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<li><a href="#settinglimit">Limiting the size of the job accepted by JABAWS Server </a></li>\r
<li><a href="#diffbin">Using a different version of the alignment program with JABAWS</a></li>\r
<li><a href="#mixuse">Load balancing </a></li>\r
- <li><a href="#confaccessright">Reviewing JABAWS configuration via web browser</a></li>\r
<li><a href="#testingJaba">Testing JABA Web Services</a></li>\r
<li><a href="#logs">JABAWS requests logging </a></li>\r
<li><a href="#logfiles">JABAWS internal logging </a></li>\r
- <li><a href="#execstat">Monitoring JABAWS</a></li>\r
<li><a href="#warfile">JABAWS War File Content</a></li>\r
+ <li><a href="#execstat">JABAWS Usage Statistics</a></li>\r
</ul>\r
<h3><a name="defjabaconf" id="defjabaconf"></a>JABAWS Configuration </h3>\r
<p>There are three parts of the system you can configure. The local\r
engine where to find DRMAA libraries. These variables\r
should be defined when the web application server starts up, e.g.</p>\r
\r
-<p><span class="code">SGE_ROOT=/gridware/sge<br />\r
- LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64</span></p>\r
+<p class="code">SGE_ROOT=/gridware/sge<br />\r
+ LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64</p>\r
\r
<p>Finally, do not forget to configure executables for the cluster\r
execution, they may be the same as for the local execution but may\r
<p>JABAWS supplied with binaries and source code of the executables which version it supports. So normally you would not need to install your own executables. However, if you have a different version of an executable (e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions JABAWS executable supported. This could be the case with more recent executable. If the options supported by your chosen executable is different when the standard JABAWS executable, than you need to edit <em>ExecutableName</em>Paramaters.xml configuration file. </p>\r
<h3><a name="mixuse" id="mixuse"></a>Load balancing </h3>\r
<p>If your cluster is busy and have significant waiting times you can achieve a faster response by allowing the server machine to calculate small tasks and the reserve the cluster for bigger jobs. This works especially well if your server is a powerful machine with many CPUs. To do this you need to enable and configure both the cluster and the local engines. Once this is done decide on the maximum size of a task to be run on the server locally. Then, edit <span class="hightlight">"# LocalEngineExecutionLimit #" </span>preset in<span class="hightlight"> <ServiceName>Limits.xml</span> file accordingly. JABAWS server then will balance the load according to the following rule: If the task size is smaller then the maximum task size for local engine, and the local engine has idle threads, then calculate task locally otherwise submit the task to the cluster. </p>\r
-<h3><a name="confaccessright" id="confaccessright"></a>Reviewing JABAWS configuration via web browser</h3>\r
-<p>Access to configuration files is prohibited to any unauthorized users by means of security constrain defined in web application descriptor file. There is a special user role called <span class="hightlight">admin</span> who can access these files. This comes handy if you would like to keep an eye on any of the task outputs stored in jobsout, or would like to view the configuration files. To access the configuration files add admin user into your application server. The way you do it depends on where you would like the user passwords to come from and your web application server. If you use Tomcat, then the simplest way is to use Tomcat Memory Realm which is linked to a plain text configuration file. To define the user in Tomcat server add an entry in <span class="hightlight">conf/tomcat-user.xml</span> file. <span class="code"><role rolename="admin"/><br />\r
- <user username="admin" password="your password here " roles="admin"/></span></p>\r
-<p>Once this is done make sure the servlet that returns the web application directory listings is enabled. Look in the <span class="hightlight"><tomcatroot>/conf/web.xml</span> file for the following <span class="code"><param-name>listings</param-name><br />\r
- <param-value>true</param-value></span></p>\r
-<p>The whole section that defines default listing servlet is below</p>\r
-<p class="code"> <servlet><br />\r
- <servlet-name>default</servlet-name><br />\r
- <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class><br />\r
- <init-param><br />\r
- <param-name>debug</param-name><br />\r
- <param-value>0</param-value><br />\r
- </init-param><br />\r
- <init-param><br />\r
- <param-name>listings</param-name><br />\r
- <param-value>true</param-value><br />\r
- </init-param><br />\r
- <load-on-startup>1</load-on-startup><br />\r
- </servlet><br />\r
-</p>\r
-<p>These listings are read only by default.</p>\r
<h3><a name="testingJaba" id="testingJaba"></a>Testing JABA Web Services</h3>\r
<p>You can use a command line client (part of the client only\r
package) to test your JABAWS installation as described <a href="man_client.html">here</a>. If you downloaded a JABAWS\r
<p>If you would like to know who is using your services, you might\r
want to <a href="#logs">enable Tomcat request\r
logging</a>.</p>\r
-<h3><a name="execstat" id="execstat"></a>Monitoring JABAWS</h3>\r
-<p>JABAWS stores cluster task ids for all tasks which were run on the cluster. Using cluster ids the detailed statistics can be extracted from cluster accounting system. Due to the fact that each cluster supported by JABAWS have different accounting system it was not possible to provide ready to use statistics. <br />\r
- For the local execution the starting and finishing time in nano seconds can be found in STARTED and FINISHED files respectively. In time we will provide the tools to extract execution time statistics, so keep the content of your working directory ready!</p>\r
<h3><a name="warfile" id="warfile"></a>JABAWS War File Content</h3>\r
<table width="100%">\r
<tr>\r
<td>images referenced by html pages</td>\r
</tr>\r
</table>\r
-<p> </p>\r
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-<div id="copyright">Last update: 1 April 2011<br />\r
+<div id="copyright">Last update: 10 August 2011<br />\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
git://source.jalview.org / jabaws.git / blobdiff