engine is disabled by default. To configure executable for cluster\r
execution un comment the X.cluster settings and change them\r
appropriately. </p>\r
-<p>By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing <span class="hightlight">conf/settings/<X>Limit.xml</span> files.<br />\r
+<p>\r
+ By default limits are set well in excess of what you may want to offer to the users outside your lab, \r
+ to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 \r
+ letters on average for all of the JABA web services. You can adjust the limits according to your \r
+ needs by editing <span class="hightlight">conf/settings/<X>Limit.xml</span> files.<br />\r
After you have completed the editing your configuration may look like\r
this:<span class="code">local.mafft.bin.windows=<br />\r
local.mafft.bin=binaries/mafft<br />\r
files that reside inside web application directory, all other paths\r
must be supplied as absolute!</p>\r
\r
-<p>Furthermore, you should avoid using environment variables within the paths or options - since these will not be evaluated correctly. Instead, please explicitly\r
-specify the absolute path to anything\r
-normally evaluated from an environment variable at execution time.</p>\r
+<p>\r
+Furthermore, you should avoid using environment variables within the paths or options - since \r
+these will not be evaluated correctly. Instead, please explicitly specify the absolute path \r
+to anything normally evaluated from an environment variable at execution time.\r
+</p>\r
\r
<p>If you are using JABAWS to submit jobs to the cluster (with\r
cluster engine enabled), executables must be available from all\r
defined in <span class=\r
"hightlight">conf/Executable.properties</span> file.</p>\r
<h3><a name="settinglimit" id="settinglimit"></a>Limiting the size of the job accepted by JABAWS </h3>\r
-<p>JABAWS can be configured to reject excessively large tasks. This is useful if you operate JABAWS service for many users. By defining a maximum allowed task size you can provide an even service for all users and prevents waist of resources on the tasks too large to complete successfully. You can define the maximum number of sequences and the maximum average sequence length that JABAWS accepts for each JABA Web Service independently. \r
-Furthermore, you can define different limits for different presets of the same web service. <br />\r
-By default limits are disabled. You can enable them by editing <span class="hightlight">conf/Executable.properties</span> file. You can adjust the limits according to your needs by editing <span class="hightlight">conf/settings/<X>Limit.xml</span> files. </p>\r
+<p>\r
+JABAWS can be configured to reject excessively large tasks. This is useful if you operate JABAWS service \r
+for many users. By defining a maximum allowed task size you can provide an even service for all users and \r
+prevents waist of resources on the tasks too large to complete successfully. You can define the maximum \r
+number of sequences and the maximum average sequence length that JABAWS accepts for each JABA Web Service \r
+independently. Furthermore, you can define different limits for different presets of the same web service. \r
+<br/>\r
+By default limits are disabled. You can enable them by editing <span class="hightlight">conf/Executable.properties</span> \r
+file. You can adjust the limits according to your needs by editing <span class="hightlight">conf/settings/<X>Limit.xml</span> \r
+files.</p>\r
+\r
<h3><a name="diffbin" id="diffbin"></a>Using a different version of the alignment program with JABAWS</h3>\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
+<p>\r
+ JABAWS supplied with binaries and source code of the executables which version it supports. So normally you \r
+ would not need to install your own executables. However, if you have a different version of an executable \r
+ (e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions \r
+ JABAWS executable supported. This could be the case with more recent executable. If the options supported \r
+ by your chosen executable is different when the standard JABAWS executable, than you need to edit \r
+ <em>ExecutableName</em>Paramaters.xml configuration file.\r
+</p>\r
+\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
+<p>\r
+ If your cluster is busy and have significant waiting times you can achieve a faster response by allowing \r
+ the server machine to calculate small tasks and the reserve the cluster for bigger jobs. This works \r
+ especially well if your server is a powerful machine with many CPUs. To do this you need to enable and \r
+ configure both the cluster and the local engines. Once this is done decide on the maximum size of a task \r
+ to be run on the server locally. Then, edit \r
+ <span class="hightlight">"# LocalEngineExecutionLimit #" </span>preset \r
+ in <span class="hightlight"> <ServiceName>Limits.xml</span> file accordingly. JABAWS server then \r
+ will balance the load according to the following rule: If the task size is smaller then the maximum task \r
+ size for local engine, and the local engine has idle threads, then calculate task locally otherwise submit \r
+ the task to the cluster.\r
+</p>\r
+\r
<h3><a name="testingJaba" id="testingJaba"></a>Testing JABA Web Services</h3>\r
-<p>Access <span class="code"><your_JABAWS_server_URL>/ServiceStatus</span> to test all web services. Each time you access this URL, all services are tested. You can test a particular web service by adding its name at the end of this URL. For example <span class="code">http://localhost:8080/jabaws/ServiceStatus/MuscleWS </span>will test MuscleWS webservice only. For production configuration we recommend prohibiting requests to this URL for non authenticated users to prevent excessive load on the server. </p>\r
+<p>\r
+ Access <span class="code"><your_JABAWS_server_URL>/ServiceStatus</span> to test all web services. \r
+ Each time you access this URL, all services are tested. \r
+ <!-- You can test a particular web service by adding \r
+ its name at the end of this URL. For example <span class="code">http://localhost:8080/jabaws/ServiceStatus/MuscleWS </span>\r
+ will test MuscleWS webservice only. -->\r
+ For production configuration we recommend prohibiting requests to this URL for non \r
+ authenticated users to prevent excessive load on the server.\r
+</p>\r
<p>Alternatively, 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
server package, you can use <span class=\r
<p> Google Analytics can be disabled or adjusted by removing/editing <span class="hightlight">conf/GA.properties</span> Google Analytics (GA) settings file. We would appreciate it greatly if you could leave it on!</p>\r
<p>All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance.</p>\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 14 October 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div><!-- page end-->\r
\r
git://source.jalview.org / jabaws.git / blobdiff