Documentation correction and improvements with methodology (EN)

[modules/adao.git] / doc / en / advanced.rst

..
   Copyright (C) 2008-2017 EDF R&D

   This file is part of SALOME ADAO module.

   This library is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public
   License as published by the Free Software Foundation; either
   version 2.1 of the License, or (at your option) any later version.

   This library is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
   Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public
   License along with this library; if not, write to the Free Software
   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA

   See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com

   Author: Jean-Philippe Argaud, jean-philippe.argaud@edf.fr, EDF R&D

.. _section_advanced:

================================================================================
**[DocU]** Advanced usage of the ADAO module
================================================================================

This section presents advanced methods to use the ADAO module, how to get more
information during calculation, or how to use it without the graphical user
interface (GUI). It requires to know how to find files or commands included
inside the whole SALOME installation. All the names to be replaced by user are
indicated by the syntax ``<...>``.

Converting and executing an ADAO command file (JDC) using a Shell script
------------------------------------------------------------------------

It is possible to convert and execute an ADAO command file (JDC, or ".comm/.py"
files pair, which resides in ``<ADAO JDC file directory>``) automatically by
using a template Shell script containing all the required steps. If the SALOME
main launching command , named ``salome``, is not available in a classical
terminal, the user has to know where are the main SALOME launching files, and in
particular the ``salome`` one. The directory in which this script resides is
symbolically named ``<SALOME main installation dir>`` and has to be replaced by
the good one in the Shell file template.

When an ADAO command file is build by the ADAO graphical editor and saved, if it
is named for example "AdaoStudy1.comm", then a companion file named
"AdaoStudy1.py" is automatically created in the same directory. It is named
``<ADAO Python file>`` in the template, and it is converted to YACS as an
``<ADAO YACS xml scheme>`` as a ".xml" file named "AdaoStudy1.xml". After that,
this last one can be executed in console mode using the standard YACS console
command (see YACS documentation for more information).

In all launching command Shell files examples, we choose to start and stop the
SALOME application server in the same script. It is not mandatory, but it is
useful to avoid stalling SALOME sessions. 

The simplest example consist in only launching the given YACS sheme, which was
previously generated by the user in the graphical interface. In this case, after
having replaced the strings between ``<...>`` symbols, one needs only to save
the following Shell script::

    #!/bin/bash
    USERDIR="<ADAO JDC file directory>"
    SALOMEDIR="<SALOME main installation directory>"
    $SALOMEDIR/salome start -k -t
    $SALOMEDIR/salome shell -- "driver $USERDIR/<ADAO YACS xml scheme>"
    $SALOMEDIR/salome shell killSalome.py

It is then required to change it to be in executable mode.

A more complete example consist in launching execution of a YACS scheme given by
the user, having previously verified its availability. For that, replacing the
text ``<SALOME main installation directory>``, one needs only to save the
following Shell script::

    #!/bin/bash
    if (test $# != 1)
    then
      echo -e "\nUsage: $0 <ADAO YACS xml scheme>\n"
      exit
    else
      USERFILE="$1"
    fi
    if (test ! -e $USERFILE)
    then
      echo -e "\nError : the XML file named $USERFILE does not exist.\n"
      exit
    else
      SALOMEDIR="<SALOME main installation directory>"
      $SALOMEDIR/salome start -k -t
      $SALOMEDIR/salome shell -- "driver $USERFILE"
      $SALOMEDIR/salome shell killSalome.py
    fi

An another example consist in adding the conversion of the ADAO command file
(JDC, or ".comm/.py" files pair) in an associated YACS scheme (".xml" file). At
the end of the script, one choose also to remove the ``<ADAO YACS xml scheme>``
because it is a generated file. For that, after having carefully replaced the
text ``<SALOME main installation directory>``, one needs only to save the
following Shell script::

    #!/bin/bash
    if (test $# != 1)
    then
      echo -e "\nUsage: $0 <ADAO .comm/.py case>\n"
      exit
    else
      D=`dirname $1`
      F=`basename -s .comm $1`
      F=`basename -s .py $F`
      USERFILE="$D/$F"
    fi
    if (test ! -e $USERFILE.py)
    then
      echo -e "\nError : the PY file named $USERFILE.py does not exist.\n"
      exit
    else
      SALOMEDIR="<SALOME main installation directory>"
      $SALOMEDIR/salome start -k -t
      $SALOMEDIR/salome shell -- "python $SALOMEDIR/bin/salome/AdaoYacsSchemaCreator.py $USERFILE.py $USERFILE.xml"
      $SALOMEDIR/salome shell -- "driver $USERFILE.xml"
      $SALOMEDIR/salome shell killSalome.py
      rm -f $USERFILE.xml
    fi

In all cases, the standard output and errors come in the launching terminal.

Running an ADAO calculation scheme in YACS using the text user mode (YACS TUI)
------------------------------------------------------------------------------

This section describes how to execute in TUI (Text User Interface) YACS mode a
YACS calculation scheme, obtained in the graphical interface by using the ADAO
"Export to YACS" function. It uses the standard YACS TUI mode, which is briefly
recalled here (see YACS documentation for more information) through a simple
example. As described in documentation, a XML scheme can be loaded in a Python.
We give here a whole sequence of command lines to test the validity of the
scheme before executing it, adding some initial supplementary ones to explicitly
load the types catalog to avoid weird difficulties::

    import pilot
    import SALOMERuntime
    import loader
    SALOMERuntime.RuntimeSALOME_setRuntime()

    r = pilot.getRuntime()
    xmlLoader = loader.YACSLoader()
    xmlLoader.registerProcCataLoader()
    try:
     catalogAd = r.loadCatalog("proc", "<ADAO YACS xml scheme>")
    except:
      pass
    r.addCatalog(catalogAd)

    try:
        p = xmlLoader.load("<ADAO YACS xml scheme>")
    except IOError,ex:
        print "IO exception:",ex

    logger = p.getLogger("parser")
    if not logger.isEmpty():
        print "The imported file has errors :"
        print logger.getStr()

    if not p.isValid():
        print "The schema is not valid and can not be executed"
        print p.getErrorReport()

    info=pilot.LinkInfo(pilot.LinkInfo.ALL_DONT_STOP)
    p.checkConsistency(info)
    if info.areWarningsOrErrors():
        print "The schema is not consistent and can not be executed"
        print info.getGlobalRepr()

    e = pilot.ExecutorSwig()
    e.RunW(p)
    if p.getEffectiveState() != pilot.DONE:
        print p.getErrorReport()

This method allows for example to edit the YACS XML scheme in TUI, or to gather
results for further use.

.. _section_advanced_R:

Running an ADAO calculation in R environment using the TUI ADAO interface
-------------------------------------------------------------------------

.. index:: single: R
.. index:: single: rPython

To extend the analysis and treatment capacities, it is possible to use ADAO
calculations in **R** environment (see [R]_ for more details). It is available
in SALOME by launching the R interpreter in the shell "``salome shell``".
Moreover, the package "*rPython*" has to be available, it can be installed by
the user if required by the following R command::

    #-*-coding:iso-8859-1-*-
    #
    # IMPORTANT: to be run in R interpreter
    # -------------------------------------
    install.packages("rPython")

One will refer to the [GilBellosta15]_ documentation for more information on
this package.

The ADAO calculations defined in text interface (API/TUI, see
:ref:`section_tui`) can be interpreted from the R environment, using some data
and information from R. The approach is illustrated in the example
:ref:`subsection_tui_example`, suggested in the API/TUI interface description.
In the R interpreter, one can run the following commands, directly coming from
the simple example::

    #-*-coding:iso-8859-1-*-
    #
    # IMPORTANT: to be run in R interpreter
    # -------------------------------------
    library(rPython)
    python.exec("
        from numpy import array
        import adaoBuilder
        case = adaoBuilder.New()
        case.set( 'AlgorithmParameters', Algorithm='3DVAR' )
        case.set( 'Background',          Vector=[0, 1, 2] )
        case.set( 'BackgroundError',     ScalarSparseMatrix=1.0 )
        case.set( 'Observation',         Vector=array([0.5, 1.5, 2.5]) )
        case.set( 'ObservationError',    DiagonalSparseMatrix='1 1 1' )
        case.set( 'ObservationOperator', Matrix='1 0 0;0 2 0;0 0 3' )
        case.set( 'Observer',            Variable='Analysis', Template='ValuePrinter' )
        case.execute()
    ")

giving the result::

    Analysis [ 0.25000264  0.79999797  0.94999939]

In writing the ADAO calculations run from R, one must take close attention to
the good use of single and double quotes, that should not collide between the
two languages.

The data can come from the R environment and should be stored in properly
assigned variables to be used later in Python for ADAO. One will refer to the
[GilBellosta15]_ documentation for the implementation work. We can transform the
above example to use data from R to feed the three variables of background,
observation and observation operator. We get in the end the optimal state also
in a R variable. The other lines are identical. The example thus becomes::

    #-*-coding:iso-8859-1-*-
    #
    # IMPORTANT: to be run in R interpreter
    # -------------------------------------
    #
    # R variables
    # -----------
    xb <- 0:2
    yo <- c(0.5, 1.5, 2.5)
    h <- '1 0 0;0 2 0;0 0 3'
    #
    # Python code
    # -----------
    library(rPython)
    python.assign( "xb",  xb )
    python.assign( "yo",  yo )
    python.assign( "h",  h )
    python.exec("
        from numpy import array
        import adaoBuilder
        case = adaoBuilder.New()
        case.set( 'AlgorithmParameters', Algorithm='3DVAR' )
        case.set( 'Background',          Vector=xb )
        case.set( 'BackgroundError',     ScalarSparseMatrix=1.0 )
        case.set( 'Observation',         Vector=array(yo) )
        case.set( 'ObservationError',    DiagonalSparseMatrix='1 1 1' )
        case.set( 'ObservationOperator', Matrix=str(h) )
        case.set( 'Observer',            Variable='Analysis', Template='ValuePrinter' )
        case.execute()
        xa = list(case.get('Analysis')[-1])
    ")
    #
    # R variables
    # -----------
    xa <- python.get("xa")

One notices the explicit ``str`` and ``list`` type conversions to ensure that
the data are transmitted as known standard types from "*rPython*" package.
Moreover, it is the data that can be transferred between the two languages, not
functions or methods. It is therefore necessary to prepare generically in Python
the functions to execute required by ADAO, and to forward them correctly the
data available in R.

The most comprehensive cases, proposed in :ref:`subsection_tui_advanced`, can be
executed in the same way, and they give the same result as in the standard
Python interface.

.. _section_advanced_observer:

Getting information on special variables during the ADAO calculation in YACS
-----------------------------------------------------------------------------

.. index:: single: Observer
.. index:: single: Observer Template

Some special internal optimization variables, used during calculations, can be
monitored during the ADAO calculation. These variables can be printed,
plotted, saved, etc. This can be done using "*observer*", that are scripts,
each associated with one variable.

Some templates are available when editing the ADAO case in graphical editor.
These simple scripts can be customized by the user, either at the embedded
edition stage, or at the edition stage before execution, to improve the tuning
of the ADAO calculation.

To implement these "*observer*" efficiently, one can look to the 
:ref:`ref_observers_requirements`.

Getting more information when running a calculation
---------------------------------------------------

.. index:: single: Logging

When running a calculation, useful data and messages are logged. There are two
ways to obtain theses information.

The first one, and the preferred way, is to use the built-in variable "*Debug*"
available in every ADAO case. It is available through the edition GUI of the
module. Setting it to "*1*" will send messages in the log window of the YACS
scheme execution.

The second one consist in using the "*logging*" native module of Python (see the
Python documentation http://docs.python.org/library/logging.html for more
information on this module). Everywhere in the YACS scheme, mainly through the
scripts entries, the user can set the logging level in accordance to the needs
of detailed information. The different logging levels are: "*DEBUG*", "*INFO*",
"*WARNING*", "*ERROR*", "*CRITICAL*". All the information flagged with a
certain level will be printed for whatever activated level above this particular
one (included). The easiest way is to change the log level by using the
following Python lines::

    import logging
    logging.getLogger().setLevel(logging.DEBUG)

The standard logging module default level is "*WARNING*", the default level in
the ADAO module is "*INFO*". 

It is also recommended to include some logging or debug mechanisms in the
simulation code, and use them in conjunction with the two previous methods. But
be careful not to store too big variables because it cost time, whatever logging
level is chosen (that is, even if these variables are not printed).

.. _subsection_ref_parallel_df:

Accelerating numerical derivatives calculations by using a parallel mode
------------------------------------------------------------------------

.. index:: single: EnableMultiProcessing
.. index:: single: NumberOfProcesses

When setting an operator, as described in
:ref:`section_ref_operator_requirements`, the user can choose a functional form
"*ScriptWithOneFunction*". This form explicitly leads to approximate the tangent
and adjoint operators by a finite differences calculation. It requires several
calls to the direct operator (user defined function), at least as many times as
the dimension of the state vector. This are these calls that can potentially be
executed in parallel.

Under some conditions, it is then possible to accelerate the numerical
derivatives calculations by using a parallel mode for the finite differences
approximation. When setting up an ADAO case, it is done by adding the optional
keyword "*EnableMultiProcessing*", set to "1", for the "*SCRIPTWITHONEFUNCTION*"
command in the operator definition. The parallel mode will only use local
resources (both multi-cores or multi-processors) of the computer on which SALOME
is running, requiring as many resources as available. If necessary, one can
reduce the available ressources by limiting the possible number of parallel
processes using the keyword "*NumberOfProcesses*", set to desired maximum (or to
"0" for automatic control, which is the default value). By default, this
parallel mode is disabled ("*EnableMultiProcessing=0*").

The main conditions to perform parallel calculations come from the user defined
function, that represents the direct operator. This function has at least to be
"thread safe" to be executed in Python parallel environment (notions out of
scope of this paragraph). It is not obvious to give general rules, so it's
recommended, for the user who enable this internal parallelism, to carefully
verify his function and the obtained results.

From a user point of view, some conditions, that have to be met to set up
parallel calculations for tangent and the adjoint operators approximations, are
the following ones:

#. The dimension of the state vector is more than 2 or 3.
#. Unitary calculation of user defined direct function "last for long time", that is, more than few minutes.
#. The user defined direct function does not already use parallelism (or parallel execution is disabled in the user calculation).
#. The user defined direct function avoids read/write access to common resources, mainly stored data, output files or memory capacities.
#. The "*observer*" added by the user avoid read/write access to common resources, such as files or memory.

If these conditions are satisfied, the user can choose to enable the internal
parallelism for the numerical derivative calculations. Despite the simplicity of
activating, by setting one variable only, the user is urged to verify the
results of its calculations. One must at least doing them one time with
parallelism enabled, and an another time with parallelism disabled, to compare
the results. If it does fail somewhere, you have to know that this parallel
scheme is working for complex codes, like *Code_Aster* in *SalomeMeca*
[SalomeMeca]_ for example. So, if it does not work in your case, check your
operator function before and during enabling parallelism...

.. warning::

  in case of doubt, it is recommended NOT TO ACTIVATE this parallelism.

It is also recalled that one have to choose the type "*multi*" for the default
container in order to launch the scheme, to allow a really parallel execution.

Switching from a version of ADAO to a newer one
-----------------------------------------------

.. index:: single: Version

The ADAO module and its ".comm" case files are identified by versions, with
"Major", "Minor" and "Revision" characteristics. A particular version is
numbered as "Major.Minor.Revision", with strong link with the numbering of the
SALOME platform.

Each version "Major.Minor.Revision" of the ADAO module can read ADAO case files
of the previous minor version "Major.Minor-1.*". In general, it can also read
ADAO case files of all the previous minor versions for one major branch, but it
is not guaranteed for all the commands or keywords. In general also, an ADAO
case file for one version can not be read by a previous minor or major version
of the ADAO module.

Switching from 8.x to 8.y with x < y
++++++++++++++++++++++++++++++++++++

There is no known incompatibility for the ADAO case files. The upgrade procedure
is to read the old ADAO case file with the new SALOME/ADAO module, and save it
with a new name.

To make future developments easier, it is strongly recommended to ensure that
your user scripts files use a Python 2 and a Python 3 compatible syntax. In
particular, it is recommended to use the functional syntax for "*print*" and not
the "*command*" syntax, for example:

    # Python 2 & 3
    x, unit = 1., "cm"
    print( "x = %s %s"%(str(x),str(unit)) )

or::

    # Python 2 & 3
    x, unit = 1., "cm"
    print( "x = {0} {1}".format(str(x),str(unit)) )

rather than::

    # Python 2 only
    x, unit = 1., "cm"
    print "x =", x, unit

Switching from 7.8 to 8.1
+++++++++++++++++++++++++

There is no known incompatibility for the ADAO case files. The upgrade procedure
is to read the old ADAO case file with the new SALOME/ADAO module, and save it
with a new name.

Switching from 7.x to 7.y with x < y
++++++++++++++++++++++++++++++++++++

There is no known incompatibility for the ADAO case files. The upgrade procedure
is to read the old ADAO case file with the new SALOME/ADAO module, and save it
with a new name.

Switching from 6.6 to 7.2
+++++++++++++++++++++++++

There is no known incompatibility for the ADAO case files. The upgrade procedure
is to read the old ADAO case file with the new SALOME/ADAO module, and save it
with a new name.

There is one incompatibility introduced for the post-processing or observer
script files. The old syntax to call a result object, such as the "*Analysis*"
one (in a script provided through the "*UserPostAnalysis*" keyword), was for
example::

    Analysis = ADD.get("Analysis").valueserie(-1)
    Analysis = ADD.get("Analysis").valueserie()

The new syntax is entirely similar to the (classical) one of a list or tuple
object::

    Analysis = ADD.get("Analysis")[-1]
    Analysis = ADD.get("Analysis")[:]

The post-processing scripts has to be modified.

Switching from 6.x to 6.y with x < y
++++++++++++++++++++++++++++++++++++

There is no known incompatibility for the ADAO case file. The upgrade procedure
is to read the old ADAO case file with the new SALOME/ADAO module, and save it
with a new name.

There is one incompatibility introduced for the operator script files, in the
naming of operators used to for the observation operator. The new mandatory
names are "*DirectOperator*", "*TangentOperator*" and "*AdjointOperator*", as
described in the last subsection of the chapter :ref:`section_reference`. The
operator script files has to be modified.