Java Heap space

Hello,

I have Heap Space problems loading a 550M sd file into the Schrodinger SD reader. the heap space goes up to 990M which is the upper limit (looking at the low right corner small bar in the knime window) and then the operation of course fail. I am using Knime 2.3 and latest Schrodinger release.

ERROR     SD Reader     Execute failed: Java heap space

Any solutions??

Thanks

Hi mining12,

did you try increasing the heap space?

 

http://tech.knime.org/faq#q4_2

 

Iris

I did, to 2048m but still reaches the limit and fail...may be some problems with the SD Schrodinnger node?

Maybe it also helps if you set a different memory policy on the node (in the configuration dialog, select tab "Memory Policy" and then "Write tables to disc").

Does "550M sd file" refer to the number of structures in the SD file or to the size in MB of the file (either way should work fine, yes).

Thanks, I'll try. It refers to 550MB. I also have a file bigger than 1 GB.

Still fails, I get this error:

ERROR     Ligfilter     Execute failed: ("OutOfMemoryError"): null
ERROR     KNIME-Worker-3 Ligfilter     Execute failed: ("OutOfMemoryError"): null
** (KNIME:24234): DEBUG: raico_blur_apply(): invalid surface status
** (KNIME:24234): DEBUG: raico_blur_apply(): invalid surface status
** (KNIME:24234): DEBUG: raico_blur_apply(): invalid surface status
** (KNIME:24234): DEBUG: raico_blur_apply(): invalid surface status
** (KNIME:24234): DEBUG: raico_blur_apply(): invalid surface status
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x0caed57b, pid=24234, tid=3078133440
#
# JRE version: 6.0_22-b04
# Java VM: Java HotSpot(TM) Client VM (17.1-b03 mixed mode linux-x86 )
# Problematic frame:
# C  [libxul.so+0x8ef57b]
#
# An error report file with more information is saved as:
# /XXXXX/XXXX/hs_err_pid24234.log
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted

 

This sounds very much like a specific problem in the "Ligfilter" class. You should contact you Schrodinger representative and describe the behavior that you see. Pleae also send them the "/XXXXX/XXXX/hs_err_pid24234.log" file as it contains useful information what library is causing the crash.

Sorry for not being more helpful.

 Bernd

Could you please contact and send the details to our technical support at help@schrodinger.com and we will look into this. We apologize for the inconvenience.

Best regards,

 

Jean-Christophe