java process hangs while launching an executible that is using the file system -


i'm trying execute 'edena' bioinformatic program within java code. process uses input files , write output files. when input files small (~1 mb) process finishes , exits perfectly. when input files larger (~ 80 mb) process hangs. invoking process cmd works fine, suspect got buffers etc.. i'm working on ubuntu 12.04.10 4gb ram (don't know if relevant). code hanging:

string edena_exe1 = "edena -m 75 -p " + workshopdir + binassembly.cliquefilesdir +          "clique_" + c.getid() + " -drpairs "+ workshopdir + binassembly.cliquefilesdir +   "/clique" + c.getid() + "pair1.fna " + workshopdir +  binassembly.cliquefilesdir + "/clique" + c.getid() + "pair2.fna "; process edena_proc1 = runtime.getruntime().exec(edena_exe1); edena_proc1.waitfor();

thanks!

i suspect larger input file process generates more output.

when process started jvm given limited buffered stream output. if not bleed stream while process running may fill , block.

private static void dir() throws ioexception {   runtime r = runtime.getruntime();   process p = r.exec("dir c:\\ /s");   bufferedreader br = new bufferedreader(new inputstreamreader(p.getinputstream()));   try {     string line;     // bleed output.     while ((line = br.readline()) != null) {       system.out.println(line);     }   } {     br.close();   }   // in case.   p.destroy(); }

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