[gmx-users] g_covar Segmentation fault problem

[Justin Lemkul]

On 7/16/15 1:09 PM, gozde ergin wrote:
> Ok by using version 4.6.6 I got this segmentation fault error which means
> number of frames should be equal or bigger than the number of degrees of
> freedom.
>

Then use 4.6.7.  Maybe my ">=" should have been ">" instead.  The best bet when 
you get failures like this is to always upgrade to the latest version in 
whatever series you're trying to use.  4.6.7 should work.  If not, 5.0.5 
definitely does.

-Justin

>
> On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/16/15 12:26 PM, gozde ergin wrote:
>>
>>> Thank for reply Justin but I have difficulty to understand which version
>>> has this bug?
>>> If  'Segmentation fault because of #DOF and frames numbers difference' is
>>> a
>>> bug than gromacs 4.6.3 is working correctly, right?
>>>
>>>
>> Offhand, I don't know which outdated versions work and which don't.  To be
>> safe:
>>
>> 4.6.x series, use version >= 4.6.6
>> 5.0.x series, use version 5.0.5
>> Any other version in the development repo (master, release-5-0, etc)
>>
>> -Justin
>>
>>
>>
>>>
>>>
>>>
>>> On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 7/16/15 10:22 AM, gozde ergin wrote:
>>>>
>>>>   Dear gromacs user,
>>>>>
>>>>> In order to estimate system absolute entropy value I want to use
>>>>> g_covar +
>>>>> g_anaeig commands.
>>>>>
>>>>> However when I *'g_covar -f nvt.trr -s nvt.tpr'*  I get a segmentation
>>>>> fault after *'Diagonalizing ....'* step from gromacs 4.6.6 and 5.0.3.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> *Constructing covariance matrix (12258x12258) ...Last frame       4000
>>>>> time
>>>>> 4000.000   Read 4001 framesTrace of the covariance matrix: 12454.6
>>>>> (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6
>>>>> (nm^2)Segmentation
>>>>> fault (core dumped)*
>>>>>
>>>>> But the same command, executed with g_covar of gromacs 4.6.3 works
>>>>> without
>>>>> any error or fault.
>>>>>
>>>>> Was it a bug and corrected for newer versions? I saw  the release note
>>>>> of
>>>>> *
>>>>> 'Fixed a complicated bug in g_anaeig and g_covar, if the number of
>>>>> frames
>>>>> for a covariance analysis is fewer than the number of degrees of
>>>>> freedom'  *for
>>>>> gromacs 4.6.6.
>>>>>
>>>>>
>>>>>   The bug was also fixed for 5.0.5.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>>> Gromacs Users mailing list
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================