[gmx-developers] Problem with g_covar diagonalizing large covariance matrices

[Mark Abraham]

On Mon, Oct 27, 2014 at 9:28 PM, Mendez Giraldez, Raul <
rmendez at email.unc.edu> wrote:

>  Hi Mark,
>
>  I've no idea about LAPACK compilation, Gromacs was installed in our
> computer cluster at UNC by the administrators.
>

Sure, but that seems like the best direction for investigation if your
observations are that you're observing some LAPACK-related memory-limit
issue.


> Regarding my system, I do not include hydrogen atoms in the covariance
> computation, but if I am not wrong, they should not be a problem because
> they are constraints by LINCS.
>

They are still nominal DOF that you don't need to have in your covariance
matrix, and since the size of the matrix limits both your ability to do the
analysis and the speed with which you can do it...


> I have a homotetramer membrane channel protein, each monomer made of 226
> residues (x4), in total about 14000 atoms protein only and about  1500 ions
> (that are close to the entrance top/bottom). The idea is to see whether low
> frequency modes of channel opening promote ion permeation. That's why I do
> not want to work with C-alpha only.
>

There's other options, e.g. all-backbone, all-heavy.

Mark


> Thanks,
> Raul
>  ------------------------------
> *From:* gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abraham at gmail.com]
> *Sent:* Monday, October 27, 2014 3:48 PM
> *To:* Discussion list for GROMACS development
> *Cc:* Liu, Shubin; gromacs.org_gmx-developers at maillist.sys.kth.se
> *Subject:* Re: [gmx-developers] Problem with g_covar diagonalizing large
> covariance matrices
>
>
>
> On Mon, Oct 27, 2014 at 2:19 PM, Mendez Giraldez, Raul <
> rmendez at email.unc.edu> wrote:
>
>>  Dear Gromacs developers,
>>
>>  I am trying to compute PCA on a 46464x46464 matrix (15488 atoms).
>> g_covar produces segmentation fault. We thought it was a lack of physical
>> memory, but when our computer cluster system administrator, Shubin Liu,
>> looked into the system logs, found that the maximum RAM used by the program
>> was 16 Gb, while I had booked up to 800 Gb of RAM. Shubin realized that the
>> actual problem arises at the eigensolver call within covar routine. So it
>> looks like eigensolver is unable to handle big matrices, but not because
>> of lack of physical memory (is it based on LAPACK libraries, still 32-bit
>> coded?).
>>
>
>  I've no idea if there are any limits, but you can choose the LAPACK
> implementation with which to link GROMACS (see install guide), so you
> should find out what you've been using (e.g. inspect CMakeCache.txt in your
> build tree), and explore alternatives.
>
>   I am using Gromacs 4.6.3.
>>
>>  Do you know an alternative to that? The reason I want to do that is
>> to have some ion atoms in addition to my protein and see how they move
>> along the low frequency modes (large variance PCs).
>>
>
>  How many of your protein atoms do you really need for that analysis? I
> presume you're already excluding the hydrogen atoms, since they're not
> doing much at low frequencies. Even if you think you really do need them, I
> suggest you start with something small that works.
>
>  Mark
>
>
>>
>>  Thank you so much,
>>
>>  Raul
>>
>> Raul Mendez Giraldez, PhD
>> Dokholyan Lab
>> Dept. Biophysics & Biochemistry
>> Genetic Medicine
>> University of North Carolina
>> 120 Mason Farm Road
>> Chapel Hill, NC 27599
>> US
>>
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>
>
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