Compiling GMIN with CHARMM - Revision history

import>Csw34 at 10:24, 14 July 2008

2008-07-14T10:24:42Z

@@ Line 1: / Line 1: @@
-So, you want to get the latest version of GMIN from the Wales Group repository. The GMIN code is managed by Subversion version control (SVN), and before you can access it, you need an account on the departmental SVN server.
+The [[GMIN]] source is managed by Subversion version control (SVN), and before you can access it, you need an account on the departmental SVN server. A detailed tutorial documenting this process can be found on the [[SVN setup]] page.
 ===Compiling CHARMM===
-As an example, lets compile GMIN with CHARMM from the code we just obtained. Before we do so, we need to compile CHARMM itself. Before we start, we need to make sure the right compiler is loaded. For this example, lets use a 64bit Portland compiler, which at the time of writing is done using the command
+Before we start, we need to make sure the right compiler is loaded. For this example, lets use a 64bit Portland compiler, which at the time of writing is done using the command
 <pre>
 module load pgi64/7.1-6
@@ Line 11: / Line 12: @@
 module swap pgi64/6.1-6 pgi64/7.1-6
 </pre>
-NOTE: These module names are from the mek-quake server and are NOT called the same thing on clust. You can see all possible modules availiable to load using
+NOTE: These module names are from the mek-quake server and are NOT called the same thing on clust. You can see all possible modules available to load using
 <pre>
 module av
@@ Line 49: / Line 50: @@
 Now it's time to compile GMIN itself. Before we do so, we need to ensure we have set the '''Makefile''' up correctly. The Makefile specifies how the code should compiled and then linked together. When you first open it, it looks pretty horrendous, but that's just because there are so many options contained within. Any line starting with a # is commented out and will not be used. The only thing you MIGHT need to change here is the path that points to the CHARMM31 directory. It is currently set to /home/CRSID/svn/CHARMM31 - and it is HIGHLY recommended that you don't place the source anywhere else.
-If you are compiling with AMBER instead, everything in the CHARMM sections should be commented out! There are also two extra flags (FREEFORMAT_FLAG and EXTRA_FLAGS) that need to be uncommented in the Makefile for an AMBGMIN compilation. Finally, I need to check that the correct bits are uncommented for the Portland compiler, pgf90. In the Makefile provided, they are. I now need to ensure that I have the correct compiler loaded, which at the time of writing is done using the command
+If you are compiling with AMBER instead, everything in the CHARMM sections should be commented out! There are also two extra flags (FREEFORMAT_FLAG and EXTRA_FLAGS) that need to be uncommented in the Makefile for an AMBGMIN compilation. Finally, you need to check that the correct bits are uncommented for the Portland compiler, pgf90. Assuming you still have the compiler from the CHARMM compilation loaded, you should be good to go. First, we want to make sure there are no random files lurking in the repository from a previous compilation. We do this using
 <pre>
 make clean
@@ Line 71: / Line 60: @@
 Cross your fingers! At present, there are some problems compiling with CHARMM and you'll see some linking errors at the end of the compilation like this:
 <pre>
-/usr/bin/ld: Warning: alignment 16 of symbol `mdi_' in /home/csw34/GMIN/CHARMM31/lib/gnu/minmiz.a(tnpack.o) is smaller than 32 in commons.o
+/usr/bin/ld: Warning: alignment 16 of symbol `nmr_' in /home/csw34/GMIN/CHARMM31/lib/gnu/minmiz.a(tnpack.o) is smaller than 32 in commons.o
 </pre>

import>Csw34: Getting GMIN from the SVN repository moved to Compiling GMIN with CHARMM

2008-07-14T10:13:48Z

Getting GMIN from the SVN repository moved to Compiling GMIN with CHARMM

← Older revision	Revision as of 10:13, 14 July 2008
(No difference)

import>Csw34 at 09:17, 14 July 2008

2008-07-14T09:17:51Z

@@ Line 1: / Line 1: @@
 So, you want to get the latest version of GMIN from the Wales Group repository. The GMIN code is managed by Subversion version control (SVN), and before you can access it, you need an account on the departmental SVN server.
 ===Compiling CHARMM===
 As an example, lets compile GMIN with CHARMM from the code we just obtained. Before we do so, we need to compile CHARMM itself. Before we start, we need to make sure the right compiler is loaded. For this example, lets use a 64bit Portland compiler, which at the time of writing is done using the command

import>Csw34 at 11:09, 9 July 2008

2008-07-09T11:09:08Z

← Older revision		Revision as of 11:09, 9 July 2008
Line 169:		Line 169:
	If you get an infinite loop going on, exit using '''CTRL+C''' to escape. Did you change any of the paths or save the code to somewhere other than ~/svn? Double check the variables point to the right places! To compile GMIN with CHARMM, we then use the command		If you get an infinite loop going on, exit using '''CTRL+C''' to escape. Did you change any of the paths or save the code to somewhere other than ~/svn? Double check the variables point to the right places! To compile GMIN with CHARMM, we then use the command
	<pre>		<pre>
	make ~~cgmin2~~		make chgmin
	</pre>		</pre>
	Cross your fingers! At present, there are some problems compiling with CHARMM and you'll see some linking errors at the end of the compilation like this:		Cross your fingers! At present, there are some problems compiling with CHARMM and you'll see some linking errors at the end of the compilation like this:
Line 187:		Line 187:
	You can then update your code without having to download everything again using the update command.		You can then update your code without having to download everything again using the update command.

	'''WARNING!: ~~You~~ ~~must~~ be ~~VERY~~ ~~careful~~ ~~using~~ ~~this~~ ~~command! If~~ you ~~have~~ ~~changed~~ ~~your~~ ~~code~~ ~~and~~ ~~not~~ ~~committed~~ ~~those~~ changes to ~~the~~ ~~SVN~~ ~~repository~~, ~~updating~~ will ~~make SVN~~ merge ~~your~~ ~~code~~ ~~with~~ ~~that~~ in the repository. ~~More~~ ~~will~~ be ~~written~~ ~~about~~ this ~~when~~ it ~~has~~ ~~happened~~ a ~~few~~ ~~times!~~		'''WARNING!: Before you commit changes to the repository - you must use this command! As long as the changes you have made are recent, it will merge you changes into the code in the repository. Any conflicts must be dealt with manually - this is described here (INSERT LINK TO CONFLICT PAGE)

	Note: you cannot actually commit your code without updating unless your BASE matches the HEAD of the repository (i.e. no-one else has committed since you updated). This is to avoid you committing code which over-writes someone else's work.--[[User:jss43\|james]] 15:38, 3 July 2008 (BST)		Note: you cannot actually commit your code without updating unless your BASE matches the HEAD of the repository (i.e. no-one else has committed since you updated). This is to avoid you committing code which over-writes someone else's work.--[[User:jss43\|james]] 15:38, 3 July 2008 (BST)

import>Sf344: /* Compiling GMIN with CHARMM */

2008-07-08T09:35:20Z

Compiling GMIN with CHARMM

← Older revision		Revision as of 09:35, 8 July 2008
Line 151:		Line 151:
	Now it's time to compile GMIN itself. Before we do so, we need to ensure we have set the '''Makefile''' up correctly. The Makefile specifies how the code should compiled and then linked together. When you first open it, it looks pretty horrendous, but that's just because there are so many options contained within. Any line starting with a # is commented out and will not be used. The only thing you MIGHT need to change here is the path that points to the CHARMM31 directory. It is currently set to /home/CRSID/svn/CHARMM31 - and it is HIGHLY recommended that you don't place the source anywhere else.		Now it's time to compile GMIN itself. Before we do so, we need to ensure we have set the '''Makefile''' up correctly. The Makefile specifies how the code should compiled and then linked together. When you first open it, it looks pretty horrendous, but that's just because there are so many options contained within. Any line starting with a # is commented out and will not be used. The only thing you MIGHT need to change here is the path that points to the CHARMM31 directory. It is currently set to /home/CRSID/svn/CHARMM31 - and it is HIGHLY recommended that you don't place the source anywhere else.

	If you are compiling with AMBER instead, everything in the CHARMM sections should be commented out! There are also two extra flags that need to be uncommented in the Makefile for an AMBGMIN compilation. Finally, I need to check that the correct bits are uncommented for the Portland compiler, pgf90. In the Makefile provided, they are. I now need to ensure that I have the correct compiler loaded, which at the time of writing is done using the command		If you are compiling with AMBER instead, everything in the CHARMM sections should be commented out! There are also two extra flags (FREEFORMAT_FLAG and EXTRA_FLAGS) that need to be uncommented in the Makefile for an AMBGMIN compilation. Finally, I need to check that the correct bits are uncommented for the Portland compiler, pgf90. In the Makefile provided, they are. I now need to ensure that I have the correct compiler loaded, which at the time of writing is done using the command
	<pre>		<pre>
	module load pgi64/7.1-6		module load pgi64/7.1-6
Line 175:		Line 175:
	/usr/bin/ld: Warning: alignment 16 of symbol `mdi_' in /home/csw34/GMIN/CHARMM31/lib/gnu/minmiz.a(tnpack.o) is smaller than 32 in commons.o		/usr/bin/ld: Warning: alignment 16 of symbol `mdi_' in /home/csw34/GMIN/CHARMM31/lib/gnu/minmiz.a(tnpack.o) is smaller than 32 in commons.o
	</pre>		</pre>
	Don't worry about this! They are the result of a naming clash between AMBER and CHARMM and will be resolved soon :) Unless you see any other errors, congratulations! You should now have a CGMIN executable in the GMIN/source directory! Go test it!		Don't worry about this! They are the result of a naming clash between AMBER and CHARMM and will be resolved soon :) Unless you see any other errors, congratulations! You should now have a CGMIN executable in the GMIN/source directory! Go test it!

	===Checking you have the latest version===		===Checking you have the latest version===

import>Csw34 at 15:57, 4 July 2008

2008-07-04T15:57:41Z

← Older revision		Revision as of 15:57, 4 July 2008
Line 178:		Line 178:

	===Checking you have the latest version===		===Checking you have the latest version===
	If it has been a while since you downloaded the code, it is likely that you don't have the latest version. This could mean than the code you have contains bugs which have been fixed, or is missing performance or functionality increases that were added recently. You can easily see recent changes to the code either by looking at the RSS feed for the trunk [http://www.google.com/reader/view/feed/http%3A%2F%2Fwww-theor.ch.cam.ac.uk%2Fwalesrss%~~2Fgmin_trunk_log~~.xml here] (note that you can see the differences between each revision and the one previously by clicking on the revision name), or using the SVN log command:		If it has been a while since you downloaded the code, it is likely that you don't have the latest version. This could mean than the code you have contains bugs which have been fixed, or is missing performance or functionality increases that were added recently. You can easily see recent changes to the code either by looking at the RSS feed for the trunk [http://www.google.com/reader/view/feed/http%3A%2F%2Fwww-theor.ch.cam.ac.uk%2Fwalesrss%2Ftrunk_log.xml here] (note that you can see the differences between each revision and the one previously by clicking on the revision name), or using the SVN log command:
	<pre>		<pre>
	svn log $SVN/GMIN/trunk		svn log $SVN/GMIN/trunk

import>Csw34 at 16:43, 3 July 2008

2008-07-03T16:43:45Z

Show changes

import>Jss43: /* Checking you have the lastest version */

2008-07-03T14:38:13Z

Checking you have the lastest version

← Older revision		Revision as of 14:38, 3 July 2008
Line 188:		Line 188:
	svn log $SVN/GMIN/trunk		svn log $SVN/GMIN/trunk
	</pre>		</pre>

			Note that by default svn commands operate on the working copy (BASE). ''svn log'' in a working directory will therefore show commits up to your last update. See the [[SVN_Page#Logs \| SVN_Page]] for more details. --[[User:jss43\|james]] 15:38, 3 July 2008 (BST)

	You can then update your code without having to download everything again using the update command.		You can then update your code without having to download everything again using the update command.

	'''WARNING!: You must be VERY careful using this command! If you have changed your code and not committed ~~theose~~ changes to the SVN repository, updating will make SVN merge your code with that in the repository. More will be written about this when it has ~~heppened~~ a few times!		'''WARNING!: You must be VERY careful using this command! If you have changed your code and not committed those changes to the SVN repository, updating will make SVN merge your code with that in the repository. More will be written about this when it has happened a few times!

			Note: you cannot actually commit your code without updating unless your BASE matches the HEAD of the repository (i.e. no-one else has committed since you updated). This is to avoid you committing code which over-writes someone else's work.--[[User:jss43\|james]] 15:38, 3 July 2008 (BST)

	While in the GMIN directory, simply type		While in the GMIN directory, simply type

import>Csw34 at 17:48, 2 July 2008

2008-07-02T17:48:09Z

← Older revision		Revision as of 17:48, 2 July 2008
Line 184:		Line 184:

	===Checking you have the lastest version===		===Checking you have the lastest version===
	If it has been a while since you downloaded the code, it is likely that you don't have the latest version. This could mean than the code you have contains bugs which have been fixed, or is missing performance or functionality increases that were added recently. You can easily see recent changes to the code either by looking at the RSS feed for the trunk [http://www-theor.ch.cam.ac.uk~~/walesrss/gmin_trunk_log~~.xml here] (note that you can see the differences between each revision and the one previously by clicking on the revision name), or using the SVN log command:		If it has been a while since you downloaded the code, it is likely that you don't have the latest version. This could mean than the code you have contains bugs which have been fixed, or is missing performance or functionality increases that were added recently. You can easily see recent changes to the code either by looking at the RSS feed for the trunk [http://www.google.com/reader/view/feed/http%3A%2F%2Fwww-theor.ch.cam.ac.uk%2Fwalesrss%2Fgmin_trunk_log.xml here] (note that you can see the differences between each revision and the one previously by clicking on the revision name), or using the SVN log command:
	<pre>		<pre>
	svn log $SVN/GMIN/trunk		svn log $SVN/GMIN/trunk

import>Csw34 at 17:32, 2 July 2008

2008-07-02T17:32:37Z

@@ Line 35: / Line 35: @@
 zwischen.f
 </pre>
-NOTE: The 'trunk' contains the non-developmental version of GMIN You're now good to download the GMIN code :)
+NOTE: The 'trunk' contains the non-developmental version of GMIN.
 ==='Checking out' the GMIN code===
@@ Line 153: / Line 190: @@
 You can then update your code without having to download everything again using the update command.
-'''WARNING!: You must be VERY careful using this command! If you have changed your code and not committed theose changes to the SVN repository, updating will most likely undo your changes!
+'''WARNING!: You must be VERY careful using this command! If you have changed your code and not committed theose changes to the SVN repository, updating will make SVN merge your code with that in the repository. More will be written about this when it has heppened a few times!
 While in the GMIN directory, simply type