[gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500

[Mark Abraham]

On Thu, Nov 6, 2014 at 4:35 PM, Machtens, Jan-Philipp <
j.machtens at fz-juelich.de> wrote:

> Hi,
> yes I will post that to redmine soon, but let me first clarify the issue,
> since I tested some more conditions in the meantime.
> (I realized that my trajectory had 1501 frames and the error occured when
> I choose more than 500 atoms, i.e. when the number of degrees of freedom
> becomes larger then the number of frames).
> So in general, if your trajectory has nf frames, g_covar will result in a
> segfault if the group to be (covariance) analyzed is larger then nf/3 atoms.
> If found this statement to be true for gromacs 4.6.6, 4.6.7 and 5.0.2.
> This error does not happen for gromacs 4.6.5
>
> So, I wonder whether this is an unwanted behaviour which has been
> introduced in 4.6.6? Do you think this behavior makes sense ? The official
> release notes for 4.6.6 do not mention changes in g_covar.
>

Correct, but a change (git hash 972032bfb8) that was intended to fix a
problem observed with g_anaeig also affected code in g_covar (which I have
now corrected in the release notes). The nature of the change seems very
consistent with your observations.

Mark

Best,
> Jan-Philipp Machtens
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abraham at gmail.com]
> Sent: Thursday, November 06, 2014 1:27 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance
> matrices bigger than 1500x1500
>
> Hi,
>
> IIRC some minor bugs were fixed, but a regression like that should be dealt
> with... please file at http://redmine.gromacs.org.
>
> Mark
>
> On Thu, Nov 6, 2014 at 12:00 PM, Machtens, Jan-Philipp <
> j.machtens at fz-juelich.de> wrote:
>
> > Dear all,
> > I observed that g_covar in Gromacs 5.0.2 segfaults at the diagonalization
> > step, if the group for the covariance analysis is bigger than 500 atoms,
> > i.e. if the covariance matrix is bigger than 1500x1500.
> > In my hands, this problem does not arise with g_covar 4.6.x. The results
> > obtained from g_covar (version 5.x) on groups <= 500 atoms that I
> obtained
> > were the same os those from version 4.6.x and also verified manually.
> > Memory is not the problem here. The problem is independent on
> single/double
> > precision.
> >
> > Before posting this on redmine.gromacs I first want to check whether
> > someone here has made a contradicting experience which would argue
> against
> > a possible bug introduced in 5.0.2?
> > Thanks.
> > Cheers,
> > Jan-Philipp Machtens
> >
> >
> >
> >
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