error while tautomer calculation

Hi, I encounter problems when running the command:


cxcalc tautomers -f sdf -c true ./Checked.sdf >> ./TMP_12032007_110405AM/Checked.sdf





where Checked.sdf is a sd-file of 3.8GB which was exported from instantjchem.





the error is:





/usr/bin/cxcalc: line 108: 12621 Aborted (core dumped) java $javaopts chemaxon.marvin.Calculator "$@"





I thought that it's an issue of heap space, so I used the -xmX2000M flag, which did not do any better. Before that, I used lower values as well.





The file was imported/exported by IJC wihtout any problems, so o am wondering what could be the problem.


Thanks in advance, Markus

Hi,





Please run the following command on your system and post the result:

Code:

ulimit -c

Zsolt

The uotpou is as silmple as:





markus@akb-30:~$ ulimit -c


0


markus@akb-30:~$





Is there a problem with that?


Cheers Markus

m.kossner wrote:

The uotpou is as silmple as: markus@akb-30:~$ ulimit -c 0 markus@akb-30:~$ Is there a problem with that?

No, it's OK.





Do you get the same error with smaller files?


Could you run the calculation using Sun JRE 1.5?





Probably it is not a memory limit issue. Generating canonical tautomers (1 tautomer / molecule) should run fine with default -Xmx settings.





We are trying to reproduce the error.





Zsolt

Hi there,


I tried the same things on other PCs, notably 32bit in stead of my 64bit machines.


All works fine there!





I think it's an issue of the java installation, rather than one of the Chemaxon code. I was running the java-6-64bit when I encountered the problem. I came along the ia32bit packages, which I have not jet testet.





Secondly I could imagine some OS<->java problems, which we had with other java issues in the past. We are using "Ubuntu Gutsy Gibbon" on 64bit as well as 32bit architectures, as mentioned above.





Thank you for your help,


Markus