SVN setup - Revision history

import>Rl201: /* Setting up your SVN details */

2011-05-11T12:22:30Z

Setting up your SVN details

← Older revision		Revision as of 12:22, 11 May 2011
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	<pre>		<pre>
	export SVN=https://svn.ch.cam.ac.uk/svn/wales/groups/wales/		export SVN=https://svn.ch.cam.ac.uk/svn/wales/groups/wales/
	export MYSVN=https://~~wwmm~~.ch.cam.ac.uk/~~svn2~~/CRSID/		export MYSVN=https://svn.ch.cam.ac.uk/svn/CRSID/
	</pre>		</pre>
	where CRSID is the user name you use to log into Raven with. When you're done, we need to save he changes, press '''ESC''' to exit insert mode (check 'Insert' isn't still showing at the bottom!) and then type:		where CRSID is the user name you use to log into Raven with. When you're done, we need to save he changes, press '''ESC''' to exit insert mode (check 'Insert' isn't still showing at the bottom!) and then type:

import>Rl201 at 12:22, 11 May 2011

2011-05-11T12:22:13Z

← Older revision		Revision as of 12:22, 11 May 2011
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	This opens the '''vi''' editor. Press '''SHIFT+G''' to go to the bottom of the file, then press '''I''' to enter insert mode. Add the following to the bottom:		This opens the '''vi''' editor. Press '''SHIFT+G''' to go to the bottom of the file, then press '''I''' to enter insert mode. Add the following to the bottom:
	<pre>		<pre>
	export SVN=https://~~wwmm~~.ch.cam.ac.uk/~~svn2~~/groups/wales/		export SVN=https://svn.ch.cam.ac.uk/svn/wales/groups/wales/
	export MYSVN=https://wwmm.ch.cam.ac.uk/svn2~~/users~~/CRSID/		export MYSVN=https://wwmm.ch.cam.ac.uk/svn2/CRSID/
	</pre>		</pre>
	where CRSID is the user name you use to log into Raven with. When you're done, we need to save he changes, press '''ESC''' to exit insert mode (check 'Insert' isn't still showing at the bottom!) and then type:		where CRSID is the user name you use to log into Raven with. When you're done, we need to save he changes, press '''ESC''' to exit insert mode (check 'Insert' isn't still showing at the bottom!) and then type:

import>Csw34: /* 'Checking out' the code */

2009-07-28T16:56:43Z

'Checking out' the code

← Older revision		Revision as of 16:56, 28 July 2009
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	*'''DOC''' contains the documentation for [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]]. Whenever you introduce a new keyword or feature, it should be documented.		*'''DOC''' contains the documentation for [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]]. Whenever you introduce a new keyword or feature, it should be documented.
	*'''SCRIPTS''' contains useful scripts developed by members of the group. For example, perm-pdb.py generates an OPTIM perm.allow file from an input PDB.		*'''SCRIPTS''' contains useful scripts developed by members of the group. For example, perm-pdb.py generates an OPTIM perm.allow file from an input PDB.
			*'''AMBERTOOLS''' contains the full version of Amber Tools 1.2 with our updated LeaP files to fix forcefield problems we have encountered using AMBER9.

	Now that you have the source codes, you should try to compile and test it. A brief tutorial on compiling GMIN with CHARMM can be found [[Compiling GMIN with CHARMM \| here]].		Now that you have the source codes, you should try to compile and test it. A brief tutorial on compiling GMIN with CHARMM can be found [[Compiling GMIN with CHARMM \| here]].

import>Csw34: /* Setting up your SVN details */

2009-07-28T16:50:21Z

Setting up your SVN details

← Older revision		Revision as of 16:50, 28 July 2009
Line 31:		Line 31:
	<pre>		<pre>
	AMBER/		AMBER/
			AMBERTOOLS/
	BLAS/		BLAS/
	CHARMM31/		CHARMM31/

import>Csw34: /* 'Checking out' the code */

2009-07-27T11:41:15Z

'Checking out' the code

← Older revision		Revision as of 11:41, 27 July 2009
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	* '''OPTIM''' contains the [[OPTIM]] code. It has the same directory structure as [[GMIN]] also.		* '''OPTIM''' contains the [[OPTIM]] code. It has the same directory structure as [[GMIN]] also.
	* '''AMBER''' contains the [[AMBER]]9 source code.		* '''AMBER''' contains the [[AMBER]]9 source code.
			* '''NAB''' contains the [[AMBER]]9 nucleic acid builder (NAB) source code.
	* '''LAPACK''' and '''BLAS''' contain the maths libraries used by all the group code.		* '''LAPACK''' and '''BLAS''' contain the maths libraries used by all the group code.
	* '''CHARMM31''' contains the [[CHARMM]] source code. You need to compile [[CHARMM]] before you compile [[GMIN]] with it, and you must use the same compiler in both cases. If you don't you'll get errors. The [[OPTIM]] compilation automatically recompiles [[CHARMM]] if necessary.		* '''CHARMM31''' contains the [[CHARMM]] source code. You need to compile [[CHARMM]] before you compile [[GMIN]] with it, and you must use the same compiler in both cases. If you don't you'll get errors. The [[OPTIM]] compilation automatically recompiles [[CHARMM]] if necessary.
	*'''DOC''' contains the documentation for [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]]. Whenever you introduce a new keyword or feature, it should be documented.		*'''DOC''' contains the documentation for [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]]. Whenever you introduce a new keyword or feature, it should be documented.
			*'''SCRIPTS''' contains useful scripts developed by members of the group. For example, perm-pdb.py generates an OPTIM perm.allow file from an input PDB.

	Now that you have the source codes, you should try to compile and test it. A brief tutorial on compiling GMIN with CHARMM can be found [[Compiling GMIN with CHARMM \| here]].		Now that you have the source codes, you should try to compile and test it. A brief tutorial on compiling GMIN with CHARMM can be found [[Compiling GMIN with CHARMM \| here]].

import>Csw34: /* Setting up your SVN details */

2009-07-27T11:39:09Z

Setting up your SVN details

← Older revision		Revision as of 11:39, 27 July 2009
Line 33:		Line 33:
	BLAS/		BLAS/
	CHARMM31/		CHARMM31/
			COPYING
	DISCONNECT		DISCONNECT/
	DOC/		DOC/
	GMIN/		GMIN/
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	OPTIM/		OPTIM/
	PATHSAMPLE/		PATHSAMPLE/
			SCRIPTS/
	</pre>		</pre>
	NOTE: The 'trunk' contains the non-developmental version of the group codes.		NOTE: The 'trunk' contains the non-developmental version of the group codes.

import>Csw34: /* Setting up your SVN details */

2009-01-21T11:14:43Z

Setting up your SVN details

← Older revision		Revision as of 11:14, 21 January 2009
Line 33:		Line 33:
	BLAS/		BLAS/
	CHARMM31/		CHARMM31/
			DISCONNECT
	DOC/		DOC/
	GMIN/		GMIN/

import>Csw34: /* 'Checking out' the code */

2008-08-02T19:06:01Z

'Checking out' the code

← Older revision		Revision as of 19:06, 2 August 2008
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	The first time you want to access the code, you need to 'check it out'. This will pull the code from the repository into a local directory for your use.		The first time you want to access the code, you need to 'check it out'. This will pull the code from the repository into a local directory for your use.

	'''WARNING: It has been found that if you put the svn directory too far from your /home/CRSID/, you will not be able to compile the CHARMM source. This is most likely due to the variable CHARMM uses to contain the locations of files is of a limited length! We hope to fix this problem, but for now you need to ensure it is close enough. ~~The path below is the MAXIMUM length that allows CHARMM to still compile, adding one more x to the svn directory name leads to all sorts of silly errors!~~'''		'''WARNING: It has been found that if you put the svn directory too far from your /home/CRSID/, you will not be able to compile the CHARMM source. This is most likely due to the variable CHARMM uses to contain the locations of files is of a limited length! We hope to fix this problem, but for now you need to ensure it is close enough. '''

	This is the furthest the CHARMM31 directory within the repository can be from your home, without causing errors. Adding one more 'x' to the svn directory name will cause problems.		This is the furthest the CHARMM31 directory within the repository can be from your home, without causing errors. Adding one more 'x' to the svn directory name will cause problems.

import>Csw34: /* Setting up your SVN details */

2008-08-02T19:05:25Z

Setting up your SVN details

← Older revision		Revision as of 19:05, 2 August 2008
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	------------		------------
	</pre>		</pre>
	Save the file by pressing '''ESC''' and then typing ''':wq'''. You're now good to download the ~~GMIN~~ code :)		Save the file by pressing '''ESC''' and then typing ''':wq'''. You're now good to download the group code :)

	==='Checking out' the code===		==='Checking out' the code===

import>Csw34: /* Setting up your SVN details */

2008-08-02T19:04:42Z

Setting up your SVN details

← Older revision		Revision as of 19:04, 2 August 2008
Line 7:		Line 7:

	===Setting up your SVN details===		===Setting up your SVN details===
	Open a shell on the machine where you plan on using ~~GMIN~~. To make subversion easy to use, you need to specify some locations in your .bashrc file as environment variables. We do this as follows:		Open a shell on the machine where you plan on using the group code. To make subversion easy to use, you need to specify some locations in your .bashrc file as environment variables. We do this as follows:
	<pre>		<pre>
	vi ~/.bashrc		vi ~/.bashrc