ARSC HPC Users' Newsletter 350, October 13, 2006

Contents

• Iceberg Software Upgrades
• Java for Fortran Programmers: Part IV
• Quick Tip

Iceberg Software Upgrades

On October 4th, the compilers on iceberg were upgraded to the latest versions.

Below are some notable new features available in the compilers:

XL Fortran 10.1.0.1

With the upgrade to version 10.1, the IBM compiler now recognizes the suffix of a file to determine which Fortran standard to use during compilation.

In the past, the "-qsuffix=f=90" flag was required to have the XL Fortran compilers recognize .f90 as a valid Fortran 90 file, etc.

E.g.

  
  % mpxlf90_r hello_fortran.f90 -o hello_fortran
  ** mympi   === End of Compilation 1 ===
  1501-510  Compilation successful for file hello_fortran.f90.

The new compilers also recognize .F90 as a file which should be passed through the C preprocessor before compilation.

E.g.

  
  % mpxlf90_r -WF,-DSHOW hello_fortran.F90 -o hello_fortran
  ** mympi   === End of Compilation 1 ===
  1501-510  Compilation successful for file hello_fortran.F90.

In the past, this would have required a cryptic set of qsuffix sub-options (i.e. -qsuffix=f=f90:cpp=F90).

Recognized suffixes now include:
   .f,.f77,.f90,.f95,.F,.F77 .F90, and .F95

XL Fortran 10 also includes:

• OpenMP 2.5 API support.
• new scalar and vector functions in the MASS library.
• support for some parts of the Fortran 2003 standard

For more details see:
    http://www-306.ibm.com/software/awdtools/fortran/xlfortran/features/aix/xlf-aix.html

XL C/C++ 8.0.0.10

The upgraded XL C/C++ also includes:

• OpenMP 2.5 API support.
• new scalar and vector functions in the MASS library.
• Some support for gcc compiler flags to make it easier to port codes written for gcc.

For more details see: http://www-306.ibm.com/software/awdtools/caix/features/

Java for Fortran Programmers: Part IV

[[ Thanks to Lee Higbie of ARSC for this tutorial. ]]

The topic today is:

    - HelloBill, a simple Java GUI program

Here is the full text of HelloBill.java. The line numbers are not part of the code but were inserted here to facilitate discussing the code. I have deleted most blank lines to keep the length low in the newsletter. Also, in a text newsletter, the best way to describe a program appears to be with embedded comments and notes about specific lines at the end. That's where mine are.

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/**  Gussied up HelloWorld.
*
*   (C) Lee Higbie    &    Arctic Region Supercomputing Center, 2006
*   higbie at arsc dot edu      www.arsc.edu
*   This program may be copied and modified provided this notice is
*   preserved .
*/
import java.awt.*;        // all the windowing stuff like Buttons
import java.awt.event.*;  // for mouse click and window listeners

public class HelloBill extends Frame
                  implements ActionListener, WindowListener {
   // The next two lines declare two class variables.  These are
   // available to all HelloBIll objects--all instances of the class
   static String  title    = "Hi Bill";   // static for use in main
   Button disposeBtn = new Button("Exit");
   /**   @param  args the command line args, an array of Strings
   */
   public static void main (String [] args) {   // appl entry point
      if (args.length > 0) {
         System.out.println ("Hello "+ args[0] +" with "
                                    + args.length +" args.");
      } else {         // end if there are really arguments
         System.out.println ("Hello Pirate (argless user).");
      }                // end else, no arguments on command line
      HelloBill cg = new HelloBill(title);  // cr. HelloBill obj
   }     // end method main

   public HelloBill (String t) {    // for creating a HelloBill obj
      super (t);                    // call the Frame constructor
      disposeBtn.addActionListener(this);// tells: resp'd to clicks
      add(disposeBtn);              // adds dispose button to this
      setVisible(true);             // allows you to see this
      addWindowListener(this);      // for clicks on window buttons
   }                  // end of constructor
   // The rest of the code is for responding to external events
   public void actionPerformed(ActionEvent ae) {
      // required by ActionListener interface
      System.out.println("Dialog @ HelloBill 37 "+ae);
      // prints a line on java console so you can see action
      this.dispose();                        // closes window
   }                 // end of actionPerformed method
   // rest of methods are required by the WindowListener interface
   public void windowClosing     (WindowEvent we){
      System.out.println ("Window closing at HelloBill 46");
      System.exit(0);
   }                  // end of windowClsing method
   public void windowActivated   (WindowEvent we){ }    // all null
   public void windowClosed      (WindowEvent we){ }    // methods
   public void windowDeactivated (WindowEvent we){ }
   public void windowDeiconified (WindowEvent we){ }
   public void windowIconified   (WindowEvent we){ }
   public void windowOpened      (WindowEvent we){ }
}      // end HelloBill class

This source is available here:
   http://people.arsc.edu/~higbie/JavaForFortran/HelloBill.java

Notes on HelloBill.java: Because the class is named HelloBill, the file must be named HelloBill.java. The name is case sensitive, even on Windows systems.

Lines 8, 9: Most classes start with a series of import statements. As described in Chapter 3, these allow referencing the classes in those packages by the class names. The AWT includes a complete set of basic widgets. The widgets are in the java.awt package and the events are in java.awt.event. Notice that the import on line 8 does not import the events. The wild card only says to import all the members of the java.awt package.

Line 11: The extends clause means that HelloBill is a subclass of Frame (java.awt.Frame) and thus has access to all its public and protected methods, variables, ...

Line 12: The implements clause implies a contract between HelloBill and Java saying that HelloBill will have all the methods of the implemented classes. Java does not permit multiple inheritance (a class can extend only one other class) but the implementing capability allows a class to take on attributes of many others. More about this much later.

Lines 15, 16: Because title is static there is only one title for the HelloBill, no matter how many HelloBill objects are created. If many instances of HelloBill were created, many HelloBill objects, each would have its own disposeBtn because this variable is not static. The keyword "new" says create an object. In this case it calls the (object) constructor for Button that has one argument, a String.

Line 19: When you run the Java interpreter, java, it starts your application at the first method it finds that is public, static, void (no return value), is called "main" and accepts a single parameter that is an array of Strings. In general, method calls are by the complete signature: the name + the classes of the arguments + the order of the arguments. In this case java passes the command line arguments to main as a String [ ]. Executing java HelloBill Amy Pam will cause java to pass an array of two Strings to HelloBill.main, the main method in the class.

Line 20: One of the field variables of Array objects is length = number of elements in the array. Because Java will not allow reference with an out-of-range subscript, the program must have the test for the number of arguments. Comment the test (insert // at the beginning), recompile and rerun with no command line argument and the program will fail with:

    Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException:
    0 at HelloBill.main(HelloBill.java:21)

Line 26: The keyword "new" causes the creation of an object, a HelloBill object in this case. In particular, it calls a constructor for the HelloBill class.

Line 29: When a method specifies no result type and has the same name as the class, it is a constructor for the class. Whenever "new HelloBill" is called with a single string as the parameter, a HelloBill object will be created. As with any other method, there can be many public HelloBill methods with different signatures.

Line 30: The keyword super indicates the parent class, the class that this class extends. In other words, super(t) call the constructor for Frame that has a single string as its argument, which creates a frame with t on the title bar.

Lines 30-34: The comments describe their meaning.

Lines 37-42: This method is required by the implements ActionListener contract. A mouse click on a button will create an ActionEvent and this method will be executed.

Lines 44-53: These methods are required by the implements WindowListener contract. A mouse click on a title bar widgets will generate a WindowEvent and a call to one of these methods. You can put print statements into the code to see when they respond. You can also comment out line 46, the System.exit(0) call, and the kill button on the title bar of your HelloBill will no longer work. You will continue to see the result of the print statement so you know the interrupt is being received by your method.

Print statements send their output to the "java console," the terminal window where you execute the java <class name> command.

To play with this yourself, copy the code to a code editor, cut out the line numbers and save as HelloBill.java. Then, in the directory where you saved it, type javac HelloBill.java to compile the program. The compilation will produce a class file, HelloBill.class. To run the program you then type java HelloBill (case sensitive, remember). Note that the java compiler is javac, with a c on the end and the java program runner is just the word java.

A:[[  I use the Unix system call:
  [[ 
  [[   int getgroups (int gidsetlen, gid_t *gidset)
  [[ 
  [[ This stores a list of values of type gid_t into the simple, 
  [[ C-style array, gidset.  However, I'm using C++, and want to use  
  [[ the vector container class from the Standard Template Library to 
  [[ operate on the list.
  [[ 
  [[ Generalizing the question, what's the best way to copy a simple 
  [[ array into an STL vector object?  Is this as good as it gets?
  [[ 
  [[   for (int i = 0; i < numberOfArrayElements; i++) 
  [[   {
  [[       theVector.push_back ( theArray[i] );
  [[   }  

  #
  # Thanks to Rich Griswold: 
  #

  The memory for an STL vector is guaranteed to be contiguous, so you
  can do something like this:

    typedef  std::vector<gid_t>  gid_array_type;
    int gidsetlen = getgroups( 0, NULL );
    if ( -1 == gidsetlen ) { return false; }
    gid_array_type gids( gidsetlen );  // Allocates memory to hold IDs
    if ( -1 == getgroups( gidsetlen, &gids[0] ) ) { return false; }

  If you've already declared your STL vector, you can allocate the
  memory by calling:

    gids.reserve( gidsetlen );

  If you already have the data in a C array called gidset, you can do
  this (after allocating the memory in the STL vector):

    memcpy( &gids[0], getset, gidsetlen * sizeof( gid_t ) );


  #
  # Here's further discussion from Rich, which he generously provided 
  # on our request: 
  #

  The original STL standard was ambiguous concerning the question
  of whether the memory allocated for a vector will be contiguous,
  but that has been fixed.  Taking the address of the zeroth element
  will return the address of the beginning of the allocated memory,
  so I haven't seen anything recently that seriously discourages this
  practice.  Before the standard was updated, some people discouraged
  it, since theoretically some implementation might use non-contiguous
  memory, but to my knowledge, no implementation actually did this.

  There are a few possible gotchas.  First, like C, you have to make
  sure the memory is actually allocated.  You can use either of the
  two methods, either through the constructor, or with reserve().
  To check if the memory is actually allocated, use capacity().

  Second, I usually use typedefs with STL containers, since it
  makes code developement easier by reducing the amount of typing.
  For example, instead of typing:

    std::vector<std::string>  strings;
    std::vector<std::string>::iterator  itr;

  I can type "typedef std::vector<std::string> strings_type;" once,
  then use it throughout my code:

    strings_type  strings; strings_type::iterator  itr;

  This becomes more important when you start nesting types like this:

    std::map< std::map::size_type, std::vector<std::string> >  foo;

  It also makes maintenance eaiser, because you can just change the
  typedef in one place if you need to make a change; for example from
  std::vector to std::list.  This is where the second gotcha comes in.
  If you are using a std::vector in a typedef, and you change it to
  another container type that does not guarantee contiguous memory
  allocation, code that depends on contiguous memory will break.

  As long as you keep this in mind, there isn't any problem I know of
  with using STL vectors in place of C arrays in this way.



  # 
  # And a response from Co-editor, Don Bahls
  # 

  Instead of copying element by element, you can use the assign
  operator:

    theVector.assign(theArray,theArray + numberOfArrayElements);

  The first operand is a pointer to the start of the array.  The second
  is a pointer past the last element of the array.  If you use this
  method make sure you declare "theVector" to be a container of the
  same type as "theArray". E.g.,

    std::vector<gid_t> theVector;



Q: I use ScaLAPACK, therefore I use BLACS.  I'm on AIX, therefore I use
  ESSL/PESSL.  I don't use MPI.  Here's my question:

  I need the global minimim value of a distributed matrix. SHMEM provides
  a routine to determine this:

     shmem_double_min_to_all : 
       "Performs a minimum reduction on array of doubles"

  I don't see anything in ScaLAPACK and the routine provided in the
  BLACS library is no help:

    DGAMN2D: 
      "Perform an elementwise absolute value max/min." ... "Remember, ... 
      The absolute value is used to determine the max/min."

  Suggestions? 

[[ Answers, Questions, and Tips Graciously Accepted ]]

Thomas J. Baring	ARSC Web Specialist	ph: 907-450-8619
Donald Bahls	ARSC User Consultant	ph: 907-450-8674
Arctic Region Supercomputing Center
University of Alaska Fairbanks
PO Box 756020
Fairbanks AK 99775-6020

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