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<h1>NWChem FAQ</h1>
<p><h3>Linux Clusters</h3></p>
<!--DO NOT REMOVE Begin Question and End Question Comments.-->
<ul>
<!--Begin Question-->
<li><a href="#0">What hardware configuration is suggested for running NWChem on Linux cluster? </a></li>
<li><a href="#1">How do I install and run NWChem on Myrinet clusters?</a></li>
<li><a href="#2">How do I install NWChem on Giganet clusters?</a></li>
<li><a href="#3">How do I increase the shared memory segment in FreeBSD?</a></li>
<!--End Question-->
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<hr>
<p>
<a name="0"></a>
<font color="purple">What hardware configuration is suggested for running NWChem on Linux cluster?
</font>
<p>
Most of the NWChem modules are not going to perform well on large Linux clusters
that use just Fast Ethernet for communication. For optimal performance,
you need to use either <a href="#giganet">Giganet</a> or <a href="#myrinet"> Myrinet</a> interconnects.
</p>
<hr>
<p>
<a name="1"></a>
<font color="purple">How do I install and run NWChem on Myrinet clusters?
</font>
<p>
Prior to installing NWChem, you must have installed the <a href="http://www.myri.com/scs/linux/index.html">GM</a> and the
<a href="http://www.myri.com/scs/index.html"> MPICH over GM</a>
softwares on the system.
<p>Before starting the NWChem compilation, the following environmental variables
must be defined
<pre>
USE_MPI=y
GM_HOME="location of GM software"
GM_INCLUDE=$GM_HOME/include
GM_LIB=$GM_HOME/lib
ARMCI_NETWORK=GM
MPI_LOC="location of MPICH-GM software"
MPI_LIB=$MPI_LOC/lib
MPI_INCLUDE=$MPI_LOC/include
LIBMPI=-lmpich
</pre>
To run NWChem, you need to set the following enviromental variable
<pre>
GMPI_SHMEM_FILE /tmp/$USER.gm
</pre>
The next step is to launch the program. One way to do it is by using
the mpirun.ch_gm script supplied in the MPICH-GM tar file. The
command to execute is
<pre>
mpirun.ch_gm --gm-use-shmem $NWCHEM_TOP/bin/LINUX/nwchem
</pre>
or
<pre>
mpiexec $NWCHEM_TOP/bin/LINUX/nwchem
</pre>
<hr>
<p>
<a name="2"></a>
<font color="purple">How do I install NWChem on Giganet clusters?
</font>
<p>
Before starting the NWChem compilation, the following environmental variables
must be defined
<pre>
ARMCI_NETWORK=VIA
LIBMPI="-lmpipro -lpthread"
</pre>
To run NWChem, you need to set the following environmental variable
<pre>
MPI_COMM=VIA
</pre>
</p>
<hr>
<p>
<a name="3"></a>
<font color="purple">How do I increase the shared memory segment in FreeBSD?</font>
<p>
To increase the shared memory segments on FreeBSD the
following two sysctl's should be added to the startup scripts
(e.g. /etc/rc.local):
<pre>
sysctl -w kern.ipc.shmmax=67108864
sysctl -w kern.ipc.shmall=16384
</pre>
the first sysctl allocates 64Mbytes of memory, the second does
the same thing in 4k pages (4k * 16384 = 64M), you <b>must</b> set both
sysctl.
</p>
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<hr>Contact: <a href="mailto:ms3distribution@emsl.pnl.gov">NWChem Support</a><br>
Updated: February 22, 2005</td>
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