a more consistent resource_monitor checking

Author: oesteban

nipype/interfaces/base.py

@@ -1066,9 +1066,9 @@ def run(self, **inputs):
         results :  an InterfaceResult object containing a copy of the instance
         that was executed, provenance information and, if successful, results
         """
-        from ..utils.profiler import resource_monitor, ResourceMonitor
+        from ..utils.profiler import ResourceMonitor
 
-        enable_rm = resource_monitor and self.resource_monitor
+        enable_rm = config.resource_monitor and self.resource_monitor
         force_raise = not getattr(self.inputs, 'ignore_exception', False)
         self.inputs.trait_set(**inputs)
         self._check_mandatory_inputs()

nipype/interfaces/tests/test_resource_monitor.py

@@ -11,10 +11,15 @@
 import pytest
 
 # Import packages
-from nipype.utils.profiler import resource_monitor as run_profile, _use_resources
+from nipype import config
+from nipype.utils.profiler import _use_resources
 from nipype.interfaces.base import traits, CommandLine, CommandLineInputSpec
 from nipype.interfaces import utility as niu
 
+# Try to enable the resource monitor
+config.enable_resource_monitor()
+run_profile = config.resource_monitor
+
 
 class UseResourcesInputSpec(CommandLineInputSpec):
     mem_gb = traits.Float(desc='Number of GB of RAM to use',

nipype/pipeline/engine/nodes.py

@@ -725,7 +725,6 @@ def update(self, **opts):
         self.inputs.update(**opts)
 
     def write_report(self, report_type=None, cwd=None):
-        from ...utils.profiler import resource_monitor
         if not str2bool(self.config['execution']['create_report']):
             return
         report_dir = op.join(cwd, '_report')
@@ -763,7 +762,7 @@ def write_report(self, report_type=None, cwd=None):
             rst_dict = {'hostname': self.result.runtime.hostname,
                         'duration': self.result.runtime.duration}
             # Try and insert memory/threads usage if available
-            if resource_monitor:
+            if config.resource_monitor:
                 rst_dict['mem_peak_gb'] = self.result.runtime.mem_peak_gb
                 rst_dict['cpu_percent'] = self.result.runtime.cpu_percent
 

nipype/pipeline/engine/utils.py

@@ -1298,6 +1298,10 @@ def write_workflow_prov(graph, filename=None, format='all'):
 
 
 def write_workflow_resources(graph, filename=None):
+    """
+    Generate a JSON file with profiling traces that can be loaded
+    in a pandas DataFrame or processed with JavaScript like D3.js
+    """
     import simplejson as json
     if not filename:
         filename = os.path.join(os.getcwd(), 'resource_monitor.json')

nipype/pipeline/engine/workflows.py

@@ -595,7 +595,7 @@ def run(self, plugin=None, plugin_args=None, updatehash=False):
             logger.info('Provenance file prefix: %s' % prov_base)
             write_workflow_prov(execgraph, prov_base, format='all')
 
-        if str2bool(self.config['execution'].get('resource_monitor', 'false')):
+        if config.resource_monitor:
             write_workflow_resources(execgraph)
         return execgraph
 

nipype/utils/config.py

@@ -18,11 +18,13 @@
 import configparser
 import numpy as np
 
-from builtins import str, object, open
+from builtins import bytes, str, object, open
 
 from simplejson import load, dump
-from ..external import portalocker
 from future import standard_library
+from ..external import portalocker
+from .misc import str2bool
+
 standard_library.install_aliases()
 
 
@@ -96,6 +98,7 @@ def __init__(self, *args, **kwargs):
         config_file = os.path.join(config_dir, 'nipype.cfg')
         self.data_file = os.path.join(config_dir, 'nipype.json')
         self._config.readfp(StringIO(default_cfg))
+        self._resource_monitor = None
         if os.path.exists(config_dir):
             self._config.read([config_file, 'nipype.cfg'])
 
@@ -202,5 +205,41 @@ def enable_provenance(self):
         self._config.set('execution', 'write_provenance', 'true')
         self._config.set('execution', 'hash_method', 'content')
 
+    @property
+    def resource_monitor(self):
+        """Check if resource_monitor is available"""
+        if self._resource_monitor is not None:
+            return self._resource_monitor
+
+        # Cache config from nipype config
+        self.resource_monitor = self._config.get(
+            'execution', 'resource_monitor') or False
+        return self._resource_monitor
+
+    @resource_monitor.setter
+    def resource_monitor(self, value):
+        # Accept string true/false values
+        if isinstance(value, (str, bytes)):
+            value = str2bool(value.lower())
+
+        if value is False:
+            self._resource_monitor = False
+        elif value is True:
+            if not self._resource_monitor:
+                # Before setting self._resource_monitor check psutil availability
+                self._resource_monitor = False
+                try:
+                    import psutil
+                    self._resource_monitor = LooseVersion(
+                        psutil.__version__) >= LooseVersion('5.0')
+                except ImportError:
+                    pass
+                finally:
+                    if not self._resource_monitor:
+                        warn('Could not enable the resource monitor: psutil>=5.0'
+                             ' could not be imported.')
+                    self._config.set('execution', 'resource_monitor',
+                                     ('%s' % self._resource_monitor).lower())
+
     def enable_resource_monitor(self):
-        self._config.set('execution', 'resource_monitor', 'true')
+        self.resource_monitor = True

nipype/utils/profiler.py

@@ -2,7 +2,7 @@
 # @Author: oesteban
 # @Date:   2017-09-21 15:50:37
 # @Last Modified by:   oesteban
-# @Last Modified time: 2017-09-29 16:42:27
+# @Last Modified time: 2017-10-02 15:44:29
 """
 Utilities to keep track of performance
 """
@@ -17,15 +17,9 @@
 
 from builtins import open, range
 from .. import config, logging
-from .misc import str2bool
 
 proflogger = logging.getLogger('utils')
-
-resource_monitor = str2bool(config.get('execution', 'resource_monitor', 'false'))
-if resource_monitor and psutil is None:
-    proflogger.warning('Switching "resource_monitor" off: the option was on, but the '
-                       'necessary package "psutil" could not be imported.')
-    resource_monitor = False
+resource_monitor = config.resource_monitor
 
 # Init variables
 _MB = 1024.0**2