[gmx-developers] Small configure.ac change

Erik Lindahl lindahl at sbc.su.se
Sun Jan 2 14:38:47 CET 2005


I've moved all symbols to use GMX_ prefixes, to make it easier 
interfacing Gromacs with other stuff (and to know which symbols are 
part of gromacs) - but apparently I missed this one :-)

On Jan 1, 2005, at 2:11 PM, Charlie Peck wrote:

> On Jan 1, 2005, at 5:15 AM, David van der Spoel wrote:
>> On Fri, 31 Dec 2004, Charlie Peck wrote:
>>> I'm working with the CVS snapshot labeled GROMACS 3.3_beta_20041226.
>>> configure.ac produces a symbol GMX_MPI when --enable-mpi is specified
>>> on the configure command line but many places in the source code are
>>> looking for the symbol USE_MPI.  The net effect is that you can't run
>>> this snapshot with MPI.
>> I haven't seen this problem in plain CVS. Maybe you should just try to
>> download the latest cvs rather than this snapshot.
> I misspoke, I am using the latest CVS cut (retrieved with $ cvs ... co 
> gmx) when I get this error.  In any event the fix on my end is easy 
> for this item.
> I ran into a second problem later on, here's the output from mdrun:
> -------------------------------------------------------
> Program mdrun, VERSION 3.3_beta_20041226
> Source code file: ns.c, line: 314
> Fatal error:
> ns.c, 315: Negative number of short range atoms.
> Call your Gromacs dealer for assistance.
> -------------------------------------------------------
> This was with the DPPC gmxbench system.  I get the same error with 
> gmxbench's villin system.  These same input files work fine with our 
> 3.2.1 code.  Unfortunately my background is computer science not 
> chemistry so this could be the result of a change in the behavior of 
> grompp/mdrun that I need to learn about, but I didn't see anything in 
> the manual (also checked-out from CVS) that referenced this.
> The folks I work with are building a wrapper for GROMACS that 
> automates running molecular systems on clusters.  There are some 
> features in the current CVS cut that we would really like to take 
> advantage of but we don't want to pester the developers with lots of 
> questions if the codeline isn't in a state for this type of testing.  
> I got the sense reading the developers page at www.gromacs.org that it 
> was pretty stable.  If you would rather we stick to 3.2.1 for now we 
> can.

Normally it's quite stable, but we recently added a _huge_ amount of 
new stuff, and haven't had time to test everything yet - it should 
stabilize in a couple of days or a week...

I'll look into the NS and MPI symbol stuff.

All the best,

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