CO2P3S Installation Guide and User Manual Version 1.0
Contents
1. hook methods this item becomes a cascaded menu item indicated by an arrow to the right and you can select the class you wish to edit Figure 14 Either a new viewer for the class will appear or an existing viewer for the selected class will be brought to the foreground The Viewing Template window is a modified HTML viewer where the links represent places where you can add or edit code The code in the viewer is generated with the framework code for a pattern template and is run through a code beautifier before being displayed If you select a link a Code Editor dialog appears shown in Figure 16 The Code Editor dialog allows you to modify the code for particular method in the viewer This editor is not the one in your preferences but rather is a dialog that was created specifically to prevent errors involving hook method signatures The combination of the Viewing Template and Code Editor dialogs do not allow you an opportunity to edit the signatures of the hook methods Further the code is generated for you saving you from having to enter these signatures This is important because the remaining framework code relies on the methods in the class in the viewer having specific signatures for the code to operate correctly This tool support ensures that these signatures cannot be changed and prevents some potential compile and logic errors As an example of the latter error consider the first two arguments to the constructor at the top of the code2. in CO2P3S can be found in our papers available through the Pub lications link at http www cs ualberta ca systems cops index html The layers of CO2P3S are listed below The current distribution only supports the topmost layer The layers are Patterns Layer At this layer you express the structure of your program by selecting the appro priate parallel design pattern templates A design pattern template is a design construct that represents a family of related design pattern implementations Each implementation has the same basic structure but each is a slight structural variation that makes the pattern more applicable to your specific problem To select the member of the family that best suits your problem you provide values for pattern template parameters associated with each template After you have provided appropriate values for the pattern template parameters you use the fully specified template to create an object oriented framework that implements the selected pattern structure An object oriented framework is a set of usually abstract classes that provide a design and partial implementation of the application independent part of a specific kind of application such as a graphical user interface In our case the application domain is the implementation of a parallel structural pattern The structural part of the framework calls a set of hook methods at execution points where application specific operations are required You co
3. indicates the format of the XML file including all legal tags Since this file is referenced through a URL your machine must have an active network connection for CO2P3S to work properly See Section 4 7 for a workaround if you plan to use CO2P3S on a machine that cannot access this URL Lines 7 and 8 define a name space for the XML document CO2P3S will work properly if you cannot access this URL The region of interest in the copsrce xml file starts at line 10 and ends at line 39 The format of the configuration fields is that of standard XML Each field starts with the XML tag 10 20 30 lt xml version 1 0 gt lt This is a sample RC file for the CO2P3S program The location for this file on the user s system is HOME copsrc xml gt lt DOCTYPE CopsCfg copsCfg SYSTEM http www cs ualberta ca systems DTD 1 0 CopsCfg dtd gt lt CopsCfg copsCfg xmlns CopsCfg http www cs ualberta ca systems cops cfg gt lt CopsCfg copsInstallationDirectory gt installation path of COPS lt CopsCfg copsInstallationDirectory gt lt CopsCfg userProgramDirectory gt path to user programs lt CopsCfg userProgramDirectory gt lt CopsCfg defaultEditor gt name of default Java code editor lt CopsCfg defaultEditor gt lt CopsCfg htmlBrowser gt name of HTML browser lt CopsCfg htmlBrowser gt lt CopsCfg patterns gt lt CopsCfg patternName gt Mesh lt CopsCfg patternName gt lt CopsCfg pa
4. template Editing Code boolean public boolean notDone return Cthis _morphogenl hasConverged amp amp this _morphogen2 hasConverged OK Cancel Restore Default Figure 16 The Code Editor dialog 18 Figure 17 The Program menu the default as generated with the framework code An important note is that because of a problem with the current implementation the code editor does not display any code for those methods with the default implementation The correct method body is still in the actual source code but is not displayed in the code editor However if you click OK on a code editor with an empty body you will overwrite the default with a blank body This will cause compilation errors later To preserve the default either cancel the change or restore the default After restoring the default or accepting a new method body CO2P3S will normally regenerate source code for the framework to incorporate this new code and display the updated code in the viewer This regeneration can incur an unwelcome time delay You can disable this regeneration by unchecking the Regenerate After Each Change checkbox at the bottom of the Viewing Template This speeds up the code editing process Changes to method bodies are no longer reflected in the viewer However the changes are still visible in the code editors If any methods are changed the background of the viewer will turn grey and a label will appear
5. COsP3S Installation Guide and User Manual Version 1 0 J Anvik S Bromling S MacDonald J Schaeffer D Szafron and K Tan Abstract This document is an installation guide and user manual for Version 1 0 of the CO2P3S parallel programming system CO2P3S is a programming system for designing coding and executing parallel programs that execute in a shared memory environment CO2P3S generates framework code from a design pattern description of the structure of a program The frame work code contains all of the necessary communication and synchronization for the selected program structure Application code is inserted by implementing sequential hook methods that are called by the larger framework structure 1 Introduction CO2P3S Correct Object Oriented Pattern based Parallel Programming System pronounced cops combines design patterns and object oriented frameworks into a process for writing high performance object oriented programs that execute on multiple processors At the highest level of application development you specify the parallel structure of your program using a set of sup ported design pattern templates Much like the patterns they are based upon pattern templates represent a family of solutions to a design problem You specialize the pattern template to se lect the most appropriate member of this family by specifying values for design pattern template parameters Once the best pattern structure is selected the patt
6. O2P3S installation the value of the copsIn stallationDirectory configuration property from Section 2 4 1 24 10 When editing code using the Viewing Template the code for methods that still have their default bodies will not appear in the Code Editor The proper code is still in the application classes but simply doesn t appear in the Code Editor dialog However you must take care not to accept an empty window by clicking OK This overwrites the default with an empty method body which will result in compile errors Either cancel the change or restore the default implementation 11 There are a number of cases when the displayed HTML and the actual code do not match The most common example is with the lt and gt operators These are not displayed correctly since they are part of HTML tags The HTML generator does not convert these for proper display In other cases we have seen extra newlines inserted into code These problems only affect the HTML and not the underlying code The code as it appears in the Code Editor dialog is properly inserted into the source 12 If no constructors are explicitly added to a class the code generator will always insert an explicit default constructor that is not editable by the user This can be a problem for pattern designers as it means that the user cannot augment the default constructor Trying to add the default constructor in user added code will result in a compile error The workaround i
7. ach time 4 5 Example Programs Supplied with CO2P3S This section briefly describes the example applications that are supplied with this distribution of CO P3S reaction diffusion texture generation parallel sorting by regular sampling and matrix product chain These programs can be found in the directory COPSINSTALL programs More information on these two programs is provided in the docs subdirectory for the program 4 5 1 Reaction diffusion Texture Generation The reaction diffusion texture generation problem is taken from computer graphics 4 The pro gram simulates two chemical called morphogens as they simultaneously react with one another and diffuse over a two dimensional surface This simulation repeatedly iterates over the surface computing new values until the values converge to their final solution When the simulation is complete one of the morphogens can be used to render a texture that resembles zebra stripes as shown in Figure 20 This texture is generated so that it can be tiled on a larger surface without any noticeable edges between tiles This is accomplished by allowing the diffusion process to wrap around the edges both horizontally and vertically during the simulation This program uses the Mesh pattern template This template parallelizes this computation by spatially decomposing the two dimensional surface into distinct partitions These partitions are then assigned to different processors for evalu
8. at the bottom of the dialog making it is clear that the displayed code is out of date An out of date viewer can be refreshed by rechecking the Regenerate After Each Change Closing an out of date viewer by clicking the Close button will force a code regeneration so current code will appear if the template is brought up again later Checking the Show Line Numbers checkbox at the bottom of the Viewing Template win dow cause line numbers for the source code to appear on the left side of the viewer This feature allows you to easily find compile errors in the code in this window Note that if you regenerate the framework code using either the Generate First Layer Code menu item or the option in the Compile dialog Section 4 4 5 all Viewing Template and associated Code Editor dialogs for that pattern template are closed It is possible for you to change some of the class names in the generated code which may mean that the class displayed in the viewer may no longer be part of your program The best way to ensure that this window always displays a relevant class is to close it and have you open another viewer which will always be on a class that is part of the current framework 4 4 5 Compile Dialog Once you have entered all of your application code you need to compile the code This is done by selecting the Compile item from the Program menu shown in Figure 17 The Compile dialog shown in Figure 18 will appear Selecting Compil
9. ately you can skip the Patterns Layer and write programs directly in this language Native Code Layer This layer provides a base object oriented programming language together with any libraries used to implement the abstractions in higher layers The libraries can be optimized for your particular execution environment 4 The CO P S Graphical User Interface 4 1 Program Organization A COzP3S program is a directory with the following subdirectories src This subdirectory contains the complete source code for a CO2P3S program This code in cludes both the generated source code and additional source file you add to your program Section 4 4 3 You should use the COPS user interface to work on all of these source files Otherwise any changes you make may be overwritten during source code generation classes This subdirectory contains the Java bytecode files for the program cops_patterns This subdirectory contains saved information on the pattern templates in your CO P3S program You should not change any of the contents of this directory cops_html This subdirectory contains HTML files for the classes with hook methods for a given framework Again the contents of this subdirectory should not be modified cops_methods This subdirectory contains the bodies of the application specific hook methods that you have implemented The contents should not be altered manually Other directories are also included in a CO2P3S program and you can crea
10. ation However the nature of a mesh computation is that each element or pixel in the texture requires data from adjacent elements Thus each parti tion needs data from adjacent partitions to compute new values for the elements on its boundary Further for each iteration the new values for the elements are computed using the values from the 21 previous iteration which requires barrier synchronization to ensure that no processor computes too far ahead The example program executes the simulation based on a set of command line parameters that are explained in the Program Options Pane of the program The initial random conditions are displayed in a window When complete the final result is displayed This window is the only output of the program You can use image manipulation software to capture this image for later use To end the program you will need to kill this window Otherwise the Run dialog will still believe the program is executing An interesting note on this program is the reuse of code from the sequential version All of the classes in the Program Options Pane except the Main java class were taken directly from a sequential implementation of this program The hook method code is used as an Adapter pattern 1 essentially translating the interface in the generated framework code to the interface required by the reused code In addition to reusing sequential code this implementation strategy also keeps the hook method code si
11. chines as necessary 25 5 Using X11 some window managers do not correctly display the user interface even on the local machine Once again this appears to be a problem with Swing In particular we have experienced serious problems with the FVWM2 window manager including the following e The region around the edge of dialog boxes does not render properly instead appearing as a blank grey region This may obscure the buttons in the dialog The buttons are still present and can be clicked but you will not be able to see what you re clicking Usually resizing the dialog will correct this Another option is to iconify and expand the window but again this doesn t always work e The size of a dialog window may change each time it is brought up The dialog may grow slightly each time until it takes up the entire screen It may shrink slightly until it is too small for all of its components The problems with FVWM2 are apparently known bugs but fixes do not appear to be forth coming The screenshots for this document were all taken using the Enlightenment window manager running under the Gnome desktop on a Linux workstation We have not experi enced any problems with this environment We cannot vouch for other desktop and window manager combinations 6 The file list dialog hangs when working on directories with a large number of files This is why we recommend that you set the userProgramDirectory attribute Section 2 4 1 either by mod
12. directory However these old files can interfere with compilation if the code they contain is out of date This button lets you clean out these old source code files It is also useful for quickly regenerating code for all of the pattern templates in a program rather than doing it template by template Arguments to the compiler can be specified in two ways Common arguments for including debugging information g on the command line deprecation warnings optimizations and ver bose output can be indicated with the check boxes Additional arguments can be inserted into the Flags text field The output of the compiler will appear in the text area at the top of the dialog The contents of this dialog are also saved when you save your program so you won t have to enter this information each time 4 4 6 Run Dialog To run your program select Run from the Program menu Figure 17 The Run dialog shown in Figure 19 will appear The Run dialog is much like the Compile dialog Common options are provided as check boxes or text areas Other options can be entered into the Flags text area The Run dialog has an 20 Figure 20 The output of the reaction diffusion texture generation additional text area for specifying the mainline class and command line parameters The output of the program is displayed in the text area The contents of this dialog are also saved when you save your program so you won t have to enter this information e
13. e releases of CO2P3S 2 Installing CO2P S 2 1 Operating System We have successfully run CO2P3S using native threaded Java virtual machines VMs on the fol lowing operating systems e Linux e Solaris e SGI Irix Since CO2P3S is a Java tool generating Java code it may run on other platforms However we did not develop the tool with portability in mind so we cannot guarantee that either the tool or the generated framework code will run correctly on other platforms You may experience problems with the CO2P3S user interface Differences in thread scheduling policies on different operating systems may cause problems in the generated frameworks If you successfully use CO2P3S on a different operating system please let us know and we will add it to the above list 2 2 Other System Requirements You will need the following hardware configuration and software installed on your system for CO2P3S to work properly e A Java distribution Version 1 2 or higher This distribution must include both a compiler and a run time environment The run time environment must support native threads to take advantage of multiple processors e A Perl distribution Version 5 or higher It must be possible to start the executable using the command usr bin perl This can be either the executable program or a link to the executable e Any version of GNU make This is required to compile your CO2P3S distribution e A computer with an active network connect
14. e will compile you program with the arguments supplied in the dialog Clean will remove all of your class files Abort stops any currently executing compilation The Regenerate All Layer One Source button performs two functions First it removes all source files except the user classes entered using the Program Options Pane Sec tion 4 4 3 class files and HTML files for the program Second it regenerates source code and HTML files for all patterns in the program using the current values of the pattern template param 19 Compile Compilation Output Compilation complete Generate Debugging Information Optimize _ Show Deprecation Warnings Verbose Output Flags Clean Regenerate All Layer One Source Abort Figure 18 The Compile dialog M E ml Execution Output warning native threads are not supported in this release Starting simulation at time 1675 Simulation converged s vi Use Native Threads Initial Heap Size optional Verbose output Maximum Heap Size optional Flags Shared Memory Distributed Memory Main Class and Command Line Parameters Main 64 2 2 Abor crese Figure 19 The Run dialog eters The reason for this is that CO2P3S may keep source files that were generated based on old values of class names We currently compile all source files in the src
15. ern template is used to generate object oriented framework code implementing the specific structure that you ve selected CO2P3S currently generates multithreaded Java code targeted at shared memory multiprocessors This framework code encapsulates all of the communication and synchronization code needed for the selected structure and is hidden from you to reduce the possibility of errors To complete a pro gram you need only implement sequential hook methods that are invoked from the generated structure Lower layers gradually expose the generated code using high level abstractions and then the implementation of these abstractions These layers provide performance tuning opportu nities and flexibility in a controlled manner This document serves as an installation guide and user manual for the CO2P3S parallel pro gramming system Section 2 describes the steps in the installation process This section describes the general process this release of CO2P3S was assembled with some of these steps already com pleted to minimize your effort Section 3 describes the execution environment and general pro gramming model of CO2P3S Section 4 shows the features of the user interface in detail Note that this section does not describe the pattern templates in detail Documentation for the templates is available through the interface Section 5 gives a glimpse of the future showing some of the research currently underway that we hope to incorporate into futur
16. es the top part of the Program Options Pane let you create additional classes for your application In all CO2P3S programs you will need to supply a mainline class but other classes perhaps from sequential versions of your program can also be included In addition to the mainline the reaction diffusion example uses three additional classes You can add new classes using the Add New Class button where you will be prompted for the name of the new class This should be entered without the java suffix You can select a user class and delete it from the program You can also select a class and edit it using the editor in your preferences The bottom part of the Program Options Pane provides space for program comments In Fig ure 11 this space is used to provide information on the command line arguments for the program 15 Mesh RDMesh Mesh State Superclass MorphogenPair Ordered Computation Figure 12 The Pattern Pane showing an instance of the Mesh pattern template Generate First Code Layer Generic View Pattern Template Operations Delete Pattern Set Mesh Class Name Set Mesh State Class Set Mesh State Superclass Set Mesh Ordering Set Mesh Baundary Conditions Pattern Template Set Number of Neighbours Parameters Pattern Template Class Names Figure 13 The background menu in the Pattern Pane 4 4 4 Pattern Pane If you select one of the pattern template instances in the Pr
17. he CO2P3S user interface this process is also described in this section This release of CO2P3S was assembled to minimize the amount of work you need to do before using the system As a result some of the steps below are not required However this information will be useful for future releases 2 4 1 CO 2P3S Properties First copy the file COPSDIR copsProj copsrc xml to SHOME copsrc xml note the extra period HOME is your home directory as defined by the Java system property user home If you are unsure about the value of this property you can get it by printing the result of the Java method call System getProperties getProperty user home In a UNIX environment this should correspond to your normal home directory Now edit the file SHOME copsrc xml The default file is shown in Figure 1 This file contains configuration properties used by the CO2P3S graphical user interface Some of these properties must be filled in before CO2P3S can be run Some can be reset or must be set through the user interface The first part of the XML file consists of header and definition information You should not find it necessary to change any part of the first 9 lines with one possible exception Lines 1 is header information regarding the XML file Lines 2 and 3 are a comment indicating the purpose and location for this file Line 4 and 5 indicate where the DTD Document Type Definition file for this document can be found The DTD file
18. hould be filled in before you open or create a program in CO2P3S for the first time defaultEditor This is the name of your favourite text editor This editor is used to edit extra program files that you wish to incorporate into a CO2P3S program This field can be entered now or entered later using the CO2P3S interface Note that the selected editor must execute in its own window as CO2P3S will not do this for you For editors such as emacs and gvim this is not a problem On the other hand vi does not start its own window On X11 systems this can be remedied by specifying xterm e vi as the value of this attribute You can replace vi with other console based editors htmlBrowser This is the name of your favourite HTML browser This browser will be used to display HTML documentation for the design pattern templates in CO2P3S This field can be entered now or entered later using the CO2P3S interface As with the editor this browser must execute in its own window so browsers such as lynx must be started the same way that the vi editor is above However most of the documentation pages also include graphics so a graphical browser is best patterns This field contains a list of the current pattern templates that have been loaded into the CO2P3S interface You should not change this field manually It will be updated as you add and remove templates in the interface as described in Section 2 4 3 This field already includes entries for the three
19. ifying the copsrc xml file manually or through the Edit Preferences menu item in the user interface 7 There are a number of exceptions that are thrown by Swing components Most of the time these can be safely ignored Unfortunately this can make it hard to find the exceptions that are important 8 Saving a CO2P3S program saves the configuration information for an individual program However changes within the program are performed immediately regardless of whether you save the configuration or not For example deleting classes or changing hook method bodies take effect immediately and cannot be undone by not saving the program This also means that it is possible for the configuration and program code to be out of step with one another We should perhaps follow the emacs approach of creating a working copy and replacing the original when you save the program but this has not been done 9 CO2P3S requires an open network connection to start The reason for this is that the format of the copsrc xml file is verified using a DTD Document Type Definition file that is accessed through the World Wide Web Line 5 of Figure 1 shows the URL of this file If you will be using CO2P3S on a computer without a network connection you should change this URL to point to the copy of the DTD file included in the CO2P3S distribution Change the URL to the following file COPSINSTALL DTD CopsCfg dtd where COPSINSTALL is the directory of your C
20. in Figure 15 These two arguments represent the location in a two dimensional data structure for the element being created If you had to write this signature or were able to change it you could accidently reverse the two parameters This error cannot be caught by the compiler since the parameter types are correct which is all the compiler checks However the framework code that uses this constructor is assuming the order in the figure Reversing the parameters causes the data to be transposed which may cause errors later In the Code Editor dialog you can also restore the default implementation of a hook method by clicking the Restore Default button This replaces the current value of the hook method with 17 Viewing Template Constructor ua public MorphogenPair int i int j int surfa Random gen Random initializer this _morphogenl new Morphogen 1 0d Cgen nextDouble 2 0d ZrO ee Old ye this _morphogen2 new Morphogen 1 0d Cgen nextDouble 2 0d 20d 2 Sid 3 ae Initialize this mesh node HA li EEE S t Returns whether this mesh node is not finished computing kari public boolean notDoner T return Cthis _morphogenl hasConverged amp amp this _morphogen2 hasConverged LENA A O Shaw Line Numbers vj Regenerate After Each Change Clase Figure 15 The Viewing Template for editing application code in the framework generated for a pattern
21. ion CO2P3S uses XML documents to store rele vant program and tool configuration information and the document descriptions are accessed via the World Wide Web It is possible to work around this requirement see Section 4 7 for details e If you want parallel speedups you will need a shared memory multiprocessor computer sys tem CO2P3S will work on uniprocessor machines but you will not likely experience any performance improvements In fact you will most likely experience performance degrada tion However when testing for the correctness of a program such a system may still be useful 2 3 COd gt P3S Installation Process To compile and install CO2P3S on your computer you will need to do the following 1 Obtain a copy of the source code distribution This comes as either a gzipped tar file or a zip file This is available through the World Wide Web at http www cs ualberta ca systems cops index html1 through the Downloads link on the left hand frame 2 Select a directory for your CO P3S installation which we will refer to as COPSDIR for the rest of this document Extract the contents of the distribution The COPS distribution will unarchive into a subdirectory copsPro 4 For the gzipped tar file use the command where is your shell prompt and replacing copsDistribution tar gz with the name of the distribution file tar xfz copsDistribution tar gz or o zcat copsDistribution tar gz
22. ks for pattern templates in the directory COPSINSTALL patterns which is where the templates bundled with your CO2P3S distribution can be found If you have downloaded other patterns navigate to the directory where you have installed them 3 Once you have navigated to the appropriate directory select the XML file for the pattern template you wish to add Select it and click OK and wait for the template to load This process can take some time as the contents of the XML file are used to generate Java source code which is then compiled 4 You can repeat the last two steps for all pattern templates you wish to add 5 As the interface instructs you quit CO2P3S by selecting Quit from the File menu The new pattern templates will be available the next time you start CO2P3S This is why we recommend you add new templates from the initial screen so you don t interrupt work on a current program 2 4 4 Removing Pattern Templates from COPS If you decide that a pattern template is no longer useful you can remove it from CO 2P3S As with adding a template this can be done from the initial CO2P3S screen However if you do so you will not be able to modify any programs that use that pattern template Environment Tools Program Import Patte rm Ctrl A Remove Pattern gt Phases Create or Edit Pattern Wavefront Preferences Ctrl E Mesh Distributor Figure 4 Removing a pattern template from CO2P3S COPS P
23. l 3 1 Execution Environment CO2P3S generates multithreaded Java code for the supported parallel design pattern templates This code can be run on a uniprocessor or shared memory multiprocessor On a multiprocessor system you can used native threads which allows the Java Virtual Machine to map the threads to different processors This will hopefully result in performance improvements by using different processors to execute different parts of your program in parallel CO P3S assumes that there is an active network connection This connection is used to verify the validity of some of the XML files contained within the CO2P3S system Section 4 7 contains instructions for removing this dependency if you need to CO2P3S has no special requirements regarding file systems Applications that use disk will need to make sure files are available to all threads that need them On most shared memory ma chines this should not be an issue 3 2 Programming Model The programming model for CO2P3S consists of three layers of user accessible abstraction Each layer provides distinct abstractions supporting different phases of program development In addi tion each layer gradually exposes more implementation details of the object oriented framework code generated by CO2P3S providing openness which in this sense means that you can access low level structures and run time code to improve the performance of your application More information on programming
24. ll options enabled To minimize the number of changes for future versions of CO2P3S most of these options are permanently grayed out in this distribution These options are e The Create or Edit Pattern menu item in the Environment menu This is pro vided for future releases that will provide tools for you to modify or create pattern templates 22 Section 5 1 e The Tools menu item on the user interface is disabled These tools are for managing machines and resources in the forthcoming distributed memory version of CO2P3S Sec tion 5 3 e The Shared Memory and Distributed Memory radio buttons in the Run dialog Shared memory is always selected e The Generate Next Code Layer in the background menu in the Pattern Pane This release of CO2P3S only supports the Pattern Layer so this menu item is disabled 4 7 Caveats There are a number of issues with the CO2P3S user interface These problems and potential workarounds where possible are 1 You must execute the runCops script while your current directory is COPSINSTALL If you run the script from elsewhere the images in the interface will not be displayed This will be fixed soon 2 When editing hook methods in the Viewing Template window the code for the complete framework is regenerated after each method body is accepted The time for this generation may be longer than you wish to wait To prevent this regeneration uncheck the Regener ate After Each Change checkbo
25. lled the Two Dimensional Mesh the Phases and the Distributor These three pattern template will appear when you create a new program or open an existing one You can use these templates in your programs However CO2P3S is an extensible system that allows you to add new pattern templates as they are developed Later distributions will include tools to help you create your own pattern templates and we hope to create a repository for you to exchange your templates with other users The process of adding a new pattern template is best done from the initial CO2P3S screen Figure 2 as follows Select Pattern File Lookin j patterns v rs tt Bo B Phases CI wavefront Bi DDistributor xml D DMesh xml D Distributor xml G Mesh xml b Phases xml Enviranment Tools Program C Wavefront xml 5 Import Pattern EA File name Mesh xml OK Remove Pattern Create or Edit Pattern Files of type All Files v Cancel Preferences Ctrl E a The Environment b The pattern file selection dialog menu Figure 3 User interface elements for adding pattern templates in CO2P3S 1 Select the Environment menu from the menu bar on the top of the interface Then select Import Pattern shown in Figure 3 a 2 After you select Import Pattern the dialog in Figure 3 b will appear You use this di alog to select a pattern template to import By default this dialog loo
26. mple 4 5 2 Parallel Sorting by Regular Sampling The second example program implements the Parallel Sorting by Regular Sampling PSRS al gorithm 2 This program sorts a specified number of uniformly distributed random Integer objects and verifies the results This is an explicitly parallel sorting algorithm that does not have a direct sequential counterpart In addition this program uses two instances of the Phases and Distributor pattern templates providing an example of composing multiple frameworks into a complete application Composing frameworks in CO2P3S is simplified because each framework uses the Facade pat tern 1 to provide a single simple interface to the code The constructor for this Facade creates all of the objects needed by the framework and assembles them into a complete program sim plifying the instantiation process The Facade also provides a simple interface for launching the computation for the framework where applicable seen in the Phases and Mesh frameworks 4 5 3 Matrix Product Chain The final example is matrix chain product one of the Cowichan problems 3 This program uses a dynamic programming matrix to find the least expensive way to multiply a set of matrices The program uses a single instance of the Wavefront pattern template computing the upper half of a matrix starting from the diagonal and working to the top right corner 4 6 Disabled Interface Options This version of CO2P3S does not have a
27. mplete a program by providing implementations of these hook methods by subclassing the framework classes and overriding the required methods For our parallel frameworks the structural code includes all of the error prone communi cation and synchronization code required by a pattern implementation The hook methods 10 are sequential code They do not require any parallel code for the framework to operate correctly In many programs the hook method code for a generated framework can be taken directly from an existing sequential program possibly using the Adapter design pattern 1 Documentation on the pattern template parameters and the generated framework code is provided with each template and is not part of this document To reduce the possibility of programmer error the structural framework code is encapsulated away from you at this layer of development Other errors are prevented through the user interface which is illustrated in Section 4 Intermediate Code Layer This layer provides a high level explicitly parallel programming lan guage based on a superset of an existing language such as Java or C It provides high level abstractions for expressing parallelism and synchronization At this layer the structural framework code generated at the Patterns Layer is made available implemented in the high level language You can optimize the code or implement a pattern variation that is not supported by the template parameters Altern
28. nd in the Pattern Pane Section 4 4 4 Right clicking on a button brings up the background menu shown in Figure 9 b You can add the pat tern to the program Insert Pattern or view the pattern template documentation Pattern 13 Palette E 1 first 2 second play Insert Pattern 3 third Pattern Help b The background menu for the pattern templates v a The Pattern Palette Figure 9 The Pattern Palette and background menu Help using the HTML browser specified in your preferences 4 4 2 Program Pane The Program Pane is the middle section of Figure 8 An expanded picture is in Figure 10 This pane shows the set of pattern templates that are part of the current program The topmost item with the CO2P3S logo followed by the program name represents the entire program Beneath itis a list of the pattern templates that are used in the current program Each item in the list is a small graphical representation of the template followed by its name The name of a pattern template is based on one of its parameter values which allows you to distinguish between different instances of the same template In our example we are using an instance of the Mesh template with the name RDMesh The Program Pane also indicates the status of each pattern template using colours for the tem plate name The colours are Red This colour indicates that the framework code is out of date This either means that you have
29. not generated code for this template or you have changed a pattern template parameter value and the generated code may not be consistent with the current parameters You can generate code from the Pattern Pane Section 4 4 4 or the Compile dialog Section 4 4 5 Green The framework code is consistent with the current parameter values The meaning of these colours is indicated by the legend that appears at the bottom of the Program Pane 14 Pragram COPS ReactionDiffusion H RDMesh Legend Generated code out of date Generated code current p Figure 10 The Program Pane Program Options User Classes Main java Add New Class Morphogen java MorphogenDisplay java GreyScaleDisplayWindow java Delete Class Edit Class Program Comments o run this application use the command line Main surfaceSize meshWidth lt meshHeight gt he surface will be square with meshWidth meshHeight partitions meshHeight defaults to meshWidth if not given on w Figure 11 The Program Options Pane 4 4 3 Program Options Pane When the topmost item in the Program Pane is selected the Program Options Pane appears on the right side of the interface This is the case in Figure 8 shown again in Figure 11 The Program Options Pane allows you to provide information for the entire program This consists of two components user classes and program comments User class
30. ogram Pane the Program Options Pane is replaced by the Pattern Pane for the selected instance of a pattern template The Pattern Pane on an instance of the Mesh is shown in Figure 12 The Pattern Pane shows details on a specific instance of a pattern template such as the current values of its parameters This information is depicted using a combination of text and graphics In Figure 12 we can see several class names RDMesh and MorphogenPair as well as other parameter values a four point mesh a fully toroidal topology and an ordered computation The Pattern Pane is also used to work with the pattern template and generated framework code The pane allows you to change parameter values to refine the template generate code from a fully specified template and insert hook method bodies to complete the implementation of a program Some aspects of this functionality are common to all pattern templates and are discussed here Other aspects are necessarily specific to a particular pattern template and are covered in more detail in the template documentation The pattern template is refined using a background menu in the Pattern Pane obtained by right clicking anywhere in the pane The menu for the Mesh pattern template is shown in Figure 13 The operations in this menu can be broken down into three categories generic operations that apply to all pattern templates pattern template class names and pattern template parameters The latter two categ
31. ories are specific to each pattern template and are discussed in the template documentation The first menu item in the generic operations Generate First Layer Code generates 16 Generate First Cade Layer View Pattern Template gt PSRSDistributor Delete Pattern PSRSDistributorChild Set Parent Class Name Edit Method List Figure 14 The background menu for the Pattern Pane with multiple viewable templates Patterns Layer code from the pattern template using the current template parameter values If code is successfully generated the label for the template in the Program Pane will turn green The Generate Next Code Layer item is disabled since this release only supports the Patterns Layer It will be enabled in the future when there is more support for the two lower layers in the CO2P3S programming model The last menu item in the generic operations Delete Pattern deletes the current pattern and associated files from your program Note that this deletion takes place immediately and cannot be undone later The middle menu item is View Pattern Template This item allows you to add hook method bodies to generated framework code and so is only available when the generated frame work code is up to date Selecting this item brings up a Viewing Template window shown in Figure 15 that allows you to view and edit hook method bodies for the current framework If there are multiple classes in a framework that have
32. pattern templates provided with this distribution of CO2P3S jiniPolicyDirectory This field is for future releases of CO2P3S that will include distributed pattern templates This field is not used in this distribution but the field must still appear in the configuration file Simply use the current value Pattern Window ex ile Environment COPS Figure 2 The initial screen of CO2P3S jiniLUSAddress This field is for future releases of CO2P3S that will include distributed pattern templates Again this field is not used in this distribution but the field must still appear in the configuration file Simply use the current value Line 39 ends the configuration file 2 4 2 Running CO2P3S To run CO2P3S use the script supplied with the distribution This script can be found at COPSINSTALL runCops Right now this must be executed while your current directory is COPSINSTALL for the images in the interface to be displayed correctly When CO P3S is run a log file cops log is created in the current directory This file logs events and errors in the user interface If you experience problems you can view the log by selecting View Log from the File menu The initial screen for CO2P3S is shown in Figure 2 For the remainder of this section the menus at the top of the window are the points of interest 2 4 3 Adding Pattern Templates to COPS When you first start CO2P3S it will have three pattern templates already insta
33. references Default Editar emacs User Program Directory home stevem phd software progral Default HTML Browser netscape JINI Policy Directory JINI Lookup Service Address Figure 5 The Preferences dialog To remove a pattern template select the Environment menu item from the menu bar at the top of the interface From this menu select Remove Pattern Figure 3 a This is a cascaded menu item where the items that appear are a list of the currently imported pattern templates Select the pattern template that you wish to remove as shown in Figure 4 After you confirm your selection the pattern template will be removed from CO P3S It can be added back into CO2P3S using the process in Section 2 4 3 2 5 Setting Preferences with the Graphical User Interface From the Environment menu Figure 3 a you can set your CO2P3S preferences at any time by selecting Preferences When you select this item the dialog in Figure 5 appears This dialog allows you to set the userProgramDirectory defaultEditor htmlBrowser jiniPolicyDirectory and jiniLUSAddress properties described in Section 2 4 1 The remaining properties cannot be set through this dialog 3 About CO P S This section describes some of the more general details of the CO2P3S parallel programming sys tem This includes information on the execution environment for your programs and the program ming model supported by the too
34. repository for new or modified pattern templates It should be possible to upload new templates query the repository for a template that suits your problem and install that template into your local CO2P3S distribution 25 Even further if the format of the meta templates is system independent it is possible for other pattern based programming systems to take advantage of this repository Pattern based tools that can interpret the meta template format will find they have a large set of supported patterns that can solve a broad range of problems We believe such a format is possible 5 3 Distributed Memory Pattern Templates The current pattern templates in CO2P3S are targeted at shared memory multiprocessors Net works of workstations clusters or even grid computing systems are also potential targets for high performance applications We are working on versions of our pattern templates that use Java Remote Method Invocation to execute on these kinds of systems To make it easier for pattern designers to create distributed templates we are also including JINI as a mechanism for managing remote resources and a library supporting constructs like distribute monitors for synchronization Future pattern templates may generate boilerplate code that is required by some grid software libraries such as Globus This will make it easier to take advantage of computational grids 5 4 Support for Sequential Design Patterns CO2P3S was originally envi
35. s to explicitly add the default constructor as part of the generated framework code and make it editable Another option which is best for constructors that pass arguments to a parent constructor is to create a constructor that cannot be edited and that calls an initialize method that the user can implement 5 Future Enhancements to CO2P S 5 1 MetaCQ P S One drawback to many pattern based programming systems is their lack of extensibility The tool only supports the patterns that the tool developers supply If a pattern you need for your program is not supported then you must either abandon the tool implement the pattern manually or wait for the system developers to support the pattern Future releases of CO2P3S will include the MetaCO2P3S tool that will allow you to become a pattern designer If the pattern you need doesn t already exist you can create a pattern template and framework and add it to CO2P3S Similarly you can correct problems or limitations in existing pattern templates You can add new parameters to create pattern variations that were not originally supported by the pattern template You can also modify the framework code to better support applications that the original pattern designer did not consider or to fix bugs 5 2 Pattern Template Repository Once we enable pattern designers to create new pattern templates the next step is to find a means of exchanging them with other CO2P3S users We can envision a Web based
36. sioned as a pattern based parallel programming system It has become clear that these same ideas and programming model are equally applicable to creating programs with sequential design patterns As we create sequential pattern templates we will make them available hopefully using our pattern template repository 6 Feedback We would appreciate any feedback that you have on the COPS parallel programming system or reports of any bugs that you find Please send e mail to systems cs ualberta ca References 1 E Gamma R Helm R Johnson and J Vlissides Design Patterns Elements of Reusable Object Oriented Software Addison Wesley 1994 2 H Shi and J Schaeffer Parallel sorting by regular sampling Journal of Parallel and Dis tributed Computing 14 4 361 372 1992 3 G Wilson Assessing the usability of parallel programming systems The Cowichan problems In Proceedings of the IFIP Working Conference on Programming Environments for Massively Parallel Distributed Systems pages 183 193 1994 4 A Witkin and M Kass Reaction diffusion textures Computer Graphics SIGGRAPH 91 Proceedings 25 4 299 308 1991 26
37. tar x For a zip file use the command o unzip copsDistribution zip 3 Add the following directories and JAR files to your CLASSPATH variable using the correct means for your operating system or shell e COPSDIR copsProj e COPSDIR copsProj libs jdom jar e COPS Libs xerces jar libs xalan jar IR copsProj J e COPSDIR copsProj libs jini core jar D D e COPSDIR copsPro D D D e COPSDIR copsProj libs jini ext jar The last two items will be used by future releases of CO2P3S which will support distributed memory programs This step must be done before you compile or run CO2P3S 4 Add the following directory to your PATH variable 3 e COPSDIR binUtil This step must be done before you compile or run CO2P3S 5 The current release has already been compiled so you can skip this step However you still need to complete all of the earlier steps If you have a source only distribution you will need to build COjP3S Change to the directory COPSDIR copsProj Build the distribution using the command where is your shell prompt o make 2 4 Configuring CO2P S After compiling CO2P3S you must configure it before you can execute it CO P3S configuration consists of two stages The first stage is setting the properties for the user interface The second stage is adding pattern templates to the user interface Since the second stage requires you to run t
38. te others to manage additional data for your application It is important that you not modify the contents of any of the above directories by hand The user interface provides safe access to the files that you can modify 11 File Environment Tools New Program Ctri N Open Program Ctrl O Save Pragram Ctri S Rename Program Delete Pragram View Log Ctrl L Quit ctri Q Figure 6 The File menu Open Program Look in programs x l tt E A COPS ReactionDiffusion File name ReactionDiffusion Open Files of type Directories Only Cancel Figure 7 The dialog for opening a CO2P3S program 4 2 Opening or Creating a CO2P S Program The first step in working with CO2P3S is to open an existing program or create a new one These operations are available through the File menu Figure 6 The dialog for opening a program is given in Figure 7 This dialog starts looking for CO2P3S programs in the directory indicated by the userPro gramDirectory attribute in your preferences This is the standard file chooser in Java and can be used to navigate your files The items with the CO2P3S logo on the left are directories with a sub directory structure matching that described in Section 4 1 You can select one of these directories and select Open to work on that program Creating a new program is almost identical A similar file chooser appears again starting in the director
39. the user interface may not agree when the program is opened later For example if you change a pattern template parameter and regenerate the framework code you cannot undo the changes by not saving the program The next time you load the program the code will be that for the modified parameter value while the interface displays the old value Similarly application code is saved as you change it and will persist regardless of whether or not you save your program 4 4 Working With a CO 2P S Program To make the presentation of this section more concrete we have opened the reaction diffusion example programs provided with your CO2P3S distribution Initially it will appear as shown in Figure 8 This section describes each part of the user interface as well as the compilation and execution facilities 4 4 1 Pattern Palette The first part of the interface we will examine is the Pattern Palette on the left of Figure 8 A closeup is shown in Figure 9 a The Pattern Palette allows you to select from the set of support design pattern templates rep resented as buttons on the palette In Figure 9 a the templates from top to bottom are the Two Dimensional Mesh the Distributor and the Phases You can always get the name of the template by placing the cursor in the button and waiting for the tool tip Left clicking on a button includes the pattern template into the current program The pattern will appear in the Program Pane Section 4 4 2 a
40. tternName gt Distributor lt CopsCfg patternName gt lt CopsCfg patternName gt Phases lt CopsCfg patternName gt lt CopsCfg patterns gt lt CopsCfg jiniPolicyDirectory gt install path of COPS Distributed JINI policy policy all lt CopsCfg jiniPolicyDirectory gt lt CopsCfg jini_LUS Address gt URL for lookup service lt CopsCfg jiniLUS Address gt lt CopsCfg copsCfg gt Figure 1 The default XML file that comes with a CO2P3S distribution lt CopsCfg fieldName gt where fieldName is the name of the configuration field The field ends with the tag lt CopsCfg fieldName gt where fieldName must match the starting tag The value of the field is contained between these two tags Tags can appear inside of other tags but they must be properly nested The current CO2P3S configuration has the following fields copsInstallationDirectory This is the path to the CO2P3S installation This field has to be filled in manually before CO2P3S is run the first time The correct value for this field is COPS DIR copsProj From this point onward COPSINSTALL refers to this directory userProgramDirectory This is the full path of default directory for your CO2P3S programs If no value is entered or the supplied directory does not exist your home directory as defined earlier in this section is used This can be entered either here or through the user interface However because of interface limitations described in Section 4 7 it s
41. x The window will let you know if the code in the window is out of date Note though that the most recent code will be displayed in the Code Editor dialog It simply won t be shown in the viewer itself If you recheck this checkbox or close the viewer with out of date code the framework will be regenerated 3 When you regenerate the complete framework using either the Generate First Code Layer menu item in the Pattern Pane or the Regenerate All Layer One Source button on the Compile dialog but not if you ve changed a hook method body all template viewers and code editors are closed We cannot check to see if the class in the viewer is still relevant in the application or if the correct code is being displayed Closing the viewers and reopening them from the Pattern Pane menu ensures that the viewers always display the most recent version of a class and that the class is still relevant to the application 4 Using X11 the graphical user interface may not correctly display over a remote X connec tion You will need to run CO2P3S on the local machine As far as we can tell this is a problem in the Swing library used for the interface This means that you will not be able to use the Run dialog to execute your CO2P3S program Instead you can run the program manually In the classes directory for your program Section 4 1 are the class files for your program You can start the virtual machine using these files or copy them to other ma
42. y indicated in your preferences You navigate to where you would like your program to be kept and enter in the name of the program The directory for the program including all of its subdirectories is created The empty program is opened and you can begin work on it 4 3 Saving a CO2P S Program Of course you will want to save the state of your CO2P3S programs as you work on them This is done by selecting Save from the File menu It is important to note that this only saves the 12 Pattern Window File Environment Program Palette Program Program Options Q CO P S ReactionDiffusion User Classes H RDMesh Main java Morphogen java Add New Class MorphogenDisplay java g g Pra N Delete Class GreyScaleDisplayWindow java Edit Class Legend Pragram Comments orun this application use the command line Main surfaceSize meshWidth lt meshHeight gt he surface will be square with meshWidth meshHeight Generated code current Generated code out of date v in Figure 8 An open CO2P3S program configuration information of a program such as the current set of patterns and their values Unfortunately many other changes to a CO2P3S program take effect immediately and cannot be undone by simply not saving the program You should save your program after making structural changes to it or you will find that the program state and the state displayed in
Download Pdf Manuals
Related Search