@@ -14,93 +14,97 @@ Logging
1414~~~~~~~
1515
1616*workflow_level *
17- How detailed the logs regarding workflow should be (possible values:
18- ``INFO `` and ``DEBUG ``; default value: ``INFO ``)
19- *filemanip_level *
20- How detailed the logs regarding file operations (for example overwriting
21- warning) should be (possible values: ``INFO `` and ``DEBUG ``; default value:
22- ``INFO ``)
17+ How detailed the logs regarding workflow should be (possible values:
18+ ``INFO `` and ``DEBUG ``; default value: ``INFO ``)
19+ *utils_level *
20+ How detailed the logs regarding nipype utils, like file operations
21+ (for example overwriting warning) or the resource profiler, should be
22+ (possible values: ``INFO `` and ``DEBUG ``; default value:
23+ ``INFO ``)
2324*interface_level *
24- How detailed the logs regarding interface execution should be (possible
25- values: ``INFO `` and ``DEBUG ``; default value: ``INFO ``)
25+ How detailed the logs regarding interface execution should be (possible
26+ values: ``INFO `` and ``DEBUG ``; default value: ``INFO ``)
27+ *filemanip_level * (deprecated as of 1.0)
28+ How detailed the logs regarding file operations (for example overwriting
29+ warning) should be (possible values: ``INFO `` and ``DEBUG ``)
2630*log_to_file *
2731 Indicates whether logging should also send the output to a file (possible
2832 values: ``true `` and ``false ``; default value: ``false ``)
2933*log_directory *
30- Where to store logs. (string, default value: home directory)
34+ Where to store logs. (string, default value: home directory)
3135*log_size *
32- Size of a single log file. (integer, default value: 254000)
36+ Size of a single log file. (integer, default value: 254000)
3337*log_rotate *
34- How many rotation should the log file make. (integer, default value: 4)
38+ How many rotation should the log file make. (integer, default value: 4)
3539
3640Execution
3741~~~~~~~~~
3842
3943*plugin *
40- This defines which execution plugin to use. (possible values: ``Linear ``,
41- ``MultiProc ``, ``SGE ``, ``IPython ``; default value: ``Linear ``)
44+ This defines which execution plugin to use. (possible values: ``Linear ``,
45+ ``MultiProc ``, ``SGE ``, ``IPython ``; default value: ``Linear ``)
4246
4347*stop_on_first_crash *
44- Should the workflow stop upon first node crashing or try to execute as many
45- nodes as possible? (possible values: ``true `` and ``false ``; default value:
46- ``false ``)
48+ Should the workflow stop upon first node crashing or try to execute as many
49+ nodes as possible? (possible values: ``true `` and ``false ``; default value:
50+ ``false ``)
4751
4852*stop_on_first_rerun *
49- Should the workflow stop upon first node trying to recompute (by that we
50- mean rerunning a node that has been run before - this can happen due changed
51- inputs and/or hash_method since the last run). (possible values: ``true ``
52- and ``false ``; default value: ``false ``)
53+ Should the workflow stop upon first node trying to recompute (by that we
54+ mean rerunning a node that has been run before - this can happen due changed
55+ inputs and/or hash_method since the last run). (possible values: ``true ``
56+ and ``false ``; default value: ``false ``)
5357
5458*hash_method *
55- Should the input files be checked for changes using their content (slow, but
56- 100% accurate) or just their size and modification date (fast, but
57- potentially prone to errors)? (possible values: ``content `` and
58- ``timestamp ``; default value: ``timestamp ``)
59+ Should the input files be checked for changes using their content (slow, but
60+ 100% accurate) or just their size and modification date (fast, but
61+ potentially prone to errors)? (possible values: ``content `` and
62+ ``timestamp ``; default value: ``timestamp ``)
5963
6064*keep_inputs *
6165 Ensures that all inputs that are created in the nodes working directory are
6266 kept after node execution (possible values: ``true `` and ``false ``; default
6367 value: ``false ``)
6468
6569*single_thread_matlab *
66- Should all of the Matlab interfaces (including SPM) use only one thread?
67- This is useful if you are parallelizing your workflow using MultiProc or
68- IPython on a single multicore machine. (possible values: ``true `` and
69- ``false ``; default value: ``true ``)
70+ Should all of the Matlab interfaces (including SPM) use only one thread?
71+ This is useful if you are parallelizing your workflow using MultiProc or
72+ IPython on a single multicore machine. (possible values: ``true `` and
73+ ``false ``; default value: ``true ``)
7074
7175*display_variable *
72- What ``DISPLAY `` variable should all command line interfaces be
73- run with. This is useful if you are using `xnest
74- <http://www.x.org/archive/X11R7.5/doc/man/man1/Xnest.1.html> `_
75- or `Xvfb <http://www.x.org/archive/X11R6.8.1/doc/Xvfb.1.html >`_
76- and you would like to redirect all spawned windows to
77- it. (possible values: any X server address; default value: not
78- set)
76+ What ``DISPLAY `` variable should all command line interfaces be
77+ run with. This is useful if you are using `xnest
78+ <http://www.x.org/archive/X11R7.5/doc/man/man1/Xnest.1.html> `_
79+ or `Xvfb <http://www.x.org/archive/X11R6.8.1/doc/Xvfb.1.html >`_
80+ and you would like to redirect all spawned windows to
81+ it. (possible values: any X server address; default value: not
82+ set)
7983
8084*remove_unnecessary_outputs *
81- This will remove any interface outputs not needed by the workflow. If the
82- required outputs from a node changes, rerunning the workflow will rerun the
83- node. Outputs of leaf nodes (nodes whose outputs are not connected to any
84- other nodes) will never be deleted independent of this parameter. (possible
85- values: ``true `` and ``false ``; default value: ``true ``)
85+ This will remove any interface outputs not needed by the workflow. If the
86+ required outputs from a node changes, rerunning the workflow will rerun the
87+ node. Outputs of leaf nodes (nodes whose outputs are not connected to any
88+ other nodes) will never be deleted independent of this parameter. (possible
89+ values: ``true `` and ``false ``; default value: ``true ``)
8690
8791*try_hard_link_datasink *
88- When the DataSink is used to produce an orginized output file outside
89- of nipypes internal cache structure, a file system hard link will be
90- attempted first. A hard link allow multiple file paths to point to the
91- same physical storage location on disk if the conditions allow. By
92- refering to the same physical file on disk (instead of copying files
93- byte-by-byte) we can avoid unnecessary data duplication. If hard links
94- are not supported for the source or destination paths specified, then
95- a standard byte-by-byte copy is used. (possible values: ``true `` and
96- ``false ``; default value: ``true ``)
92+ When the DataSink is used to produce an orginized output file outside
93+ of nipypes internal cache structure, a file system hard link will be
94+ attempted first. A hard link allow multiple file paths to point to the
95+ same physical storage location on disk if the conditions allow. By
96+ refering to the same physical file on disk (instead of copying files
97+ byte-by-byte) we can avoid unnecessary data duplication. If hard links
98+ are not supported for the source or destination paths specified, then
99+ a standard byte-by-byte copy is used. (possible values: ``true `` and
100+ ``false ``; default value: ``true ``)
97101
98102*use_relative_paths *
99- Should the paths stored in results (and used to look for inputs)
100- be relative or absolute. Relative paths allow moving the whole
101- working directory around but may cause problems with
102- symlinks. (possible values: ``true `` and ``false ``; default
103- value: ``false ``)
103+ Should the paths stored in results (and used to look for inputs)
104+ be relative or absolute. Relative paths allow moving the whole
105+ working directory around but may cause problems with
106+ symlinks. (possible values: ``true `` and ``false ``; default
107+ value: ``false ``)
104108
105109*local_hash_check *
106110 Perform the hash check on the job submission machine. This option minimizes
@@ -115,10 +119,10 @@ Execution
115119 done after a job finish is detected. (float in seconds; default value: 5)
116120
117121*remove_node_directories (EXPERIMENTAL) *
118- Removes directories whose outputs have already been used
119- up. Doesn't work with IdentiInterface or any node that patches
120- data through (without copying) (possible values: ``true `` and
121- ``false ``; default value: ``false ``)
122+ Removes directories whose outputs have already been used
123+ up. Doesn't work with IdentiInterface or any node that patches
124+ data through (without copying) (possible values: ``true `` and
125+ ``false ``; default value: ``false ``)
122126
123127*stop_on_unknown_version *
124128 If this is set to True, an underlying interface will raise an error, when no
@@ -146,18 +150,27 @@ Execution
146150 crashfiles allow portability across machines and shorter load time.
147151 (possible values: ``pklz `` and ``txt ``; default value: ``pklz ``)
148152
153+ *resource_monitor *
154+ Enables monitoring the resources occupation (possible values: ``true `` and
155+ ``false ``; default value: ``false ``)
156+
157+ *resource_monitor_frequency *
158+ Sampling period (in seconds) between measurements of resources (memory, cpus)
159+ being used by an interface. Requires ``resource_monitor `` to be ``true ``.
160+ (default value: ``1 ``)
161+
149162Example
150163~~~~~~~
151164
152165::
153166
154- [logging]
155- workflow_level = DEBUG
167+ [logging]
168+ workflow_level = DEBUG
156169
157- [execution]
158- stop_on_first_crash = true
159- hash_method = timestamp
160- display_variable = :1
170+ [execution]
171+ stop_on_first_crash = true
172+ hash_method = timestamp
173+ display_variable = :1
161174
162175Workflow.config property has a form of a nested dictionary reflecting the
163176structure of the .cfg file.
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