Hi Chung-ke,
Welcome to the relax mailing lists! Thanks to the hard work of one of
the relax developers - Troels Linnet - this long calculation time
should now be much, much shorter. Have a look at the following
release announcement:
http://wiki.nmr-relax.com/Relax_3.3.0
For the 'CR72 full' model (http://wiki.nmr-relax.com/CR72_full), the
clustering example here gives a ~22x speed up so your calculation time
would then drop from ~20,000 min to ~1000 min. If you would like to
receive announcements about new relax versions, please subscribe to
the relax-announce mailing list
(https://mail.gna.org/listinfo/relax-announce/). This list only
receives ~10 emails per year. See
http://news.gmane.org/gmane.science.nmr.relax.announce.
I have a few questions about how you performed the analysis. Did you
use a non-clustered set of results to seed the clustered analysis? In
the dispersion auto-analysis protocol exposed via the GUI, the results
from the non-clustered analysis will be taken as the starting point
for optimisation of the clustered analysis, as described in Morin et
al., 2014 (http://dx.doi.org/10.1093/bioinformatics/btu166). If you
wish, and are capable with scripting, you can also create your own
analysis protocol via a relax script and not use the auto-analysis.
The relax software is very flexible and you can create quite complex
analysis protocols - the auto-analyses are just large relax scripts.
Also, did you look at the results from the non-clustered analysis to
see if the kinetics of all 13 residues are similar? Or if the
dispersion curves look reasonable? Some data might be of low quality
and causing difficulties with the optimisation. You should also note
that most dispersion data is not good enough to differentiate R20A
from R20B. Do the final results (non-clustered and clustered) look
reasonable for these two parameters? It could be that differentiating
R20A from R20B in your system is difficult and causing optimisation to
take much longer than normal. Do you see the same optimisation times
with the clustered CR72 model where R20A=R20B=R20
(http://wiki.nmr-relax.com/CR72)? Also, have a look at the log file
from the analysis and see if the total number of minimisation
iterations is much longer for the 'CR72 full' model compared to the
CR72 model. This will tell you if the optimisation problem is much
more complicated for the 'full' model.
Regards,
Edward
On 9 September 2014 09:19, Chung-ke Chang <chungke@xxxxxxxxxxxxxxxxxx> wrote:
Dear all,
This is my first post here, and I have a question regarding the time it
takes for a relaxation dispersion clustering process to finish. I have one
clustering calculation that has been running for ~ 20,000 min on a single
Xeon 2.66 GHz core. The cluster consists of 13 residues being fit to the
‘CR72 full’ model. I wonder if the long time it is taking is normal? Would
it be possible that relax has been stuck in an infinite loop of some sort,
without showing up in the log file? Any input would be greatly appreciated.
By the way, using a cluster of only 11 residues out of the 13 did finish in
~13,000 min.
Chung-ke Chang
Biomacromolecular NMR Lab
Institute of Biomedical Science
Academia Sinica, Taiwan
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Re: Relaxation dispersion clustering calculation time