Out of memory error for SD file import

Hi,





I like the Instant JChem UI very much and was wondering if there are any problems with trying to load a 40M sd file into the local (derby) database. I think I'm doing it correctly, but consistently get a java out of memory exception. I have attached the output visible in the UI during file import. Is there any other logs that may help give a better picture of what's going on?





Thanks,


Jim

Code:

Created new field SMILES Created new field MOLECULE_NAME Created new field MOLECULAR_WEIGHT Created new field MOLECULAR_FORMULA Created new field STRUCTURE_ID Created new field VENDOR_NAME Created new field CATALOG_NAME Created new field CATALOG_NUMBER Created new field QUANTITY Created new field QUANTITY_UNIT_SYMBOL Created new field PRICE Created new field CURRENCY_SYMBOL Created new field PURITY_DISPLAY Created new field CAS_NUMBER Created new field MFCDNUMBER Structure is mapped to current field Structure Starting to import data... Error: Failed to import row 11,227 org.springframework.jdbc.UncategorizedSQLException: java.io.IOException: file format not recognized; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; java.io.IOException: file format not recognized; nested exception is java.sql.SQLException: java.io.IOException: file format not recognized Error: Failed to import row 11,229 org.springframework.jdbc.UncategorizedSQLException: java.io.IOException: file format not recognized; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; java.io.IOException: file format not recognized; nested exception is java.sql.SQLException: java.io.IOException: file format not recognized Error: Failed to import row 11,231 org.springframework.jdbc.UncategorizedSQLException: java.io.IOException: file format not recognized; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; java.io.IOException: file format not recognized; nested exception is java.sql.SQLException: java.io.IOException: file format not recognized Error: Failed to import row 11,233 org.springframework.jdbc.UncategorizedSQLException: java.io.IOException: file format not recognized; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; java.io.IOException: file format not recognized; nested exception is java.sql.SQLException: java.io.IOException: file format not recognized Error: Failed to import row 11,235 org.springframework.jdbc.UncategorizedSQLException: java.io.IOException: file format not recognized; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; java.io.IOException: file format not recognized; nested exception is java.sql.SQLException: java.io.IOException: file format not recognized Error: Failed to import row 11,237 org.springframework.jdbc.UncategorizedSQLException: java.io.IOException: file format not recognized; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; java.io.IOException: file format not recognized; nested exception is java.sql.SQLException: java.io.IOException: file format not recognized Error: Failed to import row 12,499 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,500 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,501 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,502 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,503 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,504 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,505 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,506 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,507 java.lang.OutOfMemoryError: Java heap space Error: Failed to import row 12,508 java.lang.OutOfMemoryError: Java heap space Error: TOO MANY CONSECUTIVE ERRORS, TERMINATING IMPORT Import completed in 770s. 12,492 entries successfully imported. 16 Errors.

Memory settings can be adjusted.


Use Tools -> Options to open the options dialog.


Then go to the Miscellaneous options and look in the Startup options tab.


We suggest you stay comfortably under the total amount of memory you have.


e.g. if you have 1GB RAM then probably best not to use more than 0.5GB for IJC.





Tim

Tim,





Thanks for the reply. User error. I was setting the "Read More" setting during file import to a really large number. The column definitions were standard throughout the file so this action was pointless. Sorry for the confusion.





-Jim