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/GMIN/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 the files that make up GMIN displayed, ending in something like this:
... wenzel.f wham_djw.f90 zwischen.f
Congratulations! 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 GMIN directory too far from your /home/CRSID/, you will not be able to compile the CHARMM source that is included. 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 GMIN directory name leads to all sorts of silly errors!
/home/csw34/GMINxxxxxxxxxx/
The code is checked out as follows:
svn co $SVN/GMIN/trunk ~/GMIN
Notice that I'm transfering the code to:
/home/csw34/GMIN
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. It was compiled before it was added to the repository using pgi64/7.1-6, so if the compiler used with GMIN is different, or even just a different version of Portland, you'll need to recompile it yourself before you compile GMIN with CHARMM.
- 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.
- LAPACK and BLAS contain highly optimised maths algorithms used by GMIN.
Compiling GMIN with CHARMM
As an example, lets compile GMIN with CHARMM from the code we just obtained. 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 becuase there are so many options contained within. Any line starting with a # is commented out and will not be used. Scroll down until you come to the section titled AMBER9. Two variables (AMB9SRC and SANDERSRC) are defined below and you need to update them to reflect the location of the code you just downloaded. Remember, you must use the FULL path here, so no ~'s!
In my case, I need to set the variables as follows:
AMB9SRC = /home/csw34/GMIN/AMBER SANDERSRC = /home/csw34/GMIN/AMBER/src/sander
In the CHARMM31 section, I am also going to set
C31SRC = /home/csw34/GMIN/CHARMM31
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 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 and double check the variables we set above point to the right places! To compile GMIN with CHARMM, we then use the command
make cgmin2
Cross your fingers!