Examples with Comm edu.rit.pj.Comm used on opensource projects

Example 1 with Comm

use of edu.rit.pj.Comm in project ffx by mjschnie.

the class Main method startParallelJava.

/**
 * Start up the Parallel Java communication layer.
 */
private static void startParallelJava(String[] args) {
    try {
        Comm.init(args);
        Comm world = Comm.world();
        rank = world.rank();
        processes = world.size();
    } catch (Exception e) {
        String message = String.format(" Exception starting up the Parallel Java communication layer.");
        logger.log(Level.WARNING, message, e.toString());
    }
}

Example 2 with Comm

use of edu.rit.pj.Comm in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method loadPlatform.

/**
 * Load an OpenMM Platform
 */
private void loadPlatform(Platform requestedPlatform) {
    // Print out the OpenMM Version.
    Pointer version = OpenMM_Platform_getOpenMMVersion();
    logger.log(Level.INFO, " OpenMM Version: {0}", version.getString(0));
    // Print out the OpenMM plugin directory.
    Pointer pluginDir = OpenMM_Platform_getDefaultPluginsDirectory();
    String pluginDirString = pluginDir.getString(0);
    if (SystemUtils.IS_OS_WINDOWS) {
        pluginDirString = pluginDirString + "/plugins";
    }
    logger.log(Level.INFO, " OpenMM Plugin Dir: {0}", pluginDirString);
    /**
     * Load plugins and print out plugins.
     *
     * Call the method twice to avoid a bug where not all platforms are list
     * after the first call.
     */
    PointerByReference plugins = OpenMM_Platform_loadPluginsFromDirectory(pluginDirString);
    OpenMM_StringArray_destroy(plugins);
    plugins = OpenMM_Platform_loadPluginsFromDirectory(pluginDirString);
    int numPlugins = OpenMM_StringArray_getSize(plugins);
    logger.log(Level.INFO, " Number of OpenMM Plugins: {0}", numPlugins);
    boolean cuda = false;
    for (int i = 0; i < numPlugins; i++) {
        String pluginString = stringFromArray(plugins, i);
        logger.log(Level.INFO, "  Plugin: {0}", pluginString);
        if (pluginString.toUpperCase().contains("AMOEBACUDA")) {
            cuda = true;
        }
    }
    OpenMM_StringArray_destroy(plugins);
    /**
     * Extra logging to print out plugins that failed to load.
     */
    if (logger.isLoggable(Level.FINE)) {
        PointerByReference pluginFailers = OpenMM_Platform_getPluginLoadFailures();
        int numFailures = OpenMM_StringArray_getSize(pluginFailers);
        for (int i = 0; i < numFailures; i++) {
            String pluginString = stringFromArray(pluginFailers, i);
            logger.log(Level.FINE, " Plugin load failure: {0}", pluginString);
        }
        OpenMM_StringArray_destroy(pluginFailers);
    }
    int numPlatforms = OpenMM_Platform_getNumPlatforms();
    logger.log(Level.INFO, " Number of OpenMM Platforms: {0}", numPlatforms);
    /**
     * for (int i = 0; i < numPlatforms; i++) { PointerByReference
     * currentPlatform = OpenMM_Platform_getPlatform(i); Pointer
     * platformName = OpenMM_Platform_getName(currentPlatform);
     * logger.log(Level.INFO, " Platform: {0}", platformName.getString(0));
     * OpenMM_Platform_destroy(currentPlatform); }
     */
    String defaultPrecision = "mixed";
    String precision = molecularAssembly.getForceField().getString(ForceField.ForceFieldString.PRECISION, defaultPrecision).toLowerCase();
    precision = precision.replace("-precision", "");
    switch(precision) {
        case "double":
        case "mixed":
        case "single":
            logger.info(String.format(" Using precision level %s", precision));
            break;
        default:
            logger.info(String.format(" Could not interpret precision level %s, defaulting to %s", precision, defaultPrecision));
            precision = defaultPrecision;
            break;
    }
    Comm world = Comm.world();
    int size = world.size();
    int defDeviceIndex = 0;
    if (size > 1) {
        int rank = world.rank();
        CompositeConfiguration props = molecularAssembly.getProperties();
        // 0/no-arg would indicate "just put everything on device specified by CUDA_DEVICE".
        // TODO: Get the number of CUDA devices from the CUDA API as the alternate default.
        int numCudaDevices = props.getInt("numCudaDevices", 0);
        if (numCudaDevices > 0) {
            defDeviceIndex = rank % numCudaDevices;
            logger.info(String.format(" Placing energy from rank %d on device %d", rank, defDeviceIndex));
        }
    }
    int deviceID = molecularAssembly.getForceField().getInteger(ForceField.ForceFieldInteger.CUDA_DEVICE, defDeviceIndex);
    String deviceIDString = Integer.toString(deviceID);
    if (cuda && requestedPlatform != Platform.OMM_REF) {
        platform = OpenMM_Platform_getPlatformByName("CUDA");
        OpenMM_Platform_setPropertyDefaultValue(platform, pointerForString("CudaDeviceIndex"), pointerForString(deviceIDString));
        OpenMM_Platform_setPropertyDefaultValue(platform, pointerForString("Precision"), pointerForString(precision));
        logger.info(String.format(" Selected OpenMM AMOEBA CUDA Platform (Device ID: %d)", deviceID));
    } else {
        platform = OpenMM_Platform_getPlatformByName("Reference");
        logger.info(" Selected OpenMM AMOEBA Reference Platform");
    }
}

Example 3 with Comm

use of edu.rit.pj.Comm in project ffx by mjschnie.

the class Runner method main.

// Main program.
/**
 * Main program.
 *
 * @param args an array of {@link java.lang.String} objects.
 * @throws java.lang.Exception if any.
 */
public static void main(String[] args) throws Exception {
    if (args.length != 1) {
        usage();
    }
    // Initialize world communicator.
    Comm.init(args);
    world = Comm.world();
    rank = world.rank();
    // Set up worker team.
    team = new WorkerTeam();
    // Master process sets up job generator.
    if (rank == team.masterRank()) {
        omitted = new HashSet<Integer>();
        // Assume argument is a checkpoint file name and try to read it.
        Scanner scanner = null;
        try {
            scanner = new Scanner(new File(args[0]));
        } catch (IOException exc) {
        }
        // Read checkpoint file.
        if (scanner != null) {
            while (scanner.hasNextLine()) {
                Scanner linescanner = new Scanner(scanner.nextLine());
                String word;
                int jobnum;
                if (!linescanner.hasNext()) {
                    continue;
                }
                word = linescanner.next();
                if (!word.equals("***")) {
                    continue;
                }
                if (!linescanner.hasNext()) {
                    continue;
                }
                word = linescanner.next();
                if (word.equals("Generator")) {
                    if (!linescanner.hasNext()) {
                        continue;
                    }
                    if (generatorExpression == null) {
                        generatorExpression = linescanner.next();
                    }
                } else if (word.equals("Job")) {
                    if (!linescanner.hasNextInt()) {
                        continue;
                    }
                    jobnum = linescanner.nextInt();
                    if (!linescanner.hasNext()) {
                        continue;
                    }
                    word = linescanner.next();
                    if (word.equals("finished")) {
                        omitted.add(jobnum);
                    }
                }
            }
            scanner.close();
        } else // Assume argument is a job generator constructor expression.
        {
            generatorExpression = args[0];
        }
        // Create job generator.
        if (generatorExpression == null) {
            stderr.printf("Runner: No job generator in checkpoint file %s%n", args[0]);
        } else {
            try {
                generator = (JobGenerator) Instance.newInstance(generatorExpression);
                stdout.printf("*** Generator %s%n", generatorExpression);
                generator.omit(omitted);
            } catch (Throwable exc) {
                stderr.printf("Runner: Could not create job generator %s%n", generatorExpression);
                exc.printStackTrace(stderr);
            }
        }
    }
    // Abort every process if job generator was not created.
    BooleanItemBuf buf = BooleanBuf.buffer(generator != null);
    world.broadcast(team.masterRank(), buf);
    if (!buf.item) {
        System.exit(1);
    }
    // Generate and run jobs.
    team.execute(new WorkerRegion() {

        public void run() throws Exception {
            execute(generator, new WorkerIteration<Job>() {

                public void sendTaskInput(Job job, Comm comm, int wRank, int tag) {
                    stdout.printf("*** Job %d started %s %s%n", job.getJobNumber(), new Date(), job.getDescription());
                }

                public void run(Job job) {
                    job.run();
                }

                public void receiveTaskOutput(Job job, Comm comm, int wRank, int tag) {
                    stdout.printf("*** Job %d finished %s%n", job.getJobNumber(), new Date());
                }
            });
        }
    });
    if (rank == team.masterRank()) {
        stdout.printf("*** All jobs finished%n");
    }
}

Example 4 with Comm

use of edu.rit.pj.Comm in project ffx by mjschnie.

the class LogFormatter method format.

/**
 * {@inheritDoc}
 * <p>
 * Unless debugging is turned on or the LogRecord is of level WARNING or
 * greater, just return the message.
 * <p>
 * If more than one process is active, prepend the rank of the process to
 * each line of the message.
 *
 * @since 1.0
 */
@Override
public String format(LogRecord record) {
    String message = null;
    if (debug || record.getLevel().intValue() >= warningLevel) {
        message = super.format(record);
    } else {
        message = record.getMessage();
        Object[] objects = record.getParameters();
        message = MessageFormat.format(message, objects);
    }
    try {
        Comm comm = Comm.world();
        int size = comm.size();
        int rank = comm.rank();
        if (size > 1) {
            if (mpiLogging) {
                String[] lines = message.split("\n");
                message = String.format(" [%d]%s", rank, lines[0]);
                int numLines = lines.length;
                for (int i = 1; i < numLines; i++) {
                    message = message.concat(String.format("\n [%d]%s", rank, lines[i]));
                }
            } else if (rank != 0) {
                message = null;
            }
        }
    } catch (Exception e) {
    // If Comm.world does not exist, do not append the rank.
    }
    return message;
}