Examples with CmdRunner pipelite.executor.cmd.CmdRunner used on opensource projects

Example 1 with CmdRunner

use of pipelite.executor.cmd.CmdRunner in project pipelite by enasequence.

the class AbstractLsfExecutor method recoverJobs.

/**
 * Attempt to recover missing job results. This will only ever be done once and if it fails the
 * job is considered failed.
 */
private static void recoverJobs(CmdRunner cmdRunner, Map<String, LsfDescribeJobsCache.RequestContext> requestMap, List<JobResult> jobResults) {
    log.atInfo().log("Recovering LSF job results.");
    AtomicInteger remainingCount = new AtomicInteger();
    AtomicInteger attemptedCount = new AtomicInteger();
    AtomicInteger recoveredCount = new AtomicInteger();
    ZonedDateTime start = ZonedDateTime.now();
    ZonedDateTime until = start.plus(JOB_RECOVERY_TIMEOUT);
    ExecutorService executorService = Executors.newFixedThreadPool(JOB_RECOVERY_PARALLELISM);
    try {
        jobResults.stream().filter(r -> r.jobId != null && r.result == null).forEach(r -> {
            attemptedCount.incrementAndGet();
            remainingCount.incrementAndGet();
            executorService.submit(() -> {
                try {
                    // Attempt to recover missing job result using bhist.
                    if (recoverJobUsingBhist(cmdRunner, r)) {
                        recoveredCount.incrementAndGet();
                    } else {
                        // Attempt to recover missing job result using output file.
                        if (recoverJobUsingOutFile(cmdRunner, r, requestMap)) {
                            recoveredCount.incrementAndGet();
                        }
                    }
                } finally {
                    remainingCount.decrementAndGet();
                }
            });
        });
        try {
            while (remainingCount.get() > 0) {
                Time.waitUntil(JOB_RECOVERY_POLL_FREQUENCY, until);
            }
        } catch (PipeliteTimeoutException ex) {
            log.atWarning().log("LSF job recovery timeout exceeded.");
        }
    } finally {
        executorService.shutdownNow();
    }
    log.atInfo().log("Finished recovering LSF job results in " + (Duration.between(ZonedDateTime.now(), start).abs().toMillis() / 1000) + " seconds. Recovered " + recoveredCount.get() + " out of " + attemptedCount.get() + " jobs.");
}

Example 2 with CmdRunner

use of pipelite.executor.cmd.CmdRunner in project pipelite by enasequence.

the class CmdExecutor method execute.

@Override
public void execute(StageExecutorRequest request, StageExecutorResultCallback resultCallback) {
    CmdRunner cmdRunner = CmdRunner.create(getExecutorParams());
    StageExecutorResult result = cmdRunner.execute(cmd);
    if (getExecutorParams().getPermanentErrors().contains(Ints.tryParse(result.getAttribute(EXIT_CODE)))) {
        result.setPermanentError();
    }
    resultCallback.accept(result);
}