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<TITLE>NWChem Frequently Asked Questions</TITLE>
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<td align="left" width="325"><img src="../../images/nwchem_logo_dark.gif" border=0 width=200 alt="NWChem - computational chemistry on parallel computers"></td>
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<a href="../../nwchem_main.html">NWChem Home</a> |
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<td width="300" align="right"><a href="ibm_sp.html">Next FAQ Catagory</a> | <a href="NWChem_FAQ.html">Return to Main FAQ</a></td>
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<br><br>
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<h1>NWChem FAQ</h1>
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<p><h3>Linux Clusters</h3></p>
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<!--DO NOT REMOVE Begin Question and End Question Comments.-->
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<ul>
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<!--Begin Question-->
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<li><a href="#0">What hardware configuration is suggested for running NWChem on Linux cluster? </a></li>
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<li><a href="#1">How do I install and run NWChem on Myrinet clusters?</a></li>
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<li><a href="#2">How do I install NWChem on Giganet clusters?</a></li>
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<li><a href="#3">How do I increase the shared memory segment in FreeBSD?</a></li>
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<!--End Question-->
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</ul>
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<hr>
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<p>
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<a name="0"></a>
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<font color="purple">What hardware configuration is suggested for running NWChem on Linux cluster?
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</font>
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<p>
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Most of the NWChem modules are not going to perform well on large Linux clusters
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that use just Fast Ethernet for communication. For optimal performance,
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you need to use either <a href="#giganet">Giganet</a> or <a href="#myrinet"> Myrinet</a> interconnects.
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</p>
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<hr>
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<p>
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<a name="1"></a>
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<font color="purple">How do I install and run NWChem on Myrinet clusters?
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</font>
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<p>
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Prior to installing NWChem, you must have installed the <a href="http://www.myri.com/scs/linux/index.html">GM</a> and the
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<a href="http://www.myri.com/scs/index.html"> MPICH over GM</a>
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softwares on the system.
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<p>Before starting the NWChem compilation, the following environmental variables
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must be defined
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<pre>
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USE_MPI=y
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GM_HOME="location of GM software"
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GM_INCLUDE=$GM_HOME/include
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GM_LIB=$GM_HOME/lib
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ARMCI_NETWORK=GM
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MPI_LOC="location of MPICH-GM software"
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MPI_LIB=$MPI_LOC/lib
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MPI_INCLUDE=$MPI_LOC/include
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LIBMPI=-lmpich
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</pre>
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To run NWChem, you need to set the following enviromental variable
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<pre>
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GMPI_SHMEM_FILE /tmp/$USER.gm
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</pre>
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The next step is to launch the program. One way to do it is by using
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the mpirun.ch_gm script supplied in the MPICH-GM tar file. The
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command to execute is
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<pre>
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mpirun.ch_gm --gm-use-shmem $NWCHEM_TOP/bin/LINUX/nwchem
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</pre>
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or
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<pre>
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mpiexec $NWCHEM_TOP/bin/LINUX/nwchem
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</pre>
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<hr>
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<p>
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<a name="2"></a>
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<font color="purple">How do I install NWChem on Giganet clusters?
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</font>
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<p>
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Before starting the NWChem compilation, the following environmental variables
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must be defined
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<pre>
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ARMCI_NETWORK=VIA
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LIBMPI="-lmpipro -lpthread"
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</pre>
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To run NWChem, you need to set the following environmental variable
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<pre>
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MPI_COMM=VIA
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</pre>
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</p>
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<hr>
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<p>
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<a name="3"></a>
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<font color="purple">How do I increase the shared memory segment in FreeBSD?</font>
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<p>
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To increase the shared memory segments on FreeBSD the
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following two sysctl's should be added to the startup scripts
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(e.g. /etc/rc.local):
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<pre>
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sysctl -w kern.ipc.shmmax=67108864
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sysctl -w kern.ipc.shmall=16384
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</pre>
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the first sysctl allocates 64Mbytes of memory, the second does
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the same thing in 4k pages (4k * 16384 = 64M), you <b>must</b> set both
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sysctl.
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</p>
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</font>
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<hr>Contact: <a href="mailto:ms3distribution@emsl.pnl.gov">NWChem Support</a><br>
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Updated: February 22, 2005</td>
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