mirror of
https://github.com/nwchemgit/nwchem.git
synced 2026-07-28 06:05:44 -04:00
200 lines
7 KiB
HTML
200 lines
7 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
|
|
"http://www.w3.org/TR/html4/loose.dtd">
|
|
<HTML>
|
|
<HEAD>
|
|
<TITLE>NWChem Frequently Asked Questions</TITLE>
|
|
<link rel="stylesheet" type="text/css" href="../../shared/nwchem_basic.css">
|
|
</HEAD>
|
|
|
|
<body text="#000000" bgcolor="#FFFFFF" link="blue" alink="blue" vlink="blue">
|
|
<table width="650"><tr><td>
|
|
<br>
|
|
<table>
|
|
<tbody>
|
|
<tr>
|
|
<td align="left" width="325"><img src="../../images/nwchem_logo_dark.gif" border=0 width=200 alt="NWChem - computational chemistry on parallel computers"></td>
|
|
<td align="right" width="325" valign="bottom">
|
|
<a href="../../nwchem_main.html">NWChem Home</a> |
|
|
<a href="../../disclaimer.html">Security & Privacy</a> |
|
|
<a href="http://www.pnl.gov" target="_blank">PNNL</a>
|
|
</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<hr>
|
|
<table width="650">
|
|
<tbody>
|
|
<tr>
|
|
<td width="350" align="left"></td>
|
|
<td width="300" align="right"><a href="ibm.html">Next FAQ Catagory</a> | <a href="NWChem_FAQ.html">Return to Main FAQ</a></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
|
|
<br><br>
|
|
<h1>NWChem FAQ</h1>
|
|
|
|
<p><h2>IBM SP</h2>
|
|
|
|
<!--DO NOT REMOVE Begin Question and End Question Comments.-->
|
|
<ul>
|
|
<!--Begin Question-->
|
|
<li><a href="#0">What is the target for running NWChem on IBM SPs? </a></li>
|
|
<li><a href="#1">I have a lapi_init error. How do I fix this problem?</a></li>
|
|
<li><a href="#2">I have a load error when trying to run NWChem. How do I fix this problem?</a></li>
|
|
<li><a href="#3">Thread scheduling policy change from AIX 4.3 to 4.3.3 which effects performance.</a></li>
|
|
<li><a href="#4">How do I use more than 2 GB of disk space?</a></li>
|
|
<!--End Question-->
|
|
</ul>
|
|
|
|
|
|
<hr>
|
|
<p>
|
|
<a name="0"></a>
|
|
<font color="purple">What is the target for running NWChem on IBM SPs?
|
|
</font>
|
|
<p>
|
|
The right target is <pre>LAPI</pre>
|
|
IBM binaries are not going to work on IBM SP systems.
|
|
For further details, have a look at the Users's manual <a href="http://www.emsl.pnl.gov/docs/nwchem/doc/user/node40.html#SECTION004050000000000000000">Running on an IBM SP</a>.
|
|
</p>
|
|
|
|
<hr>
|
|
<p>
|
|
<a name="1"></a>
|
|
<font color="purple"> I have a lapi_init error. How do I fix this problem?</font>
|
|
<p>
|
|
If you get a message similar to:
|
|
<pre>
|
|
0: lapi_init failed 419(1a3)
|
|
system message: Operation not permitted.
|
|
ERRIR: 0031-250 task 0: terminated
|
|
</pre>
|
|
you need to set the environment variable MP_MSG_API. You can either do this in your environment:
|
|
<pre>
|
|
setenv MP_MSG_API lapi
|
|
</pre>
|
|
or you can set it in your LoadLeveller script:
|
|
<pre>
|
|
# @ network.lapi = css0, not_shared, US
|
|
</pre>
|
|
The LoadLeveller method is preferred since it sets several other useful
|
|
variables.
|
|
NOTE: If you are using SMP nodes (i.e. more than one processor per node),
|
|
change the "not_shared" to "shared".
|
|
</p>
|
|
|
|
<hr>
|
|
<p>
|
|
<a name="2"></a>
|
|
<font color="purple"> I have a load error when trying to run NWChem. How do
|
|
I fix this problem?
|
|
</font>
|
|
<p>
|
|
If you get a message similar to:
|
|
<pre>
|
|
exec(): 0509-036 Cannot load program /usr/local/NWChem/bin/nwchem because of the
|
|
following errors:
|
|
0509-023 Symbol kaio_rdwr in /usr/lpp/ppe.poe/lib/libc.a is not defined.
|
|
0509-023 Symbol listio in /usr/lpp/ppe.poe/lib/libc.a is not defined.
|
|
0509-023 Symbol acancel in /usr/lpp/ppe.poe/lib/libc.a is not defined.
|
|
0509-023 Symbol iosuspend in /usr/lpp/ppe.poe/lib/libc.a is not defined.
|
|
0509-022 Cannot load library libc.a[aio.o].
|
|
0509-026 System error: Cannot run a file that does not have a valid format.
|
|
</pre>
|
|
The problem is that Asynchronous I/O is not turned on for your system. There
|
|
are two possible solutions. The first and best solution is to have the
|
|
system administrator turn on Asynchronous I/O on all of the nodes. This can
|
|
be done by:
|
|
<ol>
|
|
<li> Enter smit </li>
|
|
<li> Go to "Devices" </li>
|
|
<li> Go to "Asynchronous I/O" </li>
|
|
<li> Go to "Change / Show Characteristics of Asynchronous I/O" </li>
|
|
<li> Change "State of fast path" to "enable" </li>
|
|
<li> Make sure "STATE to be configured at system restart" is set to "available" </li>
|
|
<li> Exit smit</li>
|
|
</ol>
|
|
The nodes will need to be rebooted for the change to take effect.
|
|
<p>
|
|
The second solution is to compile GA without Asynchronous I/O turned on.
|
|
This WILL slow down the performance of NWChem.
|
|
<ol>
|
|
<li>cd $NWCHEM_TOP/src/tools/pario</li>
|
|
<li>make TARGET=LAPI clean</li>
|
|
<li>make TARGET=LAPI CC="cc -DNOAIO" LARGE_FILES=y</li>
|
|
<li>cd $NWCHEM_TOP/src</li>
|
|
<li>make link</li>
|
|
</ol>
|
|
</p>
|
|
|
|
<hr>
|
|
<p>
|
|
<a name="3"></a>
|
|
<font color="purple">Thread scheduling policy change from AIX 4.3 to 4.3.3 which
|
|
effects performance.
|
|
</font>
|
|
<p>
|
|
The default thread scheduling policy changed from AIX version 4.3 to 4.3.3
|
|
which effects MPI and LAPI programs that rely on switch packet arrival
|
|
interrupts (such as NWChem). This directly effects the performance of
|
|
NWChem. To change the default, you need to set the environment variable
|
|
RT_GRQ. You can either do this in your environment:
|
|
<pre>
|
|
setenv RT_GRQ ON
|
|
</pre>
|
|
or you can set it in your LoadLeveller script:
|
|
<pre>
|
|
# @ environment = RT_GRQ=ON
|
|
</pre>
|
|
Note that you may have other variables to set with the environment line. Just
|
|
add the variable onto the existing line using a semi-colon as a separator. For
|
|
example:
|
|
<pre>
|
|
# @ environment = COPY_ALL; MP_INFOLEVEL=3; MP_PULSE=0;
|
|
MP_SINGLE_THREAD=yes; MP_WAIT_MODE=yield; RT_GRQ=ON; restart=no
|
|
</pre>
|
|
</p>
|
|
|
|
<hr>
|
|
<p>
|
|
<a name="4"></a>
|
|
<font color="purple">How do I use more than 2 GB of disk space?</font>
|
|
<p>
|
|
During the compilation, the environment variable LARGE_FILES needs to be
|
|
set (i.e. setenv LARGE_FILES TRUE). Also, you should make sure that the
|
|
file sizes on your system are not limited to 2 GB (type "limit" and check
|
|
the output). If the sizes are limited, ask your system adminitrator to
|
|
change the limit for you.
|
|
</p>
|
|
<p>
|
|
<hr>
|
|
<font size="0">
|
|
<center>
|
|
<a href="../../nwchem_main.html">NWChem</a> |
|
|
<a href="../../capabilities/nwchem_capab.html">Capabilities</a> |
|
|
<a href="../../platforms/platforms.html">Platforms</a> |
|
|
<a href="../../download.html">Download</a> |
|
|
<a href="../../doc/user/index.html">User's Manual</a> |
|
|
<a href="../../doc/prog/index.html">Programmer's Manual</a> |
|
|
<a href="../../release-notes/index.html">Release Notes</a> |
|
|
<a href="NWChem_FAQ.html">FAQ</a>
|
|
</center>
|
|
<br>
|
|
<center>
|
|
<a href="../known_bugs.html">Known Bugs</a> |
|
|
<a href="../support.html">Support</a> |
|
|
<a href="../../training/training.html">Tutorial</a> |
|
|
<a href="../../contributors.html">Contributors</a> |
|
|
<a href="../../benchmarks/index.html">Benchmarks</a> |
|
|
<a href="http://www.emsl.pnl.gov/forms/search_nwchem.html">Search</a> |
|
|
<a href="http://www.emsl.pnl.gov/docs/mssg/index.html" target="_blank">Mol Sci. Soft. Group</a> |
|
|
<a href="../../citation.html">Citation</a>
|
|
</center>
|
|
</font>
|
|
<hr>Contact: <a href="mailto:ms3distribution@emsl.pnl.gov">NWChem Support</a><br>
|
|
Updated: February 22, 2005
|
|
</td></tr>
|
|
</table>
|
|
</body>
|
|
</html>
|