Trouble Shooting
This site lists problems that may occur using CaTSiT and hints how to solve them.
If you encounter other problems, please send us a description of the error and what you did before it occurred, so we may extend this section.
| Problem | The simulation aborts with a java.lang.OutOfMemoryError error. |
| Solution | This error occurs when the java process running the simulation has too little RAM size.
You can evade this error by assigning a higher maximum heap size to the simulation process
via the java parameter -Xmx3g. The number represents the number of Gigabyte to
assign. E.g.:
java -jar -Xmx3g CaTSiT.jar simulate 'PathToOutputFile' 'sheetName' 'PathToConfigurationFile' 'PathToTechnicalFile'
|
| Problem | The simulation takes forever! |
| Solution | Depending on the configuration and the equipment of your pc the simulation can take between
some seconds and several minutes. As a reference, the sample main configuration file, which you
can download at the sample configuration page, takes about 20
sec to cover a duration of 1500 days and about 4:30 min to cover a duration of 2000 days. The
computer that was used to run this test simulations has an Intel Core 2 Duo 3.00 Ghz processor
and a RAM size of 8 GB. The speed of the simulation is influenced by the following parameter: duration, growth rates, colonizations rates and the option whether metastases are also able to metastasise (this has a very big influence). If a simulation takes to long, first check whether all time relevant parameter (growth rates, colonization rates, duration ...) are stated in the right unit. Growth rates are given in 1/day, colonization rates in 1/(cell*day) and the duration in days. If the simulation still takes to long, try to decrease the duration in the technical configuration file. |
| Problem | The script runMultipleSims.sh won't start on Linux. The error message says 'no permission'. |
| Solution |
To execute the script
chmod +x runMultipleSims.sh
|