structure search cache error

User e34a92cce5

16-12-2005 15:59:13

Hi,


I am caching all my stuctures and recently started getting this error. The Xmx parameter is set to 1024 and we have about 2.5 million structures. Do you think that it is a server issue. I believe that 1024M should easily handle these many structures


Thanks!


Renju





Stack trace:


------------











java.lang.NullPointerException


at


chemaxon.jchem.db.StructureCache.getEstimatedMemorySize(StructureCache.java:1079)


at


chemaxon.jchem.db.CachePool.getTotalCacheSize(CachePool.java:113)


at


chemaxon.jchem.db.StructureCache.checkMemorySizeAndFreeIfNecessary(StructureCache.java:629)


at


chemaxon.jchem.db.StructureCache.load(StructureCache.java:445)


at


chemaxon.jchem.db.StructureCache.load(StructureCache.java:220)


at


chemaxon.jchem.db.StructureCache.loadIfNeeded(StructureCache.java:672)


at


chemaxon.jchem.db.JChemSearch.loadCacheIfNeeded(JChemSearch.java:2212)


at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2002)


at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:1857)


at


chemaxon.jchem.db.JChemSearch.access$1200(JChemSearch.java:71)


at


chemaxon.jchem.db.JChemSearch$SearchThread.run(JChemSearch.java:371)

ChemAxon 9c0afc9aaf

16-12-2005 16:20:02

Hi,





Or course the mentioned amount of memory is easily enough to cache 2.5 million average drug-like structures.


(only around 100MB is needed for 1 million)





Please let us know your JChem version, so we can look for the cause of the problem.





Best regards,





Szilard

User e34a92cce5

16-12-2005 16:45:52

JChem version : 3.0.5


JVM : Apple Computer, Inc. 1.4.2_09


OS : ppc Mac OS X 10.4.2

ChemAxon 9c0afc9aaf

16-12-2005 18:19:37

Hi,





We have located and fixed the problem.





This bug could occur if the initial loading of the cache started at the same time for multiple tables.


There was also a slight chance of a deadlock in similar situations, also fixed.





The next version of JChem will contain these fixes.





Until then I have prepared a modified version of the jchem.jar of our latest version (3.1.4). It is available at:





http://chemaxon.com/shared/jchem3_1_4_mod1/jchem.jar





(You should upgrade to 3.1.4 first and then replace the jchem.jar)





Many thanks for the bug report.





Best regards,





Szilard