Download and Installation new - Revision history

Rovigattil at 15:25, 17 March 2014

2014-03-17T15:25:23Z

← Older revision		Revision as of 15:25, 17 March 2014
Line 1:		Line 1:
	In this section, we outline the procedure for compiling oxDNA.		In this section, we outline the procedure for dowloading and compiling oxDNA.

	==Requirements==		==Requirements==

Rovigattil: /* Compile options */

2014-03-17T15:17:52Z

Compile options

← Older revision		Revision as of 15:17, 17 March 2014
Line 37:		Line 37:
	*'''-DDebug=1''' oxDNA will be compiled with debug flags (both for nvcc and gcc).		*'''-DDebug=1''' oxDNA will be compiled with debug flags (both for nvcc and gcc).
	*'''-DG=1''' oxDNA will be compiled with both debug and optimization flags.		*'''-DG=1''' oxDNA will be compiled with both debug and optimization flags.
	*'''-DINTEL=1''' oxDNA will be compiled using the Intel icpc compiler~~. The resulting executable will be named oxDNA_intel~~.		*'''-DINTEL=1''' oxDNA will be compiled using the Intel icpc compiler.
	*'''-DCUDA=1''' oxDNA will be compiled with CUDA support. This requires a CUDA runtime version >= 3.2.		*'''-DCUDA=1''' oxDNA will be compiled with CUDA support. This requires a CUDA runtime version >= 3.2.
	*'''-DMPI=1''' oxDNA will be compilted with MPI support. This is currently an '''unsupported''' feature and it should be used by developers only.		*'''-DMPI=1''' oxDNA will be compilted with MPI support. This is currently an '''unsupported''' feature and it should be used by developers only.

Rovigattil: /* Installation */

2014-03-17T15:17:21Z

Installation

← Older revision		Revision as of 15:17, 17 March 2014
Line 20:		Line 20:
	''via'' a [http://subversion.apache.org/ subversion] repository, accessible [http://sourceforge.net/p/oxdna/code/HEAD/tree/ here].		''via'' a [http://subversion.apache.org/ subversion] repository, accessible [http://sourceforge.net/p/oxdna/code/HEAD/tree/ here].

	==~~Installation~~==		==Compilation==
	We recommend using an out-of-source build to compile oxDNA. A standard out-of-source build is as follows		We recommend using an out-of-source build to compile oxDNA. A standard out-of-source build is as follows

Line 30:		Line 30:
	make -j4 # use 4 threads for compilation, sensibly shortening compiling time		make -j4 # use 4 threads for compilation, sensibly shortening compiling time
	</pre>		</pre>

			===Compile options===

			The following parameters can be passed to cmake:

			*'''-DDebug=1''' oxDNA will be compiled with debug flags (both for nvcc and gcc).
			*'''-DG=1''' oxDNA will be compiled with both debug and optimization flags.
			*'''-DINTEL=1''' oxDNA will be compiled using the Intel icpc compiler. The resulting executable will be named oxDNA_intel.
			*'''-DCUDA=1''' oxDNA will be compiled with CUDA support. This requires a CUDA runtime version >= 3.2.
			*'''-DMPI=1''' oxDNA will be compilted with MPI support. This is currently an '''unsupported''' feature and it should be used by developers only.

	The compilation process will generate three executables in the build/bin folder: <tt>oxDNA</tt>, <tt>DNAnalysis</tt> and <tt>confGenerator</tt>.		The compilation process will generate three executables in the build/bin folder: <tt>oxDNA</tt>, <tt>DNAnalysis</tt> and <tt>confGenerator</tt>.
			Their usage is as follows:

	<pre>		<pre>
	oxDNA <input>		oxDNA <input>
			DNAnalysis <input>
			confGenerator <input> <box_size/density> # the second argument will be interpreted as a density if it is less than 2.0
	</pre>		</pre>

	~~The complete list of supported input options can be found [[Documentation#Input_file\|here]].~~ If you want some hands-on examples, there are some in the [[Examples\|EXAMPLES]] directory.		If you want some oxDNA hands-on examples, there are some in the [[Examples\|EXAMPLES]] directory.

	A useful analysis tool that prints out all the interactions for a configuration is in the <tt>UTILS/process_data/</tt> directory. To compile it, one needs to go into that directory and type <tt>make</tt>. The program will be called <tt>output_bonds</tt> and its usage is described in the [[Documentation#Analysis_of_configurations\|Documentation]].

Rovigattil: /* Installation */

2014-03-14T18:50:54Z

Installation

← Older revision		Revision as of 18:50, 14 March 2014
Line 21:		Line 21:

	==Installation==		==Installation==
	~~To install the program enter the oxDNA directory.~~ We recommend using an out-of-source build. A standard out-of-source build is as follows		We recommend using an out-of-source build to compile oxDNA. A standard out-of-source build is as follows

	<pre>		<pre>

Rovigattil: /* Installation */

2014-03-14T18:49:59Z

Installation

← Older revision		Revision as of 18:49, 14 March 2014
Line 27:		Line 27:
	mkdir build		mkdir build
	cd build		cd build
	cmake .. # ~~add~~ cmake options, more on this later		cmake .. # cmake options go here, more on this later
	make -j4 # use 4 threads for compilation, sensibly shortening compiling time		make -j4 # use 4 threads for compilation, sensibly shortening compiling time
	</pre>		</pre>

Rovigattil: /* Installation */

2014-03-14T18:49:38Z

Installation

← Older revision		Revision as of 18:49, 14 March 2014
Line 21:		Line 21:

	==Installation==		==Installation==
	To install the program enter the oxDNA directory. ~~Compile the code with~~		To install the program enter the oxDNA directory. We recommend using an out-of-source build. A standard out-of-source build is as follows

	~~<pre>make</pre>~~

	~~See [[Documentation]] for <tt>make</tt> options~~. ~~If you want to compile oxDNA with the Intel C++ compiler (icpc) use~~

	<pre>		<pre>
	make ~~intel=1~~		cd oxDNA
			mkdir build
			cd build
			cmake .. # add cmake options, more on this later
			make -j4 # use 4 threads for compilation, sensibly shortening compiling time
	</pre>		</pre>

	The compilation process will generate an <tt>oxDNA</tt> ~~executable in the~~ <tt>~~Release~~</tt> ~~directory~~. ~~The usage of oxDNA is~~		The compilation process will generate three executables in the build/bin folder: <tt>oxDNA</tt>, <tt>DNAnalysis</tt> and <tt>confGenerator</tt>.

	<pre>		<pre>

Rovigattil: /* Dependencies */

2014-03-14T18:41:19Z

Dependencies

← Older revision		Revision as of 18:41, 14 March 2014
Line 9:		Line 9:

	===Dependencies===		===Dependencies===
	The pre-compilation stage requires [http://www.cmake.org/ cmake], while compilation is carried out with [~~https~~://www.gnu.org/software/make/ GNU Make].		The pre-compilation stage requires [http://www.cmake.org/ cmake], while compilation is carried out with [http://www.gnu.org/software/make/ GNU Make].

	The CPU-only oxDNA does not depend on any external library apart from the standard c++ library.		The CPU-only oxDNA does not depend on any external library apart from the standard c++ library.

Rovigattil: Created page with "In this section, we outline the procedure for compiling oxDNA. ==Requirements== ===Compiler=== The recommended compiler is gcc 4.6.x. oxDNA compilation has been thoroughly teste…"

2014-03-14T18:41:00Z

Created page with "In this section, we outline the procedure for compiling oxDNA. ==Requirements== ===Compiler=== The recommended compiler is gcc 4.6.x. oxDNA compilation has been thoroughly teste…"

New page

In this section, we outline the procedure for compiling oxDNA.

==Requirements==
===Compiler===
The recommended compiler is gcc 4.6.x. oxDNA compilation has been thoroughly tested with gcc >= 4.1.x and icpc >= 10. Note that compiling with gcc 4.6.x rather than with gcc 4.1.x results in a significant increase in performances. Since oxDNA is writtern in standard c++, it '''should''' be also compatible with other compilers. Optionally, oxDNA can be compiled to run on [http://www.nvidia.com NVIDIA] GPUs by enabling [http://www.nvidia.com/object/cuda_home_new.html CUDA] support at compile time.

===Operating system===
oxDNA has been tested on Linux (kernel >= 2.6.x) and Mac OS X. Since it is written in ANSI c++, it '''should''' also work out-of-the-box on other OSes.

===Dependencies===
The pre-compilation stage requires [http://www.cmake.org/ cmake], while compilation is carried out with [https://www.gnu.org/software/make/ GNU Make].

The CPU-only oxDNA does not depend on any external library apart from the standard c++ library.

The GPU-enabled oxDNA requires CUDA >= 3.2.

==Download==
There are currently no available binary packages for oxDNA. The last stable source package can be downloaded
[http://sourceforge.net/projects/oxdna/files/ here], while bleeding edge (possibly unstable) versions are available
''via'' a [http://subversion.apache.org/ subversion] repository, accessible [http://sourceforge.net/p/oxdna/code/HEAD/tree/ here].

==Installation==
To install the program enter the oxDNA directory. Compile the code with

<pre>make</pre>

See [[Documentation]] for <tt>make</tt> options. If you want to compile oxDNA with the Intel C++ compiler (icpc) use

<pre>
make intel=1
</pre>

The compilation process will generate an <tt>oxDNA</tt> executable in the <tt>Release</tt> directory. The usage of oxDNA is

<pre>
oxDNA <input>
</pre>

The complete list of supported input options can be found [[Documentation#Input_file|here]]. If you want some hands-on examples, there are some in the [[Examples|EXAMPLES]] directory.

A useful analysis tool that prints out all the interactions for a configuration is in the <tt>UTILS/process_data/</tt> directory. To compile it, one needs to go into that directory and type <tt>make</tt>. The program will be called <tt>output_bonds</tt> and its usage is described in the [[Documentation#Analysis_of_configurations|Documentation]].