CVS HowTo

From wiki.gromacs.org

To keep track of changes and different versions of the GROMACS source code we use CVS, Concurrent Version System. CVS is free software and available on all major platforms. You can find manuals, source code and a lot of other CVS information at www.cvshome.org. If you are using Linux it should be trivial to install a cvs package, but it is probably already present on your system. Anonymous CVS read-only access The latest development version of the Gromacs source is available via anonymous CVS. You do not need any special account to retrieve the source, but of course it is read-only. We are usually quite conservative when commiting changes, so the CVS version should be functional and without major bugs, but it is entirely unsupported. We appreciate if you point out bugs or problems, but since this is development software it might take a while to fix them. In other words, check your results VERY carefully if you use CVS for any kind of production runs.

Use the following commands to retrieve the latest CVS source: (The whole command from 'cvs' to 'login' (and 'gmx' the second time) should be on one line - your browser might wrap the lines in the window below. Just hit return when you are prompted for a password) (In the case of the error "cvs login: failed to open /home/user/.cvspass for reading: No such file or directory", one should create an empty .cvspass file in the home directory)

 	$>cvs -z3 -d :pserver:anoncvs@cvs.gromacs.org:/home/gmx/cvs login
        Password:
        $>cvs -z3 -d :pserver:anoncvs@cvs.gromacs.org:/home/gmx/cvs co gmx

This will create a "gmx" subdirectory with all the Gromacs sources. To create the configure script files you should now run the "./bootstrap" script in the gmx directory. To do this you might need to install or upgrade your versions of autoconf and automake to those provided on this site. Check Development_Tools. If you don't give any special command you will check of the HEAD branch, which is the main development branch, heading for the next major Gromacs version. If you only want to check or work with the most recent bugfixes in the stable revision tree you should switch 'branch' to the patches for the stable version instead. This is easy; just write

 	$>cvs update -A -r release-3-3-patches

in the top gmx directory. The -A flag is just to make sure we remove all sticky tags - a normal 'update' will only get you the most recent version of the branch you are currently working with. You cannot commit any changes as an anonymous user. If you would like to have a bugfix or other modification incorporated into the source it is best to post it to the gmx-developers mailing list.

PLEASE NOTE: To avoid confusing normal users, try to post all CVS-related questions to the gmx-developers list and not the general gmx-users list. You can also get out the LaTeX source for the manual by checking out the module "doc", and our local regression test suite as the module "gmxtest". . Read-Write access with a user ID If you have been given full write access to the repository, you should have a user name and password. Since the pserver method above transfers all passwords in clear text we are running it in read-only mode. This means you need to use ssh as an external authentication method for CVS if you want to write to CVS. There is built-in support for this, ut we must first tell it which method to use. For bash/zsh-style shells:

 	$>export CVS_RSH=ssh

or for csh/tcsh shells:

 	$>setenv CVS_RSH ssh

It is a good idea to assign this environment variable into your login files so you don't have to do it every time you use cvs. It will not interfere with CVS pserver usage on cvs.gromacs.org or other servers. Now execute ssh with the "ext" authentication method (external):

 	$>cvs -z3 -d :ext:@cvs.gromacs.org:/home/gmx/cvs co gmx

You can get rid of the password prompt completely if you add your public key to the file ~/.ssh/authorized_keys on the server. Use ssh-keygen on the machine you will log in from if you haven't got a key yet.

Some tips for using CVS There are a couple of things you might need to know in order to get started. anonymous access:

Make your own work directory, e.g. /home/lindahl/gmxwork and cd there before you check out the sources from CVS.
It is no problem to check out several working copies of the source in different places. You might for instance want one on your portable too, or your home macine.
To compile GROMACS from CVS you need to use automake to create the intermediary Makefile.in's, and autoconf to create the configure script. All these steps are performed when you run the "bootstrap" command in the gmx directory. Note that you will probably have to upgrade your installed versions of these programs to those provided on this site.
If you at a later point want to get a new version of the software (after your colleagues have added new features), simply type

     cvs update gmx.

If you want to upload your edits to the repository use a command like

     cvs commit file1 [file2]
     to enter one or more files.

If you want to add or remove a file to/from the repository, use the (by now obvious) command

     cvs add/remove file1 [file2]
     To make this changes have any effect on the repository you will also have to commit them (cvs will tell you).

If you are done with editing for the few coming weeks use cvs release gmx. CVS will then tell you if there are any changes you haven't committed yet.
You can check out an earlier version(e.g. 1.14) of a file with

     cvs update -r 1.14 file.c. Note that this will create a sticky tag on the file, so it will NOT be updated the next time you do a normal update. To remove the sticky tags you must use the -A flag to cvs update, i.e.
     cvs update -A.