[gmx-users] Gromacs Installation troubles

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 18 15:46:37 CET 2008

Nicholas Geraedts wrote:
> Mark - I've followed the instructions on the wiki. The last step says to 
> email the mailing list, as I have done. I'm not sure about your comment 
> for not needing a complete make if we're looking for MPI. There are 
> situations where the program will be used in single-processor mode, as 
> well as MPI. I'm not too concerned with the time it takes to compile all 
> of this (it's only about 8 minutes for the whole lot).

Sure. The point is to avoid compiling and installing MPI versions that 
aren't useful, while not installing the non-MPI versions that are... 
Admittedly, the loss case for a full install of both flavours is pretty 

> Jussi - I'm trying to compile the packages myself since the pre-made 
> RPM's don't seem to install the libraries needed. Furthermore, the LAM 
> RPM would constantly complain about not being able to find gcc-g77 - a 
> package found in CentOS4 but not CentOS5 (it's now referred to as 
> compat-gcc-34-g77 - the names don't agree so rpm complains). 

So that's why you can force RPM to do things when you do happen to know 
better that it does.

> Also, 
> installing LAM from yum fails to put the required binaries where they 
> belong! There's no lamboot, mpmirun, lamhalt, etc to be found anywhere 
> in the path. 

Define "belong". :-) You can find out from yum and RPM what files were 
installed with each package... that will allow you to find the correct 
things to add to your path.

>I've found that it's often much less of a headache if you 
> can find the source and start from scratch (this is the FreeBSD child in 
> me talking). 
> My main problem so far is that the library for GSL is installed in the 
> wrong location and that mdrun_mpi doesn't seem to have been compiled. If 
> the source is provided, it should be possible to compile it into a 
> functional program...

Sure. I told you last time
a) that GSL is only useful for a tiny piece of functionality and
b) how to see what mdrun got installed where.


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