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
−  
−
===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:
  
 
<pre>
  
<pre>
  +
module load pgi64/7.1-6
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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/
  
  +
</pre>
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export MYSVN=https://wwmm.ch.cam.ac.uk/svn2/users/CRSID/
  
  +
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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<pre>
  +
module av
  +
</pre>
  +
Once the compiler is loaded, change to the CHARMM31 directory using
  +
<pre>
  +
cd ~/svn/CHARMM31
  +
</pre>
  +
CHARMM is compiled by a series of scripts which we run using a few simple commands. Firstly,
  +
<pre>
  +
./clean.csh
  +
</pre>
  +
removes any files from a previous CHARMM installation. The installation is then started using
  +
<pre>
  +
./compile.csh
  +
</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>
  +
tail build.log
  +
</pre>
  +
You should get something like this if all is well:
  +
<pre>
  +
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
  +
</pre>
  +
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
  +
<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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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>
  +
make chgmin
−
:wq
  
 
</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:
−
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>
  +
/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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source ~/.bashrc
  
 
</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!

Latest revision as of 11:24, 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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