Debug code

Author: pintohutch

nipype/interfaces/afni/base.py

@@ -147,6 +147,10 @@ def __init__(self, **inputs):
         else:
             self._output_update()
 
+        # Update num threads estimate from OMP_NUM_THREADS env var
+        import os
+        self.num_threads = int(os.getenv('OMP_NUM_THREADS', 1))
+
     def _output_update(self):
         """ i think? updates class private attribute based on instance input
          in fsl also updates ENVIRON variable....not valid in afni

nipype/interfaces/base.py

@@ -1205,7 +1205,7 @@ def _read(self, drain):
 
 
 # Get number of threads for process
-def _get_num_threads(proc):
+def _get_num_threads(proc, called_from):
     """Function to get the number of threads a process is using
     NOTE: If 
 
@@ -1227,12 +1227,16 @@ def _get_num_threads(proc):
     # Init variables
     cb_log = logging.getLogger('callback')
     cb_log.propogate = False
+    cb_log.debug('\n---------------------\nCalled from: %s' % called_from)
     cb_log.debug('proc pid: %d, parent pid: %d, name: %s, exe: %s, cmdline: %s, status: %s, num_threads: %d' \
                  % (proc.pid, proc.ppid(), proc.name(), proc.exe(), proc.cmdline(), proc.status(), proc.num_threads()))
+
+
     if proc.status() == psutil.STATUS_RUNNING:
         num_threads = proc.num_threads()
     else:
         num_threads = 0
+
     child_threads = 0
     # Iterate through child processes and get number of their threads
     try:
@@ -1241,17 +1245,18 @@ def _get_num_threads(proc):
                 # If leaf child process
                 if len(child.children()) == 0:
                     child_threads += child.num_threads()
-                    #num_threads = max(num_threads, child.num_threads()) #child.num_threads()
                 cb_log.debug('child pid: %d, parent pid: %d, name: %s, exe: %s, cmdline: %s, status: %s, num_threads: %d' \
                              % (proc.pid, proc.ppid(), proc.name(), proc.exe(), proc.cmdline(), proc.status(), child.num_threads()))
+                cb_log.debug('child_threads: %d, num_threads: %d' % (child_threads, num_threads))
 
-            #num_threads = max(num_threads, num_children,
-            #                  child.num_threads(), len(child.children()))
         num_threads = max(child_threads, num_threads)
     except psutil.NoSuchProcess:
         pass
 
+
+
     # Return number of threads found
+    cb_log.debug('RETURNING num_threads as: %d!\n---------------------------\n' % num_threads)
     return num_threads
 
 
@@ -1307,7 +1312,7 @@ def _get_ram_mb(pid, pyfunc=False):
 
 
 # Get max resources used for process
-def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False):
+def get_max_resources_used(pid, mem_mb, num_threads, called_from, pyfunc=False):
     """Function to get the RAM and threads usage of a process
 
     Paramters
@@ -1332,7 +1337,7 @@ def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False):
 
     try:
         mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc))
-        num_threads = max(num_threads, _get_num_threads(psutil.Process(pid)))
+        num_threads = max(num_threads, _get_num_threads(psutil.Process(pid), called_from))
     except Exception as exc:
         iflogger.info('Could not get resources used by process. Error: %s'\
                       % exc)
@@ -1394,7 +1399,7 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False):
 
     # Init variables for memory profiling
     mem_mb = 0
-    num_threads = 0
+    num_threads = 1
     interval = .5
 
     if output == 'stream':
@@ -1415,7 +1420,7 @@ def _process(drain=0):
         while proc.returncode is None:
             if runtime_profile:
                 mem_mb, num_threads = \
-                    get_max_resources_used(proc.pid, mem_mb, num_threads)
+                    get_max_resources_used(proc.pid, mem_mb, num_threads, cmdline)
             proc.poll()
             _process()
             time.sleep(interval)
@@ -1435,7 +1440,7 @@ def _process(drain=0):
         if runtime_profile:
             while proc.returncode is None:
                 mem_mb, num_threads = \
-                    get_max_resources_used(proc.pid, mem_mb, num_threads)
+                    get_max_resources_used(proc.pid, mem_mb, num_threads, cmdline)
                 proc.poll()
                 time.sleep(interval)
         stdout, stderr = proc.communicate()
@@ -1457,7 +1462,7 @@ def _process(drain=0):
         if runtime_profile:
             while proc.returncode is None:
                 mem_mb, num_threads = \
-                    get_max_resources_used(proc.pid, mem_mb, num_threads)
+                    get_max_resources_used(proc.pid, mem_mb, num_threads, cmdline)
                 proc.poll()
                 time.sleep(interval)
         ret_code = proc.wait()
@@ -1470,7 +1475,7 @@ def _process(drain=0):
         if runtime_profile:
             while proc.returncode is None:
                 mem_mb, num_threads = \
-                    get_max_resources_used(proc.pid, mem_mb, num_threads)
+                    get_max_resources_used(proc.pid, mem_mb, num_threads, cmdline)
                 proc.poll()
                 time.sleep(interval)
         proc.communicate()

nipype/interfaces/utility.py

@@ -492,7 +492,7 @@ def _function_handle_wrapper(queue, **kwargs):
             while proc.is_alive():
                 mem_mb, num_threads = \
                     get_max_resources_used(proc.pid, mem_mb, num_threads,
-                                           pyfunc=True)
+                                           function_handle.__name__, pyfunc=True)
 
             # Get result from process queue
             out = queue.get()

nipype/pipeline/plugins/base.py

@@ -252,10 +252,8 @@ def run(self, graph, config, updatehash=False):
         while np.any(self.proc_done == False) | \
                 np.any(self.proc_pending == True):
 
-            mem_mb, num_thr = get_max_resources_used(gpid, memory_mb, num_threads)
-            memory_mb = max(mem_mb, memory_mb)
-            num_threads = max(num_thr, num_threads)
-            gw_log.info('Memory GB usage: %.4f, Threads usage: %d' % (memory_mb/1024.0, num_threads))
+            #memory_mb, num_threads = get_max_resources_used(gpid, memory_mb, num_threads, )
+            #gw_log.info('Memory GB usage: %.4f, Threads usage: %d' % (memory_mb/1024.0, num_threads))
             toappend = []
             # trigger callbacks for any pending results
             while self.pending_tasks:

nipype/utils/draw_gantt_chart.py

@@ -183,7 +183,7 @@ def calculate_resource_timeseries(events, resource):
 
     # Iterate through the events
     for tdelta, event in sorted(events.items()):
-        if tdelta > 70.7:
+        if tdelta > 80:
             print 'hi'
         if event['event'] == "start":
             if resource in event and event[resource] != 'Unkown':