Error 35 Resource Temporarily Unavailable

[a elmas]

I'm calling a method, scrTm(), many times in a loop. In this method it executes a perl script called "hybrid2.pl".
hybrid2.pl needs two input files, "s1.seq" ve "s2.seq". I write these files in the same method, scrTm(). Method basically takes two character arrays as inputs(seq1 and seq2) and writes them into files "s1.seq" ve "s2.seq".

At first steps(up to around 100) the perl script is executed with no problem, however when the number of steps increase it gives an exception as:

Error: Cannot run program "/file_path/hybrid2.pl": error=35, Resource temporarily unavailable

I guess, I am ensuring that the files are written correctly and it is an issue of memory. There should be a simple solution to this, but I'm new in Java.
Please help me how to fix it.

Here is my code:

public static int scrTm(char[] seq1, char[] seq2) throws IOException{		
		
		
		// PERL
		String sequence1 = null;
		String sequence2 = null;
		
		while( (sequence1 == null) && (sequence2 == null) ) { 
				
			// WRITE
		     try{ // Write file s1.seq
		    	    FileWriter file1 = new FileWriter("s1.seq");
		    	        BufferedWriter out1 = new BufferedWriter(file1);
		    	    out1.write(seq1);
		    	    //Close the output stream
		    	    out1.flush();
		    	    file1.flush();
		    	 }
		     catch (Exception e1){//Catch exception if any
		     System.err.println("Error: " + e1.getMessage());
		     }
		     
		     try{ // Write file s2.seq
		    	    FileWriter file2 = new FileWriter("s2.seq");
		    	        BufferedWriter out2 = new BufferedWriter(file2);
		    	    out2.write(seq2);
		    	    //Close the output stream
		    	    out2.flush();
		    	    file2.flush();		    	  
		    	 }
		     catch (Exception e2){//Catch exception if any
		     System.err.println("Error: " + e2.getMessage());
		     }
		     
		 
			
        // READ
		FileReader reader1 = new FileReader("s1.seq"); 	    
		BufferedReader br1 = new BufferedReader(reader1); 
		sequence1 = br1.readLine();
		FileReader reader2 = new FileReader("s2.seq"); 	    
		BufferedReader br2 = new BufferedReader(reader2); 
		sequence2 = br2.readLine();
		br1.close();
		br2.close();
		reader1.close();
		reader2.close();
		}// end of while

	
			// RUN PERL
		    try{
		    // put the file path 		    	
		    Runtime.getRuntime().exec("/file_path/hybrid2.pl s1.seq s2.seq" );
		    }
		    catch(Exception perl){
		    
			System.err.println("Error: " + perl.getMessage());		    	
		    } // end of PERL
		
		



		
			// Import from file
		    int imported = 0;
		    if (seq1==seq2){
		    	try{imported = Util.importTm("s1-s1.ens.TmCp");        
		    	}catch(Exception err1_importTm){
		    	System.err.println("Error: " + err1_importTm.getMessage());		    	
		    	}	    	
			}else{ 
			    try{imported = Util.importTm("s1-s2.ens.TmCp");
			    }catch(Exception err2_importTm){		    	
			    System.err.println("Error: " + err2_importTm.getMessage());		    	
			    }
			}
		    
		    System.out.println("Tm = " + imported);
	return imported;
	} // end of scrTm

[James Sabre]

Is there some reason why you don't close stream 'out1' and 'out2' ? These streams are are still open when you use the associated files though Runtime.exec().

P.S. When you chain streams as you are doing you only need to close() the outer stream since this is required to propagate through to the chained stream.
P.S.1 You should not need to flush() a stream before closing it since the contract for close() says it should perform a flush() before actually closing.
P.S.2 You should close streams in a finally() clause to make sure that even if you have exception the streams are closed. This is a simplification of the standard forceClose() method I use in most of my work.

 public static void forceClose(Closeable c)
    {
        try
        {
            if (c != null)
                c.close();
        } catch (Exception e)
        {
            e.printStackTrace();
        }
    }

It can be used on all Java streams since they all implement Closeable.
P.S.3 Your use of Runtime.exec() is seriously flawed. See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html

[a elmas]

James Sabre wrote:
P.S.3 Your use of Runtime.exec() is seriously flawed. See http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html

Thanks for reminding the open files, but it did not fix the problem alone. I looked the web-page you referred, it is a good trouble-shooter for Runtime.exec().
Using the StreamGobbler class mentioned there fixed all the problem. It seems like flawless for now.

Thank you so much!

[fred rosenberger]

a elmas,
Your post was moved to a new topic.