User f698d0529d
29-09-2005 14:15:04
Hi
This is a question which I started to ask before, but turned into a discussion on fingerprints, which I am still following up, and has been useful.
Just to clarify, about the memory requirements, the question was about the parameter to put in the catalina.sh file. Please bear with me while I explain
export JAVA_OPTS=${JAVA_OPTS}' -Xmx800m'
the line above is my catalina.sh setting at the moment.
I worked out that for all my JChem indexes, 656M of cache memory was required (using the exact method of calculation based on fingerprint size and average smiles length). On top of this, 64M are set in the JChemstreams web application for "reserved for temporary data".
So, in total, this should be 720M needed. The reason I had to increase it to 800M was because otherwise, I was still seeing messages in the catalina.out file that tables were being dropped from the cache due to lack of memory. I don't understand why this was happening. So I thought the best thing to do was leave the 64M alone, and keep increasing the catalina setting until the messages disappeared.
But I wonder now if increasing the 64M value and the total catalina amount still further would improve the performance. We now have plenty of RAM available on the server, but I don't want to waste memory either. For example, I wonder what happens if the total catalina memory is greater than the cache requirement and the temporary computational requirement. In that case, would some memory end up being reserved, but not used?
Do you have any suggestions as to how to set the value to the "optimum" value?
This is a question which I started to ask before, but turned into a discussion on fingerprints, which I am still following up, and has been useful.
Just to clarify, about the memory requirements, the question was about the parameter to put in the catalina.sh file. Please bear with me while I explain
export JAVA_OPTS=${JAVA_OPTS}' -Xmx800m'
the line above is my catalina.sh setting at the moment.
I worked out that for all my JChem indexes, 656M of cache memory was required (using the exact method of calculation based on fingerprint size and average smiles length). On top of this, 64M are set in the JChemstreams web application for "reserved for temporary data".
So, in total, this should be 720M needed. The reason I had to increase it to 800M was because otherwise, I was still seeing messages in the catalina.out file that tables were being dropped from the cache due to lack of memory. I don't understand why this was happening. So I thought the best thing to do was leave the 64M alone, and keep increasing the catalina setting until the messages disappeared.
But I wonder now if increasing the 64M value and the total catalina amount still further would improve the performance. We now have plenty of RAM available on the server, but I don't want to waste memory either. For example, I wonder what happens if the total catalina memory is greater than the cache requirement and the temporary computational requirement. In that case, would some memory end up being reserved, but not used?
Do you have any suggestions as to how to set the value to the "optimum" value?