Polyglot - Revision history

GethinWilliams: /* Introduction */

2013-09-13T11:22:18Z

Introduction

GethinWilliams: /* Calling C/C++ and Fortran from R */

2013-08-23T12:51:36Z

Calling C/C++ and Fortran from R

GethinWilliams: /* Calling C/C++ and Fortran from Matlab using MEX Files */

2013-08-23T12:50:36Z

Calling C/C++ and Fortran from Matlab using MEX Files

GethinWilliams: /* Calling C from Python using SWIG */

2013-08-23T11:18:10Z

Calling C from Python using SWIG

GethinWilliams: /* Calling C from Python using SWIG */

2013-08-23T11:17:07Z

Calling C from Python using SWIG

GethinWilliams: /* Calling C from Python using SWIG */

2013-08-23T11:14:30Z

Calling C from Python using SWIG

GethinWilliams: /* Calling C from Python using SWIG */

2013-08-22T15:02:10Z

Calling C from Python using SWIG

GethinWilliams: /* Calling C from Python using SWIG */

2013-08-22T14:52:01Z

Calling C from Python using SWIG

GethinWilliams: /* Fortran90 Constructs */

2013-08-22T14:43:37Z

Fortran90 Constructs

GethinWilliams: /* Calling Fortran from Python using F2PY */

2013-08-22T09:42:41Z

Calling Fortran from Python using F2PY

← Older revision		Revision as of 11:22, 13 September 2013
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	What are your options? You could use something not so suitable because it happens to be written in Fortran. Hmm, that doesn't sound so good. You could translate the library from C to Fortran. Hmm, that sounds like tedious and time-consuming work. Plus you'd need to understand the C, and perhaps a direct translation can't be made anyhow? This is looking like a dead-end too. It would be far better to leave the library as it is and to call the routines from your favoured language. Is that possible? Sure it is! Read on and find out how..		What are your options? You could use something not so suitable because it happens to be written in Fortran. Hmm, that doesn't sound so good. You could translate the library from C to Fortran. Hmm, that sounds like tedious and time-consuming work. Plus you'd need to understand the C, and perhaps a direct translation can't be made anyhow? This is looking like a dead-end too. It would be far better to leave the library as it is and to call the routines from your favoured language. Is that possible? Sure it is! Read on and find out how..
		+
		+	Another scenario is that C or Fortran do number crunching well, but aren't best suited to text processing or creating GUIs. For scripting languages, like python for example, the reverse is true. Wouldn't it be nice if we could combine their strengths in a single project. Well, you can!

	In this workshop, we'll look at ways in which we can mix languages and in the process create a useful end product which plays to the strengths of it's components and gets you to where you want to be, without any laborious re-writes. In the first two examples we'll look at calling C code from Fortran and then calling Fortran from C. To get the code for examples, log into your preferred Linux machine and cut and paste the following into your terminal.		In this workshop, we'll look at ways in which we can mix languages and in the process create a useful end product which plays to the strengths of it's components and gets you to where you want to be, without any laborious re-writes. In the first two examples we'll look at calling C code from Fortran and then calling Fortran from C. To get the code for examples, log into your preferred Linux machine and cut and paste the following into your terminal.

← Older revision		Revision as of 12:51, 23 August 2013
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	* http://www.biostat.jhsph.edu/~rpeng/docs/interface.pdf		* http://www.biostat.jhsph.edu/~rpeng/docs/interface.pdf
		+	* http://users.stat.umn.edu/~geyer/rc/

	=Appendices=		=Appendices=

← Older revision		Revision as of 12:50, 23 August 2013
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	* http://www.mathworks.co.uk/help/matlab/create-mex-files.html		* http://www.mathworks.co.uk/help/matlab/create-mex-files.html
		+
		+	=Calling C/C++ and Fortran from R=
		+
		+	* http://www.biostat.jhsph.edu/~rpeng/docs/interface.pdf

	=Appendices=		=Appendices=

@@ Line 447: / Line 447: @@
 b.second is: 8
 </pre>
 =Appendices=

@@ Line 432: / Line 432: @@
 <pre>
 ./test.py
 </pre>

@@ Line 422: / Line 422: @@
 </pre>
-You will notice that in addition to the source code files, interface files--with file extension '''<file>.i''', must also be written.  This is in contrast to f2py, which automatically created the interface files. I have created a makefile to simplify the creation of the shared objects.  Just type:
+You will notice that in addition to the source code files, interface files--with file extension '''<file>.i'''--must also be written.  This is in contrast to f2py, which automatically created the interface files. I have created a makefile to simplify the creation of the shared objects.  Just type:
 <pre>

@@ Line 405: / Line 405: @@
 = Calling C from Python using SWIG =
-'''NB You will need swig installed on your machine for this example. swig is not installed on bluecrystal phases 1 & 2, but is installed on phase 3.'''
+'''NB You will need SWIG installed on your machine for this example. SWIG is not installed on bluecrystal phases 1 & 2, but is installed on phase 3.'''
 <pre>
 cd ../exampleX
 </pre>
 <pre>
 make
 </pre>
 <pre>
 ./test.py
 </pre>
 =Appendices=

@@ Line 320: / Line 320: @@
 Take some time to review the Fortran90 source code and the corresponding python test scripts.
 <pre>
 f2py --fcompiler=gnu95 -c -m moddata moddata.f90
 </pre>
 <pre>
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+  ]
 </pre>
 <pre>
 f2py --fcompiler=gnu95 -c -m allocarr allocarr.f90
 </pre>
 <pre>
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   b is not allocated
 </pre>
 <pre>
 f2py --fcompiler=gnu95 -c -m type type.f90
 </pre>
 <pre>
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    2.0000000000000000        3.0000000000000000                4           5           6
 </pre>
 <pre>

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 Another popular pairing is to use Python to create the interface, utilising it's strong support for text processing, GUI building and graphics, and to use a traditional programming language, such as Fortran or C/C++, to rapidly perform any number crunching.
-In the examples below, we'll take a quick peek at the support that '''f2py''' (provided as part of the'''numpy''' python package) gives those who wish to call Fortran routines from their Python scripts.
+In the examples below, we'll take a quick peek at the support that '''f2py''' (provided as part of the '''numpy''' python package) gives those who wish to call Fortran routines from their Python scripts.
 <pre>