[gmx-users] RE: Mark & Justin - grompp error for gmxtest-4.0.4 and 3.3.3 on new gromacs-4.0.5 install

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 3 05:44:38 CET 2009

Yirdaw, Robel Birru wrote:
> Thank you both for your reply.
> So how did you guys verify and test gromacs on your machines?
> Mark, from your response, test-set 4.0.4 is of no use?!  I have seen your
> other posts but the problem here is far more basic than that.

It is of some use, but it is not robust in non-expert hands, and there 
are many known cases of failure. To be fit for the purpose, it should 
pretty much just work in the hands of a UNIX-competent sysadmin who 
knows nothing about GROMACS or perl.

> If it happens that 4.0.4 is usable to some degree, there's still the issue
> I brought up on my initial post - the script gives the grompp error.  Now
> looking at the code I can see where the problem is:  subroutine gmx_test()
> is called before double or single precision, or any of the options for
> that matter, are determined in the for loop following the gmx_test() call.
>  And so you end up with the "ERROR: Can not find grompp in your path...." 
> again, regardless of whether or not you have provided any options -
> besides without options it should respond with usage info which it
> doesn't.  However, in test-set 3.3.2, this subroutine does not exist and
> like I said in my previous post, it does run upto a certain point.  So,
> correct me if I am wrong, but gmx_test() is out of place in versions 3.3.3
> and 4.0.4.

The parsing of command line options is one of the examples of 
non-robustness of the old script. The version in git is much better in 
this regard. However that can't get properly released until a number of 
issues are resolved that I'm not the best person to decide.

> Which takes me back to my question - how did you guys, or anyone else, do
> your testing.  I thought of modifying the script to make it run but it
> looks like it needs more than just moving that one line.  Also, I just
> can't believe that this type of modification is expected on stuff
> available for download on the site.

Sorry. I'd like a useful test set available too (and have fixed it so 
that it is a useful test for my purposes), but everyone's effectively a 
volunteer around here.

> I mean, if this is really the case can one of the developers fix this and
> put up a usable script.  And, again, would doing so make the test set
> usable to some degree?

I've updated the wiki page to suggest trying the git version - 
That's been available since August and I expect it to be fit for the 
purpose of testing GROMACS 4.0.x. I haven't had any feedback since then, 
so it is still alpha-release quality. Any commentary on that version 
would be valuable.


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