Revert code, don't catch TimeoutExpired inside system_call

sisyphus/aws_batch_engine.py

@@ -90,11 +90,8 @@ def system_call(self, command, send_to_stdin=None):
         logging.debug("shell_cmd: %s" % " ".join(system_command))
         if send_to_stdin:
             send_to_stdin = send_to_stdin.encode()
-        try:
-            p = subprocess.run(system_command, input=send_to_stdin, capture_output=True, timeout=30)
-        except subprocess.TimeoutExpired:
-            logging.warning("Timeout expired for command: %s" % " ".join(system_command))
-            return [], ["TimeoutExpired".encode()], -1
+
+        p = subprocess.run(system_command, input=send_to_stdin, capture_output=True, timeout=30)
 
         def fix_output(o):
             """

sisyphus/load_sharing_facility_engine.py

@@ -58,11 +58,8 @@ def system_call(self, command, send_to_stdin=None):
         logging.debug("shell_cmd: %s" % " ".join(system_command))
         if send_to_stdin:
             send_to_stdin = send_to_stdin.encode()
-        try:
-            p = subprocess.run(system_command, input=send_to_stdin, capture_output=True, timeout=30)
-        except subprocess.TimeoutExpired:
-            logging.warning(self._system_call_timeout_warn_msg(system_command))
-            return [], ["TimeoutExpired".encode()], -1
+
+        p = subprocess.run(system_command, input=send_to_stdin, capture_output=True, timeout=30)
 
         def fix_output(o):
             # split output and drop last empty line
@@ -189,8 +186,10 @@ def submit_helper(self, call, logpath, rqmt, name, task_name, rangestring):
         while True:
             logging.info("bsub_call: %s" % bsub_call)
             logging.info("command: %s" % command)
-            out, err, retval = self.system_call(bsub_call, command)
-            if retval != 0:
+            try:
+                out, err, retval = self.system_call(bsub_call, command)
+            except subprocess.TimeoutExpired:
+                logging.warning(self._system_call_timeout_warn_msg(bsub_call))
                 time.sleep(gs.WAIT_PERIOD_SSH_TIMEOUT)
                 continue
             break
@@ -248,8 +247,10 @@ def queue_state(self):
         # get bjobs output
         system_command = ["bjobs", "-w"]
         while True:
-            out, err, retval = self.system_call(system_command)
-            if retval != 0:
+            try:
+                out, err, retval = self.system_call(system_command)
+            except subprocess.TimeoutExpired:
+                logging.warning(self._system_call_timeout_warn_msg(system_command))
                 time.sleep(gs.WAIT_PERIOD_SSH_TIMEOUT)
                 continue
             break

sisyphus/simple_linux_utility_for_resource_management_engine.py

@@ -96,11 +96,8 @@ def system_call(self, command, send_to_stdin=None):
         logging.debug("shell_cmd: %s" % " ".join(system_command))
         if send_to_stdin:
             send_to_stdin = send_to_stdin.encode()
-        try:
-            p = subprocess.run(system_command, input=send_to_stdin, capture_output=True, timeout=30)
-        except subprocess.TimeoutExpired:
-            logging.warning(self._system_call_timeout_warn_msg(system_command))
-            return [], ["TimeoutExpired".encode()], -1
+
+        p = subprocess.run(system_command, input=send_to_stdin, capture_output=True, timeout=30)
 
         def fix_output(o):
             """
@@ -236,8 +233,10 @@ def submit_helper(self, call, logpath, rqmt, name, task_name, start_id, end_id,
         sbatch_call += ["-a", "%i-%i:%i" % (start_id, end_id, step_size)]
         sbatch_call += ["--wrap=%s" % " ".join(call)]
         while True:
-            out, err, retval = self.system_call(sbatch_call)
-            if retval != 0:
+            try:
+                out, err, retval = self.system_call(sbatch_call)
+            except subprocess.TimeoutExpired:
+                logging.warning(self._system_call_timeout_warn_msg(sbatch_call))
                 time.sleep(gs.WAIT_PERIOD_SSH_TIMEOUT)
                 continue
             break
@@ -306,8 +305,10 @@ def queue_state(self):
             "arrayjobid,arraytaskid,state,name:1000",
         ]
         while True:
-            out, err, retval = self.system_call(system_command)
-            if retval != 0:
+            try:
+                out, err, retval = self.system_call(system_command)
+            except subprocess.TimeoutExpired:
+                logging.warning(self._system_call_timeout_warn_msg(system_command))
                 time.sleep(gs.WAIT_PERIOD_SSH_TIMEOUT)
                 continue
             break

sisyphus/son_of_grid_engine.py

@@ -97,11 +97,8 @@ def system_call(self, command, send_to_stdin=None):
         logging.debug("shell_cmd: %s" % " ".join(system_command))
         if send_to_stdin:
             send_to_stdin = send_to_stdin.encode()
-        try:
-            p = subprocess.run(system_command, input=send_to_stdin, capture_output=True, timeout=30)
-        except subprocess.TimeoutExpired:
-            logging.warning(self._system_call_timeout_warn_msg(system_command))
-            return [], ["TimeoutExpired".encode()], -1
+
+        p = subprocess.run(system_command, input=send_to_stdin, capture_output=True, timeout=30)
 
         def fix_output(o):
             """
@@ -252,8 +249,10 @@ def submit_helper(self, call, logpath, rqmt, name, task_name, start_id, end_id,
         qsub_call += ["-t", "%i-%i:%i" % (start_id, end_id, step_size)]
         command = " ".join(call) + "\n"
         while True:
-            out, err, retval = self.system_call(qsub_call, command)
-            if retval != 0:
+            try:
+                out, err, retval = self.system_call(qsub_call, command)
+            except subprocess.TimeoutExpired:
+                logging.warning(self._system_call_timeout_warn_msg(qsub_call))
                 time.sleep(gs.WAIT_PERIOD_SSH_TIMEOUT)
                 continue
             break
@@ -317,8 +316,10 @@ def queue_state(self):
         # get qstat output
         system_command = ["qstat", "-xml", "-u", getpass.getuser()]
         while True:
-            out, err, retval = self.system_call(system_command)
-            if retval != 0:
+            try:
+                out, err, retval = self.system_call(system_command)
+            except subprocess.TimeoutExpired:
+                logging.warning(self._system_call_timeout_warn_msg(system_command))
                 time.sleep(gs.WAIT_PERIOD_SSH_TIMEOUT)
                 continue
             break