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Possible resource contention issue  RSS feed

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I have a problem which I am suspecting to be a contention issue on the Windows Tomcat 6 server I have. I have two production Java web applications (with JSPs, servlets) running on this same server. One (program A) has code in it that actually prints documents it retrieves from a network location through a DOS command. The other (program B) doesn't do anything like that, but does create and store documents through PDFCreator. Program A always seems to run into an issue, where when generating the command line and executing it for about 20 documents, it seems to miss about 4-5 random documents. The tomcat log file says that the commands were created by program A (I have System.outs in the app), but of course, some of the prints didn't actually happen. The log says that at the same time, in program B, it was having problems executing the calls to the PDFCreator. To see if the two apps were contending for the same resources (CPU, memory), I took A to a different server and stepped through the process of printing the documents, and every time I tested, all the 20 or so documents printed without a problem.
So my question is, does this mean I have to have the apps on separate servers, or is there a way I could configure Tomcat to share the server resources better, so I don't have to separate out the apps? Any help would be greatly appreciated.
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