Sprint session 20 march 2008
A second sprintsession was held on March 20th, 2008, in the meeting room Innovation (how appropriate) of the new institute on Delta Technology Deltares.
Agenda
The meeting started with the following agenda:
The meeting starts at 9:00 (sharp - so be on time) with three brief presentations:
- 9:00 - 9:15 Mark van Koningsveld - Introduction
- 9:15 - 9:45 Bart Jan Kelter - setting of rights on and providing access to the subversion repositories
- 9:45 - 10:15 Pieter van Geer & Kees den Heijer - presentation on useful routines that are now in McTools
This time schedule is relatively strickt so that externally interested people will be able to join if they want to. After this the programme becomes flexible (an aspect that was evaluated positively by you last time).
The following items where suggested from the developersgroup:
- addition of Fortran routines to McTools, working with dll's: from Matlab to Fortran and vice versa (Gerben de Boer, Jan Kramer, Fedor Baart)
- discussion on the new duinerosion routines: strong points, status so far, implementation and use in other projects etc. (Kees den Heijer, Pieter van Geer, Ferdinand Diermanse, Mark van Koningsveld, Sander van Rooij)
- general maintenance of McTools (Robin Morelissen, Gerben de Boer, Kees den Heijer, Pieter van Geer, Mark van Koningsveld)
- discussion on upcoming coastal projects in the framework of Sandmotor and Weak link issues (PieterKoen Tonnon, Jan Mulder, Ap van Dongeren, Jaap van Thiel de Vries, Dano Roelvink, Mark van Koningsveld)
- discussion on the setup of an operational storm impact model for DC and MICORE (Deepak Vatvani, Mark van Koningsveld, Ap van Dongeren, Jaap van Thiel de Vries, Dano Roelvink)
Everyone is obviously free to join and contribute to each of these topics or to raise other items that are not on the agenda yet. It looks like it will be a very productive day. McTools is now at revision 759. Free dinner for the person to hit 1000!
Script demonstrating useful McTools applications (by Pieter and Kees)
clear all;fclose all;close all;clc cd f:\mctools\mc_toolbox; mcsettings addpath(fileparts(mfilename('fullpath'))); % edit getCalls getIsCalledBy getInputSize getInputVariables roundoff double2evalstr getFileName getVolume writemessage('init'); %% getInputVariables / getInputSize clear;fclose all;close all;clc quickstart internet d = readTransectData('Jarkus Data','Noord-Holland','03000','2006'); xInitial = d.xe(~isnan(d.ze)); %keep only the points with non-NaN z-values zInitial = d.ze(~isnan(d.ze)); %keep only the points with non-NaN z-values dbstop in getVolume at 42 dbstopcurrent [Volume, result, Boundaries] = getVolume(xInitial, zInitial); dbclear in getVolume at 42 dbstopcurrent writemessage(3,'Example of getInputVariables completed'); %% roundoff clear;fclose all;close all;clc X = 87643.7852; for n = -2:2:4 Xround = roundoff(X, n); disp(num2str(Xround)) end %% getdefaults dbstop in roundoff at 40 Xround = roundoff(X); dbclear in roundoff at 40 %% double2evalstr clear;fclose all;close all;clc dbstop in double2evalstr_test at 9 run double2evalstr_test dbstopcurrent dbstop getHsig_t_test at 30 dbstop getHsig_t_test at 41 run getHsig_t_test dbstopcurrent writemessage(4,'Example of double2evalstr_test completed'); %% getFileName clear;fclose all;close all;clc directory = 'D:\heijer\My Documents\Work\TU Delft\PhD project\Prob2B\ParametricStudy\DenHeijer2008\Case_10'; extension = 'txt'; exception = 'DP_Case_10_maxRD=068.7.txt'; fileid = []; dbstopcurrent fname = getFileName(directory, extension, exception, fileid) writemessage(5,'Example of getFileName completed'); %% writemessage writemessage(7,'Staring example of writemessage'); dbstopcurrent SavedMessages = writemessage('get') %% IsCalls fun = 'getDuneErosion_VTV2006'; directory = 'D:\heijer\My Documents\Program Files\McTools\mc_toolbox\mc_applications\mc_ucit\getDuneErosion\'; IsCalls = getCalls(fun, directory); IsCalls = getCalls(fun, directory, 'quiet'); dbstopcurrent writemessage(1,'Example of IsCalls completed'); %% IsCalledBy clear;fclose all;close all;clc fun = 'getVolume'; directory = 'D:\heijer\My Documents\Program Files\McTools\mc_toolbox\mc_applications\mc_ucit\getDuneErosion\'; [IsCalledBy, Line, Column] = getIsCalledBy(fun, directory); [IsCalledBy, Line, Column] = getIsCalledBy(fun, directory, 'quiet'); dbstopcurrent writemessage(2,'Example of IsCalledBy completed'); %% FD_GUI_figure cd( directory); run FD_GUI_figure dbstopcurrent writemessage(6,'Example of FD_GUI completed'); clc %% guidisp guidisp('set','FD_GUI_message_panel'); guidisp('test message panel'); guidisp('set',[]); guidisp('Test Command line'); dbstopcurrent writemessage(7,'Example of guidisp completed'); %% dbstate dbstop in getDuneErosion_test at 6 dbstop in getDuneErosion_VTV2006 at 12 getDuneErosion_test('VTV2006',1); dbstopcurrent writemessage(7,'Example of dbstate completed'); %% dbstopcurrent cd('D:\heijer\My Documents\Work\Deltares\Projects\McTools'); dbstopcurrent; pause(0.1); %% writemessage SavedMessages = writemessage('get') dbclear all
Interfacing with Fortran
To use fortran functions from matlab there are a few options:
- the loadlibrary method
- the mexfile method
- the swig method
The loadlibrary method
Prerequisites:
.so/.dll -> the dynamic library with the prebuild fortran code
.h -> the header file describing the functions and arguments in c notation
Fortran doesn't use text based header files but binary mod files. These are not recognized by matlab.
To generate the h files look in the dll or shared object what the naming convention generated. Type the names in the .h file. If you used fortran to generate the dll the names might and function arguments might be mangled. Also the function arguments might change. See the following example of a simple header file.
#ifdef __cplusplus extern "C" { #endif /* entry point declarations here */ __declspec( dllexport ) long fortomatint (long& , long&); # long fortomatint_ (long&, long&); \-> for g77 __declspec( dllexport ) float fortomatreal(float& , float&); #ifdef __cplusplus } /* end extern "C" */ #endif
This header file is applicable for the following fortran code when compiled to dll. Note that you have to add the compiler directives to your fortran code for every fortran function you want to be visible in the dll.
INTEGER*4 FUNCTION fortomat(val1,val2) !DEC$ ATTRIBUTES DLLEXPORT,ALIAS : "fortomat" :: fortomat INTEGER*4 val1,val2 FORTOMAT=val1*val2 END FUNCTION real*4 FUNCTION fortomatreal(val1,val2) !DEC$ ATTRIBUTES DLLEXPORT,ALIAS : "fortomatreal" :: fortomatreal real*4 val1,val2 fortomatreal=val1*val2 END FUNCTION
Use nm (linux) or depends (windows) to look inside a dynamic library.
To use the library within matlab you have to tell matlab about the library and the header file. Matlab should check if the naming convention used in the header file is consistent with the naming in the dll/so. See the following example:
if libisloaded('lib')~=1 if ispc loadlibrary endecdll.dll endecdll.h alias lib else % lunix loadlibrary libendecdll.so endecdll.h alias lib % \-> for linux end; %libfunctions lib libfunctions lib \-full %calllib('lib','fortomatint',5,5) %calllib('lib','fortomatreal',5.4,3.7) if libisloaded('lib')==1 unloadlibrary lib; end;
You can make matlab wrapper that loads the library, calls the function, and unloads the libray again. With this matlab wrapper, the matlab doe snot even need to be aware that he is calling a ddll:
function out = fortomat(var1,var2) %FORTOMAT % % fortomat(val1,val2) % where var* can be integer or float OPT.libname = 'ekufbqegjhbgoebgo'; OPT.dllname = 'endecdll.dll';; OPT.hdrname = 'endecdll.h' OPT.debug = 1; %% Load library %% ------------ if libisloaded(OPT.libaliasname)~=1 loadlibrary(OPT.dllname,OPT.hdrname,'alias',OPT.libname) end; %% Inquire library %% ------------ if OPT.debug libfunctions(OPT.libaliasname,'-full') end %% Call library function %% ------------ if isa(var1,'integer') && isa(var1,'integer') out = calllib(OPT.libname,'fortomat',var1,var2); elseif isa(var1,'float') && isa(var1,'float') out = calllib(OPT.libname,'fortomat',var1,var2); else error(['No matching datatype in ',]) end %% Unload library %% ------------ if libisloaded(OPT.libname)==1 unloadlibrary(OPT.libname); end; %% EOF
This method is described in detail at the mathworks site
The mexfile method
This method uses the mex files (matlab specific dll's) to communicate between matlab and fortran. You make fortran (or c) aware of the internals of matlab. You wrap your method with the matlab function calling method (lhs, rhs, etc...) .
Matlab Fortran
See a simple example.
C C CHECK FOR PROPER NUMBER OF ARGUMENTS C IF (NRHS .NE. 2) THEN CALL MEXERRMSGTXT('YPRIME requires two input arguments') ELSEIF (NLHS .GT. 1) THEN CALL MEXERRMSGTXT('YPRIME requires one output argument') ENDIF C C CHECK THE DIMENSIONS OF Y. IT CAN BE 4 X 1 OR 1 X 4. C M = MXGETM(PRHS(2)) N = MXGETN(PRHS(2)) C IF ((MAX(M,N) .NE. 4) .OR. (MIN(M,N) .NE. 1)) THEN CALL MEXERRMSGTXT('YPRIME requires that Y be a 4 x 1 vector') ENDIF
Using SWIG.
SWIG is an open source program to use native c/c++/fortran routines from dynamic and modern languages. This is used in tcl/python/c#/R and many other languages. There has been some work to extend this method to matlab. This however doesnt seem to be completely implemented.
SWIG & Matlab
SWIG->octave
SWIG -> Matlab
Items that came up during the day
migrate Refference Guide generation to Build Server
- use http://www.artefact.tk/software/matlab/m2html/
- generate set of HTML pages nightly
- provide access to generated pages (upload to external Apache web server) or:
- install external TeamCity for all external projects and then embed them as
{panel:borderStyle=solid|borderColor=#3C78B5|borderWidth=1px} {html} <script type="text/javascript" src="http://<build-server>/externalStatus.html?js=1&buildTypeId=bt8"></script> {html} {panel}
- (optional) add serach engine for HTML pages
merge ucit.wldelft.nl into public.wldelft.nl
- !! possible only after documentation generation will be migrated to build server and published on web-site
P: with copy of UCIT files
- try to mount it using WebDAV on unix - check if it is used
BUG in repository: svn co http://svn.wldelft.nl/repos/mctools/trunk/ mctools gives:
... A mctools\UCIT_Actions\ModelActions\Support\template\hwgxytot.def A mctools\UCIT_Actions\ModelActions\Support\template\default.sed A mctools\UCIT_Actions\ModelActions\Support\template\ym6.sco A mctools\UCIT_Actions\ModelActions\Support\template\run.bat.new svn: REPORT request failed on '/repos/mctools/!svn/vcc/default' svn: REPORT of '/repos/mctools/!svn/vcc/default': 200 OK (http://svn.wldelft.nl)