Download and Installation - Revision history

Rovigattil: /* Compiler */

2014-12-03T14:58:51Z

Compiler

← Older revision		Revision as of 14:58, 3 December 2014
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	==Requirements==		==Requirements==
	===Compiler===		===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.		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 written 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===		===Operating system===

Sulc at 18:45, 17 March 2014

2014-03-17T18:45:41Z

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	</pre>		</pre>

	If you want some oxDNA hands-on examples, there are some in the <tt>EXAMPLES</tt> ~~directory~~, some of which are documented in more detail in [[:Category:Examples\|Examples]] section.		If you want some oxDNA hands-on examples, there are some in the <tt>EXAMPLES</tt> subdirectory, some of which are documented in more detail in [[:Category:Examples\|Examples]] section.

Sulc at 18:45, 17 March 2014

2014-03-17T18:45:28Z

← Older revision		Revision as of 18:45, 17 March 2014
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	</pre>		</pre>

	If you want some oxDNA hands-on examples, there are some in the [[:Category:Examples\|Examples]] ~~directory~~.		If you want some oxDNA hands-on examples, there are some in the <tt>EXAMPLES</tt> directory, some of which are documented in more detail in [[:Category:Examples\|Examples]] section.

Sulc at 18:44, 17 March 2014

2014-03-17T18:44:27Z

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	</pre>		</pre>

	If you want some oxDNA hands-on examples, there are some in the [[Examples]] directory.		If you want some oxDNA hands-on examples, there are some in the [[:Category:Examples\|Examples]] directory.

Sulc at 18:43, 17 March 2014

2014-03-17T18:43:53Z

← Older revision		Revision as of 18:43, 17 March 2014
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	</pre>		</pre>

	If you want some oxDNA 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]] directory.

Sulc at 18:42, 17 March 2014

2014-03-17T18:42:44Z

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	In this section, we outline the procedure for compiling oxDNA~~. Before starting, we recall that the only supported features of oxDNA are~~		In this section, we outline the procedure for dowloading and compiling oxDNA.

	*Molecular and Brownian dynamics
	*Regular Monte Carlo
	*External forces
	*A stand-alone single- and double-strand generator (<tt>UTILS/generate-sa.py</tt>)
	*An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (<tt>UTILS/traj2vis.py</tt>)

	~~[[Features\|This]] page contains a more detailed list~~.

	==Requirements==		==Requirements==
	===Compiler===		===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.		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===		===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 on other OSes~~, provided that the makefile is changed accordingly~~.		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===		===Dependencies===
	~~oxDNA does not depend on any external library apart from the standard c++ library and therefore~~ is ~~completely self-contained~~.		The pre-compilation stage requires [http://www.cmake.org/ cmake], while compilation is carried out with [http://www.gnu.org/software/make/ GNU Make].

	~~==Download==~~		The CPU-only oxDNA does not depend on any external library apart from the standard c++ library.
	The ~~source package can be downloaded [http://pacci.phys.uniroma1.it/sites/default/files/oxdna/index.php here]. There are currently no available binary packages.~~
	~~A new version, more extensible and redesigned to provide additional flexibility, will be released soon. A pre~~-~~release of this new~~ oxDNA ~~is available upon request~~.

	=~~=Installation==~~		The GPU-enabled oxDNA requires CUDA >= 3.2.
	~~To install the program, untar <tt>oxDNA~~.~~tar</tt> and enter the oxDNA directory~~. ~~Compile the code with~~

	~~<pre>make<~~/~~pre>~~		==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].

	~~See [[Documentation]] for <tt>make</tt> options. If you want~~ to compile oxDNA ~~with the Intel C++ compiler (icpc) use~~		==Compilation==
			We recommend using an out-of-source build to compile oxDNA. A standard out-of-source build is as follows

	<pre>		<pre>
	make ~~intel=1~~		cd oxDNA
			mkdir build
			cd build
			cmake .. # cmake options go here, 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		===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.
			*'''-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>.
			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: /* Download */

2014-01-21T08:12:39Z

Download

← Older revision		Revision as of 08:12, 21 January 2014
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	==Download==		==Download==
	The source package can be downloaded [http://pacci.phys.uniroma1.it/sites/default/files/oxdna/index.php here]. There are currently no available binary packages. A new version, more extensible and redesigned to provide additional flexibility, will be released soon. A pre-release of ~~the~~ new oxDNA is available upon request.		The source package can be downloaded [http://pacci.phys.uniroma1.it/sites/default/files/oxdna/index.php here]. There are currently no available binary packages.
			A new version, more extensible and redesigned to provide additional flexibility, will be released soon. A pre-release of this new oxDNA is available upon request.

	==Installation==		==Installation==

Rovigattil: /* Download */

2014-01-21T08:12:21Z

Download

← Older revision		Revision as of 08:12, 21 January 2014
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	==Download==		==Download==
	The source package can be downloaded ~~<!--[http://kratos.phys.uniroma1.it/download_oxdna_code.php here]-->~~[http://pacci.phys.uniroma1.it/sites/default/files/oxdna/index.php here]. There are currently no available binary packages.		The source package can be downloaded [http://pacci.phys.uniroma1.it/sites/default/files/oxdna/index.php here]. There are currently no available binary packages. A new version, more extensible and redesigned to provide additional flexibility, will be released soon. A pre-release of the new oxDNA is available upon request.

	==Installation==		==Installation==

Romano: /* Download */

2012-08-14T21:12:26Z

Download

← Older revision		Revision as of 21:12, 14 August 2012
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	==Download==		==Download==
	The source package can be downloaded <!--[http://kratos.phys.uniroma1.it/download_oxdna_code.php here]-->[http://pacci.phys.uniroma1.it/sites/default/files/oxdna/ here]. There are currently no available binary packages.		The source package can be downloaded <!--[http://kratos.phys.uniroma1.it/download_oxdna_code.php here]-->[http://pacci.phys.uniroma1.it/sites/default/files/oxdna/index.php here]. There are currently no available binary packages.

	==Installation==		==Installation==

Romano: /* Download */

2012-08-14T21:11:59Z

Download

← Older revision		Revision as of 21:11, 14 August 2012
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	==Download==		==Download==
	The source package can be downloaded <!--[http://kratos.phys.uniroma1.it/download_oxdna_code.php here]-->[http://pacci.phys.uniroma1.it/sites/default/files/~~oxDNA_1.0.2.tar~~ here]. There are currently no available binary packages.		The source package can be downloaded <!--[http://kratos.phys.uniroma1.it/download_oxdna_code.php here]-->[http://pacci.phys.uniroma1.it/sites/default/files/oxdna/ here]. There are currently no available binary packages.

	==Installation==		==Installation==