2 Copyright (C) 2008-2019 EDF R&D
4 This file is part of SALOME ADAO module.
6 This library is free software; you can redistribute it and/or
7 modify it under the terms of the GNU Lesser General Public
8 License as published by the Free Software Foundation; either
9 version 2.1 of the License, or (at your option) any later version.
11 This library is distributed in the hope that it will be useful,
12 but WITHOUT ANY WARRANTY; without even the implied warranty of
13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
14 Lesser General Public License for more details.
16 You should have received a copy of the GNU Lesser General Public
17 License along with this library; if not, write to the Free Software
18 Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
20 See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com
22 Author: Jean-Philippe Argaud, jean-philippe.argaud@edf.fr, EDF R&D
26 ================================================================================
27 **[DocU]** Advanced usage of the ADAO module
28 ================================================================================
30 This section presents advanced methods to use the ADAO module, how to get more
31 information during calculation, or how to use it without the graphical user
32 interface (GUI). It requires to know how to find files or commands included
33 inside the whole SALOME installation. All the names to be replaced by user are
34 indicated by the syntax ``<...>``.
36 Converting and executing an ADAO command file (JDC) using a Shell script
37 ------------------------------------------------------------------------
39 It is possible to convert and execute an ADAO command file (JDC, or ".comm/.py"
40 files pair, which resides in ``<ADAO JDC file directory>``) automatically by
41 using a template Shell script containing all the required steps. If the SALOME
42 main launching command , named ``salome``, is not available in a classical
43 terminal, the user has to know where are the main SALOME launching files, and in
44 particular the ``salome`` one. The directory in which this script resides is
45 symbolically named ``<SALOME main installation dir>`` and has to be replaced by
46 the good one in the Shell file template.
48 When an ADAO command file is build by the ADAO graphical editor and saved, if it
49 is named for example "AdaoStudy1.comm", then a companion file named
50 "AdaoStudy1.py" is automatically created in the same directory. It is named
51 ``<ADAO Python file>`` in the template, and it is converted to YACS as an
52 ``<ADAO YACS xml scheme>`` as a ".xml" file named "AdaoStudy1.xml". After that,
53 this last one can be executed in console mode using the standard YACS console
54 command (see YACS documentation for more information).
56 In all launching command Shell files examples, we choose to start and stop the
57 SALOME application server in the same script. It is not mandatory, but it is
58 useful to avoid stalling SALOME sessions.
60 The simplest example consist in only launching the given YACS sheme, which was
61 previously generated by the user in the graphical interface. In this case, after
62 having replaced the strings between ``<...>`` symbols, one needs only to save
63 the following Shell script::
66 USERDIR="<ADAO JDC file directory>"
67 SALOMEDIR="<SALOME main installation directory>"
68 $SALOMEDIR/salome start -k -t
69 $SALOMEDIR/salome shell -- "driver $USERDIR/<ADAO YACS xml scheme>"
70 $SALOMEDIR/salome shell killSalome.py
72 It is then required to change it to be in executable mode.
74 A more complete example consist in launching execution of a YACS scheme given by
75 the user, having previously verified its availability. For that, replacing the
76 text ``<SALOME main installation directory>``, one needs only to save the
77 following Shell script::
82 echo -e "\nUsage: $0 <ADAO YACS xml scheme>\n"
87 if (test ! -e $USERFILE)
89 echo -e "\nError : the XML file named $USERFILE does not exist.\n"
92 SALOMEDIR="<SALOME main installation directory>"
93 $SALOMEDIR/salome start -k -t
94 $SALOMEDIR/salome shell -- "driver $USERFILE"
95 $SALOMEDIR/salome shell killSalome.py
98 An another example consist in adding the conversion of the ADAO command file
99 (JDC, or ".comm/.py" files pair) in an associated YACS scheme (".xml" file). At
100 the end of the script, one choose also to remove the ``<ADAO YACS xml scheme>``
101 because it is a generated file. For that, after having carefully replaced the
102 text ``<SALOME main installation directory>``, one needs only to save the
103 following Shell script::
108 echo -e "\nUsage: $0 <ADAO .comm/.py case>\n"
112 F=`basename -s .comm $1`
113 F=`basename -s .py $F`
116 if (test ! -e $USERFILE.py)
118 echo -e "\nError : the PY file named $USERFILE.py does not exist.\n"
121 SALOMEDIR="<SALOME main installation directory>"
122 $SALOMEDIR/salome start -k -t
123 $SALOMEDIR/salome shell -- "python $SALOMEDIR/bin/AdaoYacsSchemaCreator.py $USERFILE.py $USERFILE.xml"
124 $SALOMEDIR/salome shell -- "driver $USERFILE.xml"
125 $SALOMEDIR/salome shell killSalome.py
129 In all cases, the standard output and errors come in the launching terminal.
131 Running an ADAO calculation scheme in YACS using the text user mode (YACS TUI)
132 ------------------------------------------------------------------------------
134 This section describes how to execute in TUI (Text User Interface) YACS mode a
135 YACS calculation scheme, obtained in the graphical interface by using the ADAO
136 "Export to YACS" function. It uses the standard YACS TUI mode, which is briefly
137 recalled here (see YACS documentation for more information) through a simple
138 example. As described in documentation, a XML scheme can be loaded in a Python.
139 We give here a whole sequence of command lines to test the validity of the
140 scheme before executing it, adding some initial supplementary ones to explicitly
141 load the types catalog to avoid weird difficulties::
146 SALOMERuntime.RuntimeSALOME_setRuntime()
148 r = pilot.getRuntime()
149 xmlLoader = loader.YACSLoader()
150 xmlLoader.registerProcCataLoader()
152 catalogAd = r.loadCatalog("proc", "<ADAO YACS xml scheme>")
153 r.addCatalog(catalogAd)
158 p = xmlLoader.load("<ADAO YACS xml scheme>")
160 print("IO exception:",ex)
162 logger = p.getLogger("parser")
163 if not logger.isEmpty():
164 print("The imported file has errors :")
165 print(logger.getStr())
168 print("The schema is not valid and can not be executed")
169 print(p.getErrorReport())
171 info=pilot.LinkInfo(pilot.LinkInfo.ALL_DONT_STOP)
172 p.checkConsistency(info)
173 if info.areWarningsOrErrors():
174 print("The schema is not consistent and can not be executed")
175 print(info.getGlobalRepr())
177 e = pilot.ExecutorSwig()
179 if p.getEffectiveState() != pilot.DONE:
180 print(p.getErrorReport())
182 This method allows for example to edit the YACS XML scheme in TUI, or to gather
183 results for further use.
185 .. _section_advanced_R:
187 Running an ADAO calculation in R environment using the TUI ADAO interface
188 -------------------------------------------------------------------------
191 .. index:: single: rPython
193 To extend the analysis and treatment capacities, it is possible to use ADAO
194 calculations in **R** environment (see [R]_ for more details). It is available
195 in SALOME by launching the R interpreter in the shell "``salome shell``".
196 Moreover, the package "*rPython*" has to be available, it can be installed by
197 the user if required by the following R command::
200 # IMPORTANT: to be run in R interpreter
201 # -------------------------------------
202 install.packages("rPython")
204 One will refer to the [GilBellosta15]_ documentation for more information on
207 The ADAO calculations defined in text interface (API/TUI, see
208 :ref:`section_tui`) can be interpreted from the R environment, using some data
209 and information from R. The approach is illustrated in the example
210 :ref:`subsection_tui_example`, suggested in the API/TUI interface description.
211 In the R interpreter, one can run the following commands, directly coming from
215 # IMPORTANT: to be run in R interpreter
216 # -------------------------------------
219 from numpy import array
220 from adao import adaoBuilder
221 case = adaoBuilder.New()
222 case.set( 'AlgorithmParameters', Algorithm='3DVAR' )
223 case.set( 'Background', Vector=[0, 1, 2] )
224 case.set( 'BackgroundError', ScalarSparseMatrix=1.0 )
225 case.set( 'Observation', Vector=array([0.5, 1.5, 2.5]) )
226 case.set( 'ObservationError', DiagonalSparseMatrix='1 1 1' )
227 case.set( 'ObservationOperator', Matrix='1 0 0;0 2 0;0 0 3' )
228 case.set( 'Observer', Variable='Analysis', Template='ValuePrinter' )
234 Analysis [ 0.25000264 0.79999797 0.94999939]
236 In writing the ADAO calculations run from R, one must take close attention to
237 the good use of single and double quotes, that should not collide between the
240 The data can come from the R environment and should be stored in properly
241 assigned variables to be used later in Python for ADAO. One will refer to the
242 [GilBellosta15]_ documentation for the implementation work. We can transform the
243 above example to use data from R to feed the three variables of background,
244 observation and observation operator. We get in the end the optimal state also
245 in a R variable. The other lines are identical. The example thus becomes::
248 # IMPORTANT: to be run in R interpreter
249 # -------------------------------------
254 yo <- c(0.5, 1.5, 2.5)
255 h <- '1 0 0;0 2 0;0 0 3'
260 python.assign( "xb", xb )
261 python.assign( "yo", yo )
262 python.assign( "h", h )
264 from numpy import array
265 from adao import adaoBuilder
266 case = adaoBuilder.New()
267 case.set( 'AlgorithmParameters', Algorithm='3DVAR' )
268 case.set( 'Background', Vector=xb )
269 case.set( 'BackgroundError', ScalarSparseMatrix=1.0 )
270 case.set( 'Observation', Vector=array(yo) )
271 case.set( 'ObservationError', DiagonalSparseMatrix='1 1 1' )
272 case.set( 'ObservationOperator', Matrix=str(h) )
273 case.set( 'Observer', Variable='Analysis', Template='ValuePrinter' )
275 xa = list(case.get('Analysis')[-1])
280 xa <- python.get("xa")
282 One notices the explicit ``str`` and ``list`` type conversions to ensure that
283 the data are transmitted as known standard types from "*rPython*" package.
284 Moreover, it is the data that can be transferred between the two languages, not
285 functions or methods. It is therefore necessary to prepare generically in Python
286 the functions to execute required by ADAO, and to forward them correctly the
289 The most comprehensive cases, proposed in :ref:`subsection_tui_advanced`, can be
290 executed in the same way, and they give the same result as in the standard
293 .. _section_advanced_execution_mode:
295 Change the default execution mode of nodes in YACS
296 --------------------------------------------------
298 .. index:: single: YACS
300 Various reasons may lead to want to change the default mode of node execution
301 in YACS (see [#]_ for the correct use of these possibilities). This may be for
302 performance reasons, or for example for reasons of resource conflicts.
304 One may want to use this change in execution mode to extend the use of local
305 computing resources or to set remote calculations for a node that requires it.
306 This is particularly the case for a node that should use a simulation resource
307 available on a cluster, for example.
309 In addition, the various calculations that are carried out (user-provided
310 operators, results retrieval functions, etc.) may also present conflicts if
311 they are performed in a single process, and in particular in the main process
312 of SALOME. This is the default YACS operating mode for performance and
313 simplicity reasons. However, it is recommended to change this functioning when
314 encountering execution instabilities or error messages in the graphical
317 In any case, in the YACS schema being edited, it is sufficient to change the
318 execution mode of the node(s) that require it. They have to be executed in a
319 new container created for the occasion (it is not enough to use the default
320 container, it is explicitly necessary to create a new one) and whose properties
321 are adapted to the intended use. The procedure is therefore as follows:
323 #. Create a new YACS container, using the context menu in the tree view of the YACS schema (usually on the left),
324 #. Adapt the characteristics of the container, for example by selecting a "*type*" property with the value "*multi*" for a truly parallel execution, or by choosing a remote computing resource defined by the "*Resource*" property, or by using advanced parameters,
325 #. Graphically select in the central view the node whose execution mode you want to change,
326 #. In the panel to the right of the node entries, unfold the execution choices (named "*Execution Mode*"), check the "*Container*" box instead of the "*YACS*" default, and choose the newly created container (it is usually named "*container0*"),
327 #. Save the modified schema
329 This can be repeated for each node that requires it, by reusing the same new
330 container for all nodes, or by creating a new container for each node.
334 this change in execution mode is extremely powerful and flexible. It is
335 therefore recommended that the user both use it, and at the same time be
336 attentive to the interaction of the different choices he makes, to avoid, for
337 example, an unintended performance deterioration, or computer conflicts that
338 are complicated to diagnose.
340 .. _section_advanced_observer:
342 Getting information on special variables during the ADAO calculation
343 --------------------------------------------------------------------
345 .. index:: single: Observer
346 .. index:: single: Observer Template
348 Some special internal optimization variables, used during calculations, can be
349 monitored during the ADAO calculation. These variables can be printed, plotted,
350 saved, etc. This can be done using "*observer*", that are commands gathered in
351 scripts, each associated with one variable.
353 Some templates are available when editing the ADAO case in graphical editor.
354 These simple scripts can be customized by the user, either at the embedded
355 edition stage, or at the edition stage before execution, to improve the tuning
356 of the ADAO calculation.
358 To implement these "*observer*" efficiently, one can look to the
359 :ref:`section_ref_observers_requirements`.
361 Getting more information when running a calculation
362 ---------------------------------------------------
364 .. index:: single: Logging
366 When running a calculation, useful data and messages are logged. There are two
367 ways to obtain theses information.
369 The first one, and the preferred way, is to use the built-in variable "*Debug*"
370 available in every ADAO case. It is available through the edition GUI of the
371 module. Setting it to "*1*" will send messages in the log window of the YACS
374 The second one consist in using the "*logging*" native module of Python (see the
375 Python documentation http://docs.python.org/library/logging.html for more
376 information on this module). Everywhere in the YACS scheme, mainly through the
377 scripts entries, the user can set the logging level in accordance to the needs
378 of detailed information. The different logging levels are: "*DEBUG*", "*INFO*",
379 "*WARNING*", "*ERROR*", "*CRITICAL*". All the information flagged with a
380 certain level will be printed for whatever activated level above this particular
381 one (included). The easiest way is to change the log level by using the
382 following Python lines::
385 logging.getLogger().setLevel(logging.DEBUG)
387 The standard logging module default level is "*WARNING*", the default level in
388 the ADAO module is "*INFO*".
390 It is also recommended to include some logging or debug mechanisms in the
391 simulation code, and use them in conjunction with the two previous methods. But
392 be careful not to store too big variables because it cost time, whatever logging
393 level is chosen (that is, even if these variables are not printed).
395 .. _subsection_ref_parallel_df:
397 Accelerating numerical derivatives calculations by using a parallel mode
398 ------------------------------------------------------------------------
400 .. index:: single: EnableMultiProcessing
401 .. index:: single: NumberOfProcesses
403 When setting an operator, as described in
404 :ref:`section_ref_operator_requirements`, the user can choose a functional form
405 "*ScriptWithOneFunction*". This form explicitly leads to approximate the tangent
406 and adjoint operators by a finite differences calculation. It requires several
407 calls to the direct operator (user defined function), at least as many times as
408 the dimension of the state vector. This are these calls that can potentially be
409 executed in parallel.
411 Under some conditions, it is then possible to accelerate the numerical
412 derivatives calculations by using a parallel mode for the finite differences
413 approximation. When setting up an ADAO case, it is done by adding the optional
414 keyword "*EnableMultiProcessing*", set to "1", for the "*SCRIPTWITHONEFUNCTION*"
415 command in the operator definition. The parallel mode will only use local
416 resources (both multi-cores or multi-processors) of the computer on which SALOME
417 is running, requiring as many resources as available. If necessary, one can
418 reduce the available ressources by limiting the possible number of parallel
419 processes using the keyword "*NumberOfProcesses*", set to desired maximum (or to
420 "0" for automatic control, which is the default value). By default, this
421 parallel mode is disabled ("*EnableMultiProcessing=0*").
423 The main conditions to perform parallel calculations come from the user defined
424 function, that represents the direct operator. This function has at least to be
425 "thread safe" to be executed in Python parallel environment (notions out of
426 scope of this paragraph). It is not obvious to give general rules, so it's
427 recommended, for the user who enable this internal parallelism, to carefully
428 verify his function and the obtained results.
430 From a user point of view, some conditions, that have to be met to set up
431 parallel calculations for tangent and the adjoint operators approximations, are
434 #. The dimension of the state vector is more than 2 or 3.
435 #. Unitary calculation of user defined direct function "last for long time", that is, more than few minutes.
436 #. The user defined direct function does not already use parallelism (or parallel execution is disabled in the user calculation).
437 #. The user defined direct function avoids read/write access to common resources, mainly stored data, output files or memory capacities.
438 #. The "*observer*" added by the user avoid read/write access to common resources, such as files or memory.
440 If these conditions are satisfied, the user can choose to enable the internal
441 parallelism for the numerical derivative calculations. Despite the simplicity of
442 activating, by setting one variable only, the user is urged to verify the
443 results of its calculations. One must at least doing them one time with
444 parallelism enabled, and an another time with parallelism disabled, to compare
445 the results. If it does fail somewhere, you have to know that this parallel
446 scheme is working for complex codes, like *Code_Aster* in *SalomeMeca*
447 [SalomeMeca]_ for example. So, if it does not work in your case, check your
448 operator function before and during enabling parallelism...
452 in case of doubt, it is recommended NOT TO ACTIVATE this parallelism.
454 It is also recalled that one have to choose the type "*multi*" for the default
455 container in order to launch the scheme, to allow a really parallel execution.
457 Switching from a version of ADAO to a newer one
458 -----------------------------------------------
460 .. index:: single: Version
462 The ADAO module and its ".comm" case files are identified by versions, with
463 "Major", "Minor" and "Revision" characteristics. A particular version is
464 numbered as "Major.Minor.Revision", with strong link with the numbering of the
467 Each version "Major.Minor.Revision" of the ADAO module can read ADAO case files
468 of the previous minor version "Major.Minor-1.*". In general, it can also read
469 ADAO case files of all the previous minor versions for one major branch, but it
470 is not guaranteed for all the commands or keywords. In general also, an ADAO
471 case file for one version can not be read by a previous minor or major version
474 Switching from 9.x to 9.y with y > x
475 ++++++++++++++++++++++++++++++++++++
477 There is no known incompatibility for the ADAO case files. The upgrade procedure
478 is to read the old ADAO case file with the new SALOME/ADAO module, and save it
481 Switching from 8.5 to 9.2
482 +++++++++++++++++++++++++
484 There is no known incompatibility for the ADAO case files. The upgrade procedure
485 is to read the old ADAO case file with the new SALOME/ADAO module, and save it
488 However, there may be incompatibilities from user script files that would not
489 have a syntax compatible with Python 3. The most immediate error is the use of
490 printing "*print*" with "*command*" syntax instead of functional syntax
491 "*print(...)*". In this case, it is suggested to correct the syntax of user
492 files in environment 8 before switching to environment 9.
494 Switching from 8.x to 8.y with y > x
495 ++++++++++++++++++++++++++++++++++++
497 There is no known incompatibility for the ADAO case files. The upgrade procedure
498 is to read the old ADAO case file with the new SALOME/ADAO module, and save it
501 To make future developments easier, it is strongly recommended to ensure that
502 your user scripts files use a Python 2 and a Python 3 compatible syntax. In
503 particular, it is recommended to use the functional syntax for "*print*" and not
504 the "*command*" syntax, for example:
508 print( "x = %s %s"%(str(x),str(unit)) )
514 print( "x = {0} {1}".format(str(x),str(unit)) )
522 Switching from 7.8 to 8.1
523 +++++++++++++++++++++++++
525 There is no known incompatibility for the ADAO case files. The upgrade procedure
526 is to read the old ADAO case file with the new SALOME/ADAO module, and save it
529 Switching from 7.x to 7.y with y > x
530 ++++++++++++++++++++++++++++++++++++
532 There is no known incompatibility for the ADAO case files. The upgrade procedure
533 is to read the old ADAO case file with the new SALOME/ADAO module, and save it
536 Switching from 6.6 to 7.2
537 +++++++++++++++++++++++++
539 There is no known incompatibility for the ADAO case files. The upgrade procedure
540 is to read the old ADAO case file with the new SALOME/ADAO module, and save it
543 There is one incompatibility introduced for the post-processing or observer
544 script files. The old syntax to call a result object, such as the "*Analysis*"
545 one (in a script provided through the "*UserPostAnalysis*" keyword), was for
548 Analysis = ADD.get("Analysis").valueserie(-1)
549 Analysis = ADD.get("Analysis").valueserie()
551 The new syntax is entirely similar to the (classical) one of a list or tuple
554 Analysis = ADD.get("Analysis")[-1]
555 Analysis = ADD.get("Analysis")[:]
557 The post-processing scripts has to be modified.
559 Switching from 6.x to 6.y with y > x
560 ++++++++++++++++++++++++++++++++++++
562 There is no known incompatibility for the ADAO case file. The upgrade procedure
563 is to read the old ADAO case file with the new SALOME/ADAO module, and save it
566 There is one incompatibility introduced for the operator script files, in the
567 naming of operators used to for the observation operator. The new mandatory
568 names are "*DirectOperator*", "*TangentOperator*" and "*AdjointOperator*", as
569 described in the last subsection of the chapter :ref:`section_reference`. The
570 operator script files has to be modified.
572 .. [#] For more information on YACS, see the *YACS module* and its integrated help available from the main menu *Help* of the SALOME platform.