Compiling GMIN with CHARMM

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.

Getting an account on the SVN server

The SVN server we use is run by the good people in the Unilever Centre, so you should email ucc-support@ch.cam.ac.uk, CCing in David (dw34) to request access to the Wales Group repository. Make sure you include your CRSID, the bit before @cam.ac.uk in your email address.

Once they reply, you should be able to set up your password here after logging into Raven. To check you have access to the repository, try logging in here. If you can't, you've done something wrong! Get help!

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:

vi ~/.bashrc

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:

export SVN=https://wwmm.ch.cam.ac.uk/svn2/groups/wales/
export MYSVN=https://wwmm.ch.cam.ac.uk/svn2/users/CRSID/

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:

:wq

and press ENTER. This should exit the editor, and return you to the directory you were in before. These variables will now be automatically set when you open a new shell, but for now, we need to load them manually. We do this using the source command:

source ~/.bashrc

We're now ready to check if you have access to the repository from your chosen machine. Lets try listing the contents of the GMIN trunk directory. Type the following ($SVN is the environmental variable we set to the location of the Wales Group repository above):

svn ls $SVN/trunk 

You will be prompted to validate a security certificate so press p and then ENTER to accept it permenantly. Now enter the password you set above (you only need to do this once!). You should see a list of the directories in the repository, something like this:

AMBER/
AMH/
CHARMM31/
GMIN/

NOTE: The 'trunk' contains the non-developmental version of the group codes.

Finally, before you download the code, you need to set up the log file template. This ensures that everyone submitting changes to the repository writes their log files in a similar fashion. Firstly, we need to edit the SVN config file

vi ~/.subversion/config

There is a section in the config file that begins as follows:

# [helpers]
# editor-cmd = editor (vi, emacs, notepad, etc.)

This should be changed to the following:

[helpers]
editor-cmd = vim +"r ~/template"

This tell subversion to open the file /home/CRSID/template when it asks for a commit log message to be written. Lets create this file now

vi ~/template

Enter insert mode by pressing i and paste the following into vi:

SUMMARY OF CHANGES 
------------------


SUBROUTINES AFFECTED
--------------------


KEYWORDS AFFECTED
-----------------


KNOWN ISSUES 
------------

Save the file by pressing ESC and then typing :wq. You're now good to download the GMIN code :)

'Checking out' the GMIN code

The first time you want to access the code, you need to 'check it out'. This will pull the entire 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!

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.

/home/csw34/svnxxxxxxxxxxx/CHARMM31

As a result, it is HIGHLY recommended that you transfer the code to ~/svn as shown below. This also prevents you from having to edit the Makefile more than is necessary. The code is checked out as follows:

svn co $SVN/trunk ~/svn

Notice that I'm transferring the code to:

/home/csw34/svn

This path is clearly shorter than that above, and so we should have no problem compiling CHARMM. You'll need to wait a while for the code to transfer! Once it has finished, you'll see a message like this:

Checked out revision 9853.

The number given is the version number you have just obtained. Whenever changes are make to the code and uploaded to the repository, this number is incremented. It might be increased by more than one between versions as the counter is common for all software, not just GMIN. That's it! You now have a copy of the GMIN code. Here are a few notes on its structure for new users.

• 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.
• GMIN/source contains the GMIN source code itself.
• GMIN/source/CHARMMinterface contains the CHARMM interface files which link GMIN to the CHARMM source. We try to change the CHARMM source itself as little as possible, so most changes are made here.
• AMBER contains the AMBER9 source code.
• AMH contains the files used for the AMH potential as implemented by Dr Mike Prentiss.
• GMIN/source/LAPACK and GMIN/source/BLAS contain highly optimised maths algorithms used by GMIN.

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

module load pgi64/7.1-6

If you get a conflict error message, you already have a version of pgf90 loaded and need to swap it out, for example:

module swap pgi64/6.1-6 pgi64/7.1-6

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

module av

Once the compiler is loaded, change to the CHARMM31 directory using

cd ~/svn/CHARMM31

CHARMM is compiled by a series of scripts which we run using a few simple commands. Firstly,

./clean.csh

removes any files from a previous CHARMM installation. The installation is then started using

./compile.csh

It takes a while...so if you see it finish quickly, within a minute - you probably have problems! You can check by using

tail build.log

You should get something like this if all is well:

install.com> Phase 2 completed.

 install.com> Processing CHARMM source on gnu...


 install.com> CHARMM Installation is completed.
              The CHARMM executable is /home/csw34/svn/CHARMM31/exec/gnu/charmm.

 install.com> Phase 3 completed.
Tue Jul  1 20:46:11 BST 2008

If you do, congratulations! You have just compiled CHARMM :)

Compiling GMIN with CHARMM

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

module load pgi64/7.1-6

If you get a module conflict error message, you already have a version of pgf90 loaded and need to swap it out, for example:

module swap pgi64/6.1-6 pgi64/7.1-6

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

module av

Right! Lets try compiling some code! First, we want to make sure there are no random files lurking in the repository from a previous compilation. We do this using

 
make clean

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

make chgmin

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:

/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

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

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 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:

svn log $SVN/GMIN/trunk

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 for more details. --james 15:38, 3 July 2008 (BST)

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

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.--james 15:38, 3 July 2008 (BST)

While in the svn directory, simply type

svn update

You will then be shown which files have been added, changed or removed and finally told which version number you now have. Committing and merging changes is covered on the SVN Page.