">IISER
Bhopal</font></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
<div hspace="streak-pt-mark" style="max-height:1px"><img
alt="" style="width: 0px; max-height: 0px; overflow:
hidden;"
src="https://mailfoogae.appspot.com/t?sender=ac2hhbWltc0BpaXNlcmIuYWMuaW4%3D&type=zerocontent&guid=1bfbface-450a-422e-bbc9-02ec895c8f53"
moz-do-not-send="true"><font size="1" color="#ffffff">ᐧ</font></div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Aug 12, 2021
at 12:48 AM Steven R. Brandt <<a
href="mailto:sbrandt@cct.lsu.edu" target="_blank"
moz-do-not-send="true">sbrandt@cct.lsu.edu</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>
<p>What SubmitScript and RunScript are you using?
Can you show us? Thanks.</p>
<p>--Steve<br>
</p>
<div>On 8/10/2021 2:35 AM, Shamim Haque wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default"
style="color:rgb(0,0,0)">Hello,</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">I am trying to run
the BNS simulation on the cluster at IISER
Bhopal. Upon using 2 nodes (16x2 cores) my
simulation stalled at this message:</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"> </div>
<div class="gmail_default"><i><font
color="#a64d79">The environment variable
CACTUS_NUM_PROCS is set to 32, but there
are 1 MPI processes. This may indicate a
severe problem with the MPI startup
mechanism.</font></i></div>
<i><font color="#a64d79">APPLICATION TERMINATED
WITH THE EXIT STRING: Aborted (signal 6)</font><br>
</i>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">The command fed into
the simfactory via jobscript is as follows:</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"><font color="#a64d79"><i>time
mpirun
/home2/mallick/ET/Cactus/simfactory/bin/sim
create-submit nsns30
--basedir=/home2/mallick/simulations
--procs=32 --ppn=16 --num-threads=1
--num-smt=1 --ppn-used=16 --parfile
/home2/mallick/ET/Cactus/parfile/nsns_vlr_mass_diff.par
--walltime=24:00:00</i></font><i><b><font
color="#a64d79"><br>
</font></b></i></div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">I could not figure
out the issue. I am also struggling with
setting up the machine scripts as per the
cluster, so I am not sure if that is somehow
hampering the simulation.</div>
<div class="gmail_default"
style="color:rgb(0,0,0)"><br>
</div>
<div class="gmail_default"
style="color:rgb(0,0,0)">Thanks in advance for
helping me with this issue. I have attached
the concerned scripts and outputs for
reference.</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">Regards</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr"><font
color="#666666">Shamim Haque</font></div>
<div dir="ltr"><font
color="#666666">Junior
Research Fellow (JRF)<br>
</font>
<div><font color="#666666">Department
of Physics</font></div>
<div><font color="#666666">IISER
Bhopal</font></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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style="max-height:1px"><img alt="" style="width:
0px; max-height: 0px; overflow: hidden;"
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