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

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 2 22:39:23 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.
> 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.
> 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.
> 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?

No such modifications should be necessary.  The script should work "out of the 
box," so to speak.  Let me go back to my original question - do you have a 
single-precision Gromacs installation, or just double-precision?  I seem to 
recall you saying that you were testing by running luck_d only.  How are you 
calling the script?  Just "./gmxtest.pl all"?  Because doing so only tests 
single-precision.  If there is a problem testing double-precision, it certainly 
needs to be addressed.

Whether or not the tests are meaningful is a bit more complex, as you note. 
Failures aren't always failures, per the many threads in the archive on this 
topic :)  Since Mark did quite a bit of work some time ago, the test set has 
been much more robust, but as you'll note from our discussion, more features and 
combinations should be implemented.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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