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<p class="MsoNormal"><span style="color:#1F497D">Sorry, I should have mentioned that our file system is NFS hosted on the cluster head node, with infiniband from the compute nodes to the head.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">******</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am attempting to run an MPI Monte Carlo: multiple instances of a simulation “Mav” under the control of MPI. Mav does a huge amount of output to disk, but the MPI processes that oversee the Mav instances are lightweight and only wake
up every 5 seconds.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The MPI Monte Carlo is much slower than running each Mav as an independent PBS Torque job, and according to “iotop”, the MPI-supervised Mav instances regularly become blocked waiting for I/O. iotop often shows the Mavs’s spending 99%
of their time waiting for I/O. The independent Torque jobs don’t do that.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I got some significant improvement in the MPI performance by telling qsub not to save the stdout and stderr output (qusb –k n) to a file. My question is: are there any other optional types of disk activity performed by MPI that I can disable?
What else could be happening here?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m using MPICH 3.3.2 compiled with pgc++, PBS Torque 5.1.1, CentOS 3.10.0.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here are my MPICH configure options:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">'--disable-option-checking' '--prefix=/opt/mpich_pgc' '--with-pbs=/opt/torque' 'CC=pgcc' 'CXX=pgc++' '-enable-debuginfo' '--cache-file=/dev/null' '--srcdir=.' 'CFLAGS= -O2' 'LDFLAGS=' 'LIBS=' 'CPPFLAGS= -I/home/kmccall/mpich-3.3.2/src/mpl/include
-I/home/kmccall/mpich-3.3.2/src/mpl/include -I/home/kmccall/mpich-3.3.2/src/openpa/src -I/home/kmccall/mpich-3.3.2/src/openpa/src -D_REENTRANT -I/home/kmccall/mpich-3.3.2/src/mpi/romio/include' 'MPLLIBNAME=mpl'<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">Kurt<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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