- updated some SGE and PBS commands with input validity checks

 . in particular, this prevents "qsub" with no parameters which waits indefinitely on stdin
- added parsing for some SGE outputs (submitJob, checkJobs, deleteJobs)

rsmcore/queuepbs.cc

@@ -7,14 +7,27 @@ QString QueuePBS::listAllNodeInfo() { return "pbsnodes -a"; }
 QString QueuePBS::listAllQueues() { return "qstat -q"; }
 QString QueuePBS::checkJobs(QStringList jobIDs)
 {
-  // TODO: optional -f job_id job_id ...
-  return "qstat ";
+  QString command = "qstat";
+  if (jobIDs.length() > 0) command += " -f " + jobIDs.join(" ");
+  return command;
 }
 QString QueuePBS::deleteJobs(QStringList jobIDs)
-{  // TODO: qdel job_id job_id ...
-  return "qdel ";
+{
+  if (jobIDs.length() == 0) return "";
+  int totalLen = 0;
+  for (auto id : jobIDs)
+  {
+    totalLen += id.trimmed().length();
+  }
+  if (totalLen == 0) return "";
+  return "qdel " + jobIDs.join(" ");
+}
+QString QueuePBS::submitJob(QString params)
+{
+  // do not allow calling qsub using stdin since it will wait indefinitely
+  if (params.trimmed().length() == 0) return "";
+  return "qsub " + params;
 }
-QString QueuePBS::submitJob(QString params) { return "qsub " + params; }
 QString QueuePBS::showQueueInfo(QString queueName)
 {
   return "showq " + queueName;

rsmcore/queuesge.cc

@@ -16,9 +16,20 @@ QString QueueSGE::checkJobs(QStringList jobIDs)
 QString QueueSGE::deleteJobs(QStringList jobIDs)
 {
   if (jobIDs.length() == 0) return "";
+  int totalLen = 0;
+  for (auto id : jobIDs)
+  {
+    totalLen += id.trimmed().length();
+  }
+  if (totalLen == 0) return "";
   return "qdel " + jobIDs.join(" ");
 }
-QString QueueSGE::submitJob(QString params) { return "qsub " + params; }
+QString QueueSGE::submitJob(QString params)
+{
+  // do not allow calling qsub using stdin since it will wait indefinitely
+  if (params.trimmed().length() == 0) return "";
+  return "qsub " + params;
+}
 QString QueueSGE::showQueueInfo(QString queueName)
 {
   return "qconf -sq " + queueName;
@@ -28,4 +39,79 @@ QString QueueSGE::showFreeProcs(QString params)
   (void)sizeof(params);
   return "qstat -g c";
 }
+
+// returns job ID on success or -1 on failure
+int QueueSGE::parseSubmitJobReturn(QString str)
+{
+  // examples:
+  //  Your job 99 ("spin_test") has been submitted
+  //  Your job - array 90.1 - 16 : 1(" test ")has been submitted;
+  int jobID                   = -1;
+  QRegularExpression re       = QRegularExpression("job[^0-9]*([0-9]+)");
+  QRegularExpressionMatch rem = re.match(str);
+  if (rem.hasMatch())
+  {
+    jobID = rem.captured(1).toInt();
+  }
+  return jobID;
+}
+
+// returns QSet of job IDs on success or emtpy QSet on failure or if no jobs
+// running
+QSet<int> QueueSGE::parseCheckJobsReturn(QString str)
+{
+  // examples:
+  //  job-ID  prior   name       user         state submit/start at     queue
+  //  slots ja-task-ID
+  //  -----------------------------------------------------------------------------------------------------------------
+  //      105 0.50000 spintest   mpi_user     r     04/14/2020 13:48:03
+  //      all.q@rpi3-compute-node-1.clus     1 1 105 0.50000 spintest   mpi_user
+  //      r     04/14/2020 13:48:03 all.q@rpi3-compute-node-2.clus     1 2
+  QSet<int> jobIDs;
+  QRegularExpression re = QRegularExpression("[^0-9]*([0-9]+)");
+  QStringList subStrList =
+      str.split(QRegExp("[\r\n]"), QString::SkipEmptyParts);
+  for (auto subStr : subStrList)
+  {
+    QRegularExpressionMatch rem = re.match(subStr);
+    if (rem.hasMatch())
+    {
+      int jobID = rem.captured(1).toInt();
+      jobIDs.insert(jobID);
+    }
+  }
+  return jobIDs;
+}
+
+// returns QSet of job IDs on success or emtpy QSet on failure or if no jobs
+// running
+QSet<int> QueueSGE::parseDeleteJobsReturn(QString str)
+{
+  // examples:
+  // mpi_user has registered the job-array task 112.1 for deletion
+  // mpi_user has registered the job-array task 112.2 for deletion
+  // ...
+  // mpi_user has deleted job 113
+  //
+  //  denied: job "111" does not exist
+  //  denied: job "112" does not exist
+  //
+  //
+
+  QSet<int> jobIDs;
+  QRegularExpression re = QRegularExpression("[^0-9]*([0-9]+)");
+  QStringList subStrList =
+      str.split(QRegExp("[\r\n]"), QString::SkipEmptyParts);
+  for (auto subStr : subStrList)
+  {
+    QRegularExpressionMatch rem = re.match(subStr);
+    if (rem.hasMatch())
+    {
+      int jobID = rem.captured(1).toInt();
+      jobIDs.insert(jobID);
+    }
+  }
+  return jobIDs;
+}
+
 }  // namespace rsm

rsmcore/queuesge.hh

 #ifndef RSMSGE_QUEUESGE_HH_
 #define RSMSGE_QUEUESGE_HH_
 
+#include <QRegularExpression>
+#include <QRegularExpressionMatch>
+#include <QSet>
+
 #include "rsmcore/queuebase.hh"
 
 namespace rsm
@@ -16,6 +20,9 @@ class QueueSGE : public QueueBase
   QString submitJob(QString params) override;
   QString showQueueInfo(QString queueName) override;
   QString showFreeProcs(QString params) override;
+  int parseSubmitJobReturn(QString str);
+  QSet<int> parseCheckJobsReturn(QString str);
+  QSet<int> parseDeleteJobsReturn(QString str);
 };  // class QueueSGE
 }  // namespace rsm
 

rsmcore/sessionworker.cc

@@ -394,6 +394,7 @@ void SessionWorker::requestExec(QString command)
     ssh_channel_free(channel);
     return;
   }
+  // TODO: should we use timeout or non-blocking version of this call?
   int nbytes = ssh_channel_read(channel, buffer, sizeof(buffer), 0);
   while (nbytes > 0)
   {
@@ -419,4 +420,4 @@ void SessionWorker::requestExec(QString command)
   emit execFinished();
 }
 
-}  // namespace rsm
\ No newline at end of file
+}  // namespace rsm

rsmwidgets/examples/rsmportalexample.cc

@@ -34,7 +34,7 @@ ExamplePortalWidget::ExamplePortalWidget(QWidget *parent)
   mUserNameEdit         = new QLineEdit("", this);
   mConnectButton        = new QPushButton("Connect", this);
   mCommandEdit          = new QLineEdit(this);
-  mCommandSubmitButton  = new QPushButton("Submit", this);
+  mCommandSubmitButton  = new QPushButton("Submit Command", this);
   mSchedulerBox         = new QGroupBox(this);
   mPBSRadioButton       = new QRadioButton("PBS", this);
   mSGERadioButton       = new QRadioButton("SGE", this);
@@ -43,8 +43,10 @@ ExamplePortalWidget::ExamplePortalWidget(QWidget *parent)
   mGetQueueInfoTextEdit = new QLineEdit(this);
   mGetAllNodeInfoButton = new QPushButton("Node Info", this);
   mGetAllJobInfoButton  = new QPushButton("Job Info", this);
-  mDeleteJobButton      = new QPushButton("Delete Job", this);
+  mSubmitJobButton      = new QPushButton("Submit Job", this);
+  mDeleteJobButton      = new QPushButton("Delete Job(s)", this);
   mDeleteJobTextEdit    = new QLineEdit(this);
+  mSubmitJobTextEdit    = new QLineEdit("", this);
 
   mTextEdit = new QTextEdit(this);
 
@@ -75,6 +77,8 @@ ExamplePortalWidget::ExamplePortalWidget(QWidget *parent)
   layout->addWidget(mGetQueueInfoButton, row, 1);
   layout->addWidget(mGetQueueInfoTextEdit, row, 2);
   layout->addWidget(mGetAllNodeInfoButton, ++row, 1);
+  layout->addWidget(mSubmitJobButton, ++row, 1);
+  layout->addWidget(mSubmitJobTextEdit, row, 2);
   layout->addWidget(mGetAllJobInfoButton, ++row, 1);
   layout->addWidget(mDeleteJobButton, ++row, 1);
   layout->addWidget(mDeleteJobTextEdit, row, 2);
@@ -86,6 +90,7 @@ ExamplePortalWidget::ExamplePortalWidget(QWidget *parent)
 
   connect(mSchedulerButtonGroup,
           QOverload<int>::of(&QButtonGroup::buttonClicked), [=](int id) {
+            (void)sizeof(id);
             QString name = mSchedulerButtonGroup->checkedButton()->text();
             if ("PBS" == name)
               queue = &queuePBS;
@@ -104,6 +109,8 @@ ExamplePortalWidget::ExamplePortalWidget(QWidget *parent)
           &ExamplePortalWidget::submitGetAllNodeInfoToHost);
   connect(mGetAllJobInfoButton, &QPushButton::pressed, this,
           &ExamplePortalWidget::submitGetAllJobInfoToHost);
+  connect(mSubmitJobButton, &QPushButton::pressed, this,
+          &ExamplePortalWidget::submitSubmitJobToHost);
   connect(mDeleteJobButton, &QPushButton::pressed, this,
           &ExamplePortalWidget::submitDeleteJobToHost);
 
@@ -166,37 +173,43 @@ void ExamplePortalWidget::submitCommandToHost()
 {
   radix_tagged_line("submitCommandToHost()");
   QString command = mCommandEdit->text();
-  mSession->requestExec(command);
+  submitCommand("custom", command);
 }
 
 void ExamplePortalWidget::submitListAllQueuesToHost()
 {
   radix_tagged_line("submitListAllQueuesToHost()");
   QString command = queue->listAllQueues();
-  mSession->requestExec(command);
+  submitCommand("listAllQueues", command);
 }
 
 void ExamplePortalWidget::submitGetQueueInfoToHost()
 {
   radix_tagged_line("submitGetQueueInfoToHost()");
   QString command = queue->showQueueInfo(mGetQueueInfoTextEdit->text());
-  fprintf(stderr, "%s\n", command.toStdString().c_str());
-  mSession->requestExec(command);
+  submitCommand("showQueueInfo", command);
 }
 
 void ExamplePortalWidget::submitGetAllNodeInfoToHost()
 {
   radix_tagged_line("submitGetAllNodeInfoToHost()");
   QString command = queue->listAllNodeInfo();
-  mSession->requestExec(command);
+  submitCommand("listAllNodeInfo", command);
 }
 
 void ExamplePortalWidget::submitGetAllJobInfoToHost()
 {
   radix_tagged_line("submitGetAllJobInfoToHost()");
   QString command = queue->checkJobs(QStringList());
-  fprintf(stderr, "%s\n", command.toStdString().c_str());
-  mSession->requestExec(command);
+  submitCommand("checkJobs", command);
+}
+
+void ExamplePortalWidget::submitSubmitJobToHost()
+{
+  radix_tagged_line("submitSubmitJobToHost()");
+  QStringList jobIDs = QStringList();
+  QString command    = queue->submitJob(mSubmitJobTextEdit->text());
+  submitCommand("submitJob", command);
 }
 
 void ExamplePortalWidget::submitDeleteJobToHost()
@@ -206,15 +219,14 @@ void ExamplePortalWidget::submitDeleteJobToHost()
   if (mDeleteJobTextEdit->text().length() > 0)
     jobIDs = mDeleteJobTextEdit->text().split(QRegExp("[ ,]"));
   QString command = queue->deleteJobs(jobIDs);
-  fprintf(stderr, "%d\n", jobIDs.size());
-  fprintf(stderr, "%s\n", command.toStdString().c_str());
-  mSession->requestExec(command);
+  submitCommand("deleteJobs", command);
 }
 
-void ExamplePortalWidget::slotExecOutputReady()
+void ExamplePortalWidget::submitCommand(QString commandType, QString command)
 {
-  QByteArray output = mSession->readExecOutput();
-  mTextEdit->append(output);
+  if ("" != execingCommandType) return;
+  execingCommandType = commandType;
+  mSession->requestExec(command);
 }
 
 void ExamplePortalWidget::connectionFailed(QString message)
@@ -377,12 +389,36 @@ void ExamplePortalWidget::execFailed(QString message)
   radix_tagged_line(message.toStdString());
   mTextEdit->append(message);
   mTextEdit->append("\n");
+  execingCommandType = "";
 }
 
 void ExamplePortalWidget::execFinished()
 {
   mTextEdit->append("Execution finished.\n");
+  if ("submitJob" == execingCommandType)
+  {
+    int jobID = queueSGE.parseSubmitJobReturn(mSession->readExecOutput());
+    fprintf(stderr, "%d\n", jobID);
+  }
+  if ("checkJobs" == execingCommandType)
+  {
+    QSet<int> jobIDs =
+        queueSGE.parseCheckJobsReturn(mSession->readExecOutput());
+    fprintf(stderr, "--\n");
+    for (auto jobID : jobIDs) fprintf(stderr, "%d\n", jobID);
+    fprintf(stderr, "--\n");
+  }
+  if ("deleteJobs" == execingCommandType)
+  {
+    QSet<int> jobIDs =
+        queueSGE.parseDeleteJobsReturn(mSession->readExecOutput());
+    fprintf(stderr, "--\n");
+    for (auto jobID : jobIDs) fprintf(stderr, "%d\n", jobID);
+    fprintf(stderr, "--\n");
+  }
+  execingCommandType = "";
 }
+
 MainWindow::MainWindow(QWidget *parent)
     : QMainWindow(parent)
 {

rsmwidgets/examples/rsmportalexample.hh

@@ -44,8 +44,10 @@ class ExamplePortalWidget : public QWidget
   QLineEdit *mGetQueueInfoTextEdit;
   QPushButton *mGetAllNodeInfoButton;
   QPushButton *mGetAllJobInfoButton;
+  QPushButton *mSubmitJobButton;
   QPushButton *mDeleteJobButton;
   QLineEdit *mDeleteJobTextEdit;
+  QLineEdit *mSubmitJobTextEdit;
   QTextEdit *mTextEdit;
 
   rsm::SessionController::SP mSession;
@@ -53,6 +55,9 @@ class ExamplePortalWidget : public QWidget
   rsm::QueueSGE queueSGE;
   rsm::QueueBase *queue;
 
+  void submitCommand(QString commandType, QString command);
+  QString execingCommandType;
+
  public:
   ExamplePortalWidget(QWidget *parent = nullptr);
 
@@ -63,8 +68,8 @@ class ExamplePortalWidget : public QWidget
   void submitGetQueueInfoToHost();
   void submitGetAllNodeInfoToHost();
   void submitGetAllJobInfoToHost();
+  void submitSubmitJobToHost();
   void submitDeleteJobToHost();
-  void slotExecOutputReady();
 
   void connectionFailed(QString message);
   void connectionSuccessful();