User e05b1833aa
10-09-2010 09:23:14
Hi Tim,
I want to do an admittetly demanding overlap analysis with a 2000 cpd query against a 2.1 miljon cpd database. I get the following error message after a few minutes:
Starting overalap analysis
Running Similarity overlap analysis for Sprint_20 as query and Compounds as target
Options are: sep=, t:i,dissimilarityThreshold:0.19999999,maxResults:20,dissimilarityMetric:TANIMOTO,dissimilarityMetricParameters:
Created field Screen_80 count
Created field Screen_80 max
Created field Screen_80 hits
Using max hit count of 20
Starting searches...
Error: Unexpected error during search for structure 1
chemaxon.jchem.db.DatabaseSearchException: ERROR: Table "COMPOUNDS" could not fit into structure cache (out of memory).
Please visit http://www.chemaxon.com/jchem/FAQ.html#outofmemory and
http://www.chemaxon.com/jchem/FAQ.html#cacheSize
at chemaxon.jchem.db.JChemSearch.loadCacheIfNeeded(JChemSearch.java:1977)
at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:1678)
at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:1516)
at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:1369)
at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:1392)
at com.im.df.query.JChemSearchCapability.execute(JChemSearchCapability.java:240)
at com.im.df.query.JChemSearchCapability$SimilaritySearch.executeOverlapAnalysis(JChemSearchCapability.java:621)
at com.im.ijc.chem.overlap.wizard.OverlapAnalysisWizardAction$1.run(OverlapAnalysisWizardAction.java:81)
at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:577)
at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:1030)
Error: Unexpected error during search for structure 2
chemaxon.jchem.db.DatabaseSearchException: ERROR: Table "COMPOUNDS" could not fit into structure cache (out of memory).
Please visit http://www.chemaxon.com/jchem/FAQ.html#outofmemory and
http://www.chemaxon.com/jchem/FAQ.html#cacheSize
IJC cleary runs out of memory. Is there a way to increase the memory allocated to IJC? I'm running this on linux, have 4Gb of physical ram.