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Jarwulf

Exception in thread "Thread-4" java.lang.OutOfMemoryError: Java heap space

2 posts in this topic

Hi, I'm getting a crash in Java. Basically a txt file circa 150mb is being processed


[CODE]fileHandler.shrinkFile();[/CODE]


goes into


[CODE]

public void shrinkFile() throws FileNotFoundException, IOException, FileFormatException{
BufferedWriter outputTempFileWriter = null;
BufferedReader inputFileReader = null;


for(int i=0;i<choseFilesVector.size();i++){
String inputFile = choseFilesVector.get(i).toString();
inputFileReader = new BufferedReader(new FileReader( inputFile ), readBufferSize);

txtArea.append(" Processing "+inputFile+"\n");
txtArea.setCaretPosition(txtArea.getText().length());

//decide format
String strLine = null;
String format = null;
do{

//CRASH HAPPENS HERE
strLine = inputFileReader.readLine();
//CRASH HAPPENS HERE

if(strLine!=null && (strLine.split("\t").length>=4)){
String [] info = strLine.split("\t");
if((info[0].trim().toLowerCase().matches("chr(x|y|[0-9]+)"))&&(info[1].trim().matches("[0-9]+"))&&(info[2].trim().matches("[0-9]+"))){
//data of tagAlign
format = "tagAlign";
[/CODE]

It gets into the above loop and then simply crashes on line
[CODE]
strLine = inputFileReader.readLine(); [/CODE]

the first time through giving me the error

[CODE]Exception in thread "Thread-4" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Unknown Source)
at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)[/CODE]

etc etc. Maybe the file I'm processing is too big but the program has happened gigantic files before the only difference this time is that the files being processed were autoconverted from a different format.
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Actually its not because the file size, but I bet this new file has a gigantic [b]line [/b]on it.

The readLine() method will try and allocate the full line as a string in memory. If the line of text gets to big, you'll eventually run out of heap.

There's two courses of action that you can take :[list=1]
[*]Raise the amount of memory avaliable to the JVM (It'll work, but eventually you may run on OutOfMemory erros again)
[*]Refactor the code without relying on the readLine() method. (Instead of reading the full string and spliting it on memory, you should create a FSM and parse the file on a more "streaming" fashion)
[/list]
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