Is there an log option that can let tomcat log the bad query instead just throwing this ?
SEVERE: java.lang.OutOfMemoryError: Requested array size exceeds VM limit
(Tried log level to FULL, but only capture the above)
This is not enough information to further debug
Alternatively, if this can be fixed by allocated more memory by tweaking the following?
-Xms1024M -Xmx4096M -XX:MaxPermSize=256M
-Xms6G -Xmx6G -XX:MaxPermSize=1G -XX:PermSize=512M
(the above seems works better, keep monitoring)
I suspect you might be using sorts on a large index. That's one thing I definitely know can require a large array size with Lucene. Either way, you might want to try using a 64-bit JVM with these options:
-Xmx6G -XX:MaxPermSize=128M -XX:+UseCompressedOops
The last option will reduce 64-bit memory pointers to 32-bit (as long the heap is under 32GB). This typically reduces the memory overhead by about 40%, so it can help stretch your memory significantly.
Update: Most likely you don't need such a large permanent generation size, certainly not 1G. You're probably fine with 128M, and you'll get a specific error if you go over with Java 6. Since you're limited to 8G in your server you might be able to get away with 7G for the heap with a smaller perm gen. Be careful about not going into swap, that can seriously slow things down for Java.
I noticed you didn't mention -XX:+UseCompressedOops
in your update. That can make a huge difference if you haven't tried it yet. You might be able to squeeze a little more space out by reducing the size of eden to give the tenured generation more room. Beyond that I think you'll simply need more memory or fewer sort fields.