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

Yirdaw, Robel Birru robel.b.yirdaw at Vanderbilt.Edu
Sat Dec 5 03:29:12 CET 2009

Thanks Mark and Justin for all your input.  I will try the git version and
do any necessary modifications to test my install.

> 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 -
> http://www.gromacs.org/index.php?title=Download_%26_Installation/Test-Set.
> 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.
> Mark
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