Difference between revisions of "Compiling GMIN with CHARMM"

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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.
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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.
   
  +
Once you have the source, you need to first compile [[CHARMM]]. This procedure is different from that when compiling [[OPTIM]], where a build.csh script recompiles [[CHARMM]] automatically if required. In the future, this may be extended to [[GMIN]].
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===Getting an account on the SVN server===
  
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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.
 
   
  ⚫
===Compiling CHARMM===
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Once they reply, you should be able to set up your password [https://wwmm.ch.cam.ac.uk/svnpassword/modify.py here] after logging into Raven. To check you have access to the repository, try logging in [https://wwmm.ch.cam.ac.uk/svn2/ here]. If you can't, you've done something wrong! Get help!
  
  +
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
−  
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===Setting up your SVN details===
  
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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:
  
 
<pre>
  
<pre>
  +
module load pgi64/7.1-6
−
vi ~/.bashrc
  
 
</pre>
  
</pre>
  +
If you get a conflict error message, you already have a version of pgf90 loaded and need to swap it out, for example:
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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:
  
 
<pre>
  
<pre>
  +
module swap pgi64/6.1-6 pgi64/7.1-6
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export SVN=https://wwmm.ch.cam.ac.uk/svn2/groups/wales/
  
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export MYSVN=https://wwmm.ch.cam.ac.uk/svn2/users/CRSID/
  
 
</pre>
  
</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 available to load using
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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:
  
 
<pre>
  
<pre>
  +
module av
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:wq
  
 
</pre>
  
</pre>
  +
Once the compiler is loaded, change to the CHARMM31 directory using
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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:
  
 
<pre>
  
<pre>
  +
cd ~/svn/CHARMM31
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source ~/.bashrc
  
 
</pre>
  
</pre>
  +
CHARMM is compiled by a series of scripts which we run using a few simple commands. Firstly,
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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):
  
 
<pre>
  
<pre>
  +
./clean.csh
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svn ls $SVN/GMIN/trunk
 
 
</pre>
  
</pre>
  +
removes any files from a previous CHARMM installation. The installation is then started using
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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:
  
  ⚫
<pre>
  +
./compile.csh
 
</pre>
  
</pre>
  +
It takes a while...so if you see it finish quickly, within a minute - you probably have problems! You can check by using
−
...
  
  ⚫
<pre>
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wenzel.f
  
  +
tail build.log
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wham_djw.f90
  
−
zwischen.f
  
 
</pre>
  
</pre>
  +
You should get something like this if all is well:
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Congratulations! You're now good to download the GMIN code :)
  
  +
<pre>
  +
install.com> Phase 2 completed.
   
  +
install.com> Processing CHARMM source on gnu...
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==='Checking out' the GMIN code===
  
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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!'''
  
  +
install.com> CHARMM Installation is completed.
⚫
<pre>
  
−
/home/csw34/svn/GMINxxxxxx/
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The CHARMM executable is /home/csw34/svn/CHARMM31/exec/gnu/charmm.
  +
  +
install.com> Phase 3 completed.
  +
Tue Jul 1 20:46:11 BST 2008
 
</pre>
  
</pre>
  +
If you do, congratulations! You have just compiled CHARMM :)
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The code is checked out as follows:
  
  +
⚫
<pre>
  
  +
===Compiling GMIN with CHARMM===
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svn co $SVN/GMIN/trunk ~/GMIN
  
  ⚫
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, 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
 
</pre>
  
</pre>
  +
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
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Notice that I'm transfering the code to:
  
 
<pre>
  
<pre>
  +
make chgmin
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/home/csw34/GMIN
  
 
</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:
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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:
  
 
<pre>
  
<pre>
  +
/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
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Checked out revision 9853.
  
 
</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/bin directory! Go test it!
−
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.
  
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* '''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.
  
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* '''AMBER''' contains the AMBER9 source code.
 
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* '''AMH''' contains the files used for the AMH potential as implemented by Dr Mike Prentiss.
  
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* '''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!
  

Latest revision as of 10:24, 14 July 2008

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.

Once you have the source, you need to first compile CHARMM. This procedure is different from that when compiling OPTIM, where a build.csh script recompiles CHARMM automatically if required. In the future, this may be extended to GMIN.

Compiling CHARMM

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 available 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, 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 

 
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 `nmr_' 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/bin directory! Go test it!

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