add new [monitoring] section to nipype config

Author: oesteban

doc/users/config_file.rst

@@ -153,20 +153,28 @@ Execution
     crashfiles allow portability across machines and shorter load time.
     (possible values: ``pklz`` and ``txt``; default value: ``pklz``)
 
-*resource_monitor*
+
+Resource Monitor
+~~~~~~~~~~~~~~~~
+
+*enabled*
     Enables monitoring the resources occupation (possible values: ``true`` and
-    ``false``; default value: ``false``)
+    ``false``; default value: ``false``). All the following options will be
+    dismissed if the resource monitor is not enabled.
 
-*resource_monitor_frequency*
+*sample_frequency*
     Sampling period (in seconds) between measurements of resources (memory, cpus)
-    being used by an interface. Requires ``resource_monitor`` to be ``true``.
-    (default value: ``1``)
+    being used by an interface (default value: ``1``)
 
-*resource_monitor_append*
-    Append to an existing ``resource_monitor.json`` in the workflow ``base_dir``.
-    Requires ``resource_monitor`` to be ``true``. (unset by default,
-    possible values: ``true`` or ``false``, the resource monitor will append 
-    unless explicitly set to ``false``).
+*summary_path*
+    Path where the summary ``resource_monitor.json`` should be stored, when running
+    a workflow (``summary_path`` does not apply to interfaces run independently).
+    (unset by default, in which case the summary file will be written out to 
+    ``<base_dir>/resource_monitor.json`` of the top-level workflow).
+
+*summary_append*
+    Append to an existing summary file (only applies to workflows).
+    (default value: ``true``, possible values: ``true`` or ``false``).
 
 Example
 ~~~~~~~
@@ -181,6 +189,10 @@ Example
     hash_method = timestamp
     display_variable = :1
 
+    [monitoring]
+    enabled = false
+
+
 Workflow.config property has a form of a nested dictionary reflecting the
 structure of the .cfg file.
 

docker/files/run_examples.sh

@@ -20,8 +20,9 @@ echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
 echo 'crashfile_format = txt' >> ${HOME}/.nipype/nipype.cfg
 
 if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then
-    echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg
-    echo 'resource_monitor_frequency = 3' >> ${HOME}/.nipype/nipype.cfg
+	echo '[monitoring]' >> ${HOME}/.nipype/nipype.cfg
+    echo 'enabled = true' >> ${HOME}/.nipype/nipype.cfg
+    echo 'sample_frequency = 3' >> ${HOME}/.nipype/nipype.cfg
 fi
 
 # Set up coverage

nipype/interfaces/tests/test_resource_monitor.py

@@ -54,7 +54,7 @@ def test_cmdline_profiling(tmpdir, mem_gb, n_procs):
     of a CommandLine-derived interface
     """
     from nipype import config
-    config.set('execution', 'resource_monitor_frequency', '0.2')  # Force sampling fast
+    config.set('monitoring', 'sample_frequency', '0.2')  # Force sampling fast
 
     tmpdir.chdir()
     iface = UseResources(mem_gb=mem_gb, n_procs=n_procs)
@@ -72,7 +72,7 @@ def test_function_profiling(tmpdir, mem_gb, n_procs):
     of a Function interface
     """
     from nipype import config
-    config.set('execution', 'resource_monitor_frequency', '0.2')  # Force sampling fast
+    config.set('monitoring', 'sample_frequency', '0.2')  # Force sampling fast
 
     tmpdir.chdir()
     iface = niu.Function(function=_use_resources)

nipype/utils/config.py

@@ -31,8 +31,8 @@
 
 
 CONFIG_DEPRECATIONS = {
-    'profile_runtime': ('resource_monitor', '1.0'),
-    'filemanip_level': ('utils_level', '1.0'),
+    'profile_runtime': ('monitoring.enabled', '1.0'),
+    'filemanip_level': ('logging.utils_level', '1.0'),
 }
 
 NUMPY_MMAP = LooseVersion(np.__version__) >= LooseVersion('1.12.0')
@@ -71,8 +71,11 @@
 parameterize_dirs = true
 poll_sleep_duration = 2
 xvfb_max_wait = 10
-resource_monitor = false
-resource_monitor_frequency = 1
+
+[monitoring]
+enabled = false
+sample_frequency = 1
+summary_append = true
 
 [check]
 interval = 1209600
@@ -105,12 +108,12 @@ def __init__(self, *args, **kwargs):
             self._config.read([config_file, 'nipype.cfg'])
 
         for option in CONFIG_DEPRECATIONS:
-            for section in ['execution', 'logging']:
+            for section in ['execution', 'logging', 'monitoring']:
                 if self.has_option(section, option):
-                    new_option = CONFIG_DEPRECATIONS[option][0]
-                    if not self.has_option(section, new_option):
+                    new_section, new_option = CONFIG_DEPRECATIONS[option][0].split('.')
+                    if not self.has_option(new_section, new_option):
                         # Warn implicit in get
-                        self.set(section, new_option, self.get(section, option))
+                        self.set(new_section, new_option, self.get(section, option))
 
     def set_default_config(self):
         self._config.readfp(StringIO(default_cfg))
@@ -138,7 +141,7 @@ def get(self, section, option, default=None):
                    '"%s" instead.') % (option, CONFIG_DEPRECATIONS[option][1],
                                        CONFIG_DEPRECATIONS[option][0])
             warn(msg)
-            option = CONFIG_DEPRECATIONS[option][0]
+            section, option = CONFIG_DEPRECATIONS[option][0].split('.')
 
         if self._config.has_option(section, option):
             return self._config.get(section, option)
@@ -154,7 +157,7 @@ def set(self, section, option, value):
                    '"%s" instead.') % (option, CONFIG_DEPRECATIONS[option][1],
                                        CONFIG_DEPRECATIONS[option][0])
             warn(msg)
-            option = CONFIG_DEPRECATIONS[option][0]
+            section, option = CONFIG_DEPRECATIONS[option][0].split('.')
 
         return self._config.set(section, option, value)
 
@@ -222,8 +225,8 @@ def resource_monitor(self):
             return self._resource_monitor
 
         # Cache config from nipype config
-        self.resource_monitor = self._config.get(
-            'execution', 'resource_monitor') or False
+        self.resource_monitor = str2bool(self._config.get(
+            'monitoring', 'enabled')) or False
         return self._resource_monitor
 
     @resource_monitor.setter
@@ -248,7 +251,7 @@ def resource_monitor(self, value):
                     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',
+                    self._config.set('monitoring', 'enabled',
                                      ('%s' % self._resource_monitor).lower())
 
     def enable_resource_monitor(self):

nipype/utils/profiler.py

@@ -2,7 +2,7 @@
 # @Author: oesteban
 # @Date:   2017-09-21 15:50:37
 # @Last Modified by:   oesteban
-# @Last Modified time: 2017-10-20 09:12:36
+# @Last Modified time: 2017-11-15 11:14:07
 """
 Utilities to keep track of performance
 """
@@ -202,8 +202,8 @@ def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False):
     """
 
     if not resource_monitor:
-        raise RuntimeError('Attempted to measure resources with '
-                           '"resource_monitor" set off.')
+        raise RuntimeError('Attempted to measure resources with option '
+                           '"monitoring.enabled" set off.')
 
     try:
         mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc))