[gmx-users] g_wham error analysis hangs

Magnus Andersson magnus.andersson at scilifelab.se
Mon Aug 12 13:55:40 CEST 2013 

Hi Jochen,

Seems as if this error was associated with the mpi version. Everything worked ok when running it locally.

Best regards /

Magnus

On Aug 12, 2013, at 1:50 PM, Jochen Hub <jhub at gwdg.de> wrote:

> Hi Magnus,
> 
> I just read your mail. Sound very much like a bug, which never occurred
> to me though. But I did not use -bs-method traj-gauss a lot. Does the
> error also occur with -bs-method traj?
> 
> Btw: with -bs-method traj-gauss or traj, you need realistic estimates of
> the autocorrelation times (ACTs). If you underestimate the ACTs, you
> will underestimate your errors.
> 
> If this error still occurs with the latest version, could you make a
> tar-ball of your tpr and pullf files, put them online, and send me the link?
> 
> Then I will try to fix the bug.
> 
> Best,
> Jochen
> 
> 
> Am 8/5/13 8:29 AM, schrieb Magnus Andersson:
>> Hi,
>> 
>> I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do:
>> 
>> g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist  -nBootstrap 50 -bins 50  -bs-method traj-gauss -bsres -ac yes -bsprof -vbs
>> 
>> This is the output after which it just hangs:
>> 
>> Estimating integrated autocorreltion times ... [100%] ... done
>> 
>> Back Off! I just backed up iact.xvg to ./#iact.xvg.4#
>> Wrote iact.xvg
>> win 0, aver = 3.413503  sig = 0.091051
>> win 1, aver = 3.440995  sig = 0.060213
>> win 2, aver = 3.536864  sig = 0.069048
>> win 3, aver = 3.462364  sig = 0.041276
>> win 4, aver = 3.508488  sig = 0.041967
>> win 5, aver = 3.474703  sig = 0.038848
>> win 6, aver = 3.546181  sig = 0.042018
>> win 7, aver = 3.558158  sig = 0.047886
>> win 8, aver = 3.870348  sig = 0.053350
>> win 9, aver = 3.895024  sig = 0.047226
>> win 10, aver = 3.905363  sig = 0.039718
>> win 11, aver = 3.989860  sig = 0.048854
>> win 12, aver = 4.033406  sig = 0.045494
>> win 13, aver = 4.077549  sig = 0.042215
>> win 14, aver = 4.096139  sig = 0.036315
>> win 15, aver = 4.174044  sig = 0.040574
>> win 16, aver = 4.119622  sig = 0.052487
>> win 17, aver = 4.177672  sig = 0.036798
>> win 18, aver = 4.148724  sig = 0.033967
>> win 19, aver = 4.228320  sig = 0.039398
>> win 20, aver = 4.161365  sig = 0.039424
>> win 21, aver = 4.176532  sig = 0.041844
>> win 22, aver = 4.224519  sig = 0.030001
>> win 23, aver = 4.468429  sig = 0.046136
>> win 24, aver = 4.536401  sig = 0.049635
>> win 25, aver = 4.666026  sig = 0.054179
>> win 26, aver = 4.670022  sig = 0.045487
>> win 27, aver = 4.866098  sig = 0.046887
>> win 28, aver = 4.935376  sig = 0.050013
>> win 29, aver = 4.891905  sig = 0.042927
>> Getting initial potential by integration.
>> Initialized rapid wham stuff (contrib tolerance 3.33333e-08)
>> Evaluating only 474 of 1500 expressions.
>> 
>> 	   1) Maximum change 2.849816e-01
>> 	 100) Maximum change 2.216439e-03
>> 	 200) Maximum change 1.866839e-03
>> 	 300) Maximum change 1.612522e-03
>> 	 400) Maximum change 1.419577e-03
>> 	 500) Maximum change 1.266497e-03
>> 	 600) Maximum change 1.140793e-03
>> 	 700) Maximum change 1.034780e-03
>> 	 800) Maximum change 9.434951e-04
>> 	 900) Maximum change 8.635977e-04
>> 	1000) Maximum change 7.927633e-04
>> 	1100) Maximum change 7.293254e-04
>> 	1200) Maximum change 6.720574e-04
>> 	1300) Maximum change 6.200347e-04
>> 	1400) Maximum change 5.725450e-04
>> 	1500) Maximum change 5.290277e-04
>> 	1600) Maximum change 4.890329e-04
>> 	1700) Maximum change 4.521924e-04
>> 	1800) Maximum change 4.181996e-04
>> 	1900) Maximum change 3.867947e-04
>> 	2000) Maximum change 3.577540e-04
>> 	2100) Maximum change 3.308822e-04
>> 	2200) Maximum change 3.060068e-04
>> 	2300) Maximum change 2.829734e-04
>> 	2400) Maximum change 2.616429e-04
>> 	2500) Maximum change 2.418887e-04
>> 	2600) Maximum change 2.235951e-04
>> 	2700) Maximum change 2.066558e-04
>> 	2800) Maximum change 1.909727e-04
>> 	2900) Maximum change 1.764550e-04
>> 	3000) Maximum change 1.630186e-04
>> 	3100) Maximum change 1.505854e-04
>> 	3200) Maximum change 1.390827e-04
>> 	3300) Maximum change 1.284431e-04
>> 	3400) Maximum change 1.186038e-04
>> 	3500) Maximum change 1.095063e-04
>> 	3600) Maximum change 1.010962e-04
>> 	3700) Maximum change 9.332302e-05
>> 	3800) Maximum change 8.613974e-05
>> 	3900) Maximum change 7.950267e-05
>> 	4000) Maximum change 7.337121e-05
>> 	4100) Maximum change 6.770765e-05
>> 	4200) Maximum change 6.247700e-05
>> 	4300) Maximum change 5.764678e-05
>> 	4400) Maximum change 5.318686e-05
>> 	4500) Maximum change 4.906931e-05
>> 	4600) Maximum change 4.526823e-05
>> 	4700) Maximum change 4.175964e-05
>> 	4800) Maximum change 3.852131e-05
>> 	4900) Maximum change 3.553267e-05
>> 	5000) Maximum change 3.277469e-05
>> 	5100) Maximum change 3.022973e-05
>> 	5200) Maximum change 2.788151e-05
>> 	5300) Maximum change 2.571494e-05
>> 	5400) Maximum change 2.371608e-05
>> 	5500) Maximum change 2.187205e-05
>> 	5600) Maximum change 2.017093e-05
>> 	5700) Maximum change 1.860172e-05
>> 	5800) Maximum change 1.715425e-05
>> 	5900) Maximum change 1.581912e-05
>> 	6000) Maximum change 1.458767e-05
>> 	6100) Maximum change 1.345187e-05
>> 	6200) Maximum change 1.240432e-05
>> 	6300) Maximum change 1.143820e-05
>> 	6400) Maximum change 1.054720e-05
>> 	6500) Maximum change 9.725497e-06
>> 	6600) Maximum change 8.967716e-06
>> 	6700) Maximum change 8.268901e-06
>> 	6800) Maximum change 7.624473e-06
>> 	6900) Maximum change 7.030212e-06
>> 	7000) Maximum change 6.482219e-06
>> 	7100) Maximum change 5.976900e-06
>> 	7200) Maximum change 5.510938e-06
>> 	7300) Maximum change 5.081272e-06
>> 	7400) Maximum change 4.685081e-06
>> 	7500) Maximum change 4.319759e-06
>> 	7600) Maximum change 3.982905e-06
>> 	7700) Maximum change 3.672303e-06
>> 	7800) Maximum change 3.385910e-06
>> 	7900) Maximum change 3.121841e-06
>> 	8000) Maximum change 2.878356e-06
>> 	8100) Maximum change 2.653854e-06
>> 	8200) Maximum change 2.446856e-06
>> 	8300) Maximum change 2.255997e-06
>> 	8400) Maximum change 2.080021e-06
>> 	8500) Maximum change 1.917767e-06
>> 	8600) Maximum change 1.768166e-06
>> 	8700) Maximum change 1.630232e-06
>> 	8800) Maximum change 1.503056e-06
>> 	8900) Maximum change 1.385799e-06
>> 	9000) Maximum change 1.277687e-06
>> 	9100) Maximum change 1.178008e-06
>> 	9200) Maximum change 1.086104e-06
>> 	9300) Maximum change 1.001369e-06
>> Switched to exact iteration in iteration 9302
>> Converged in 9303 iterations. Final maximum change 9.98417e-07
>> 
>> Back Off! I just backed up profile.xvg to ./#profile.xvg.8#
>> Wrote profile.xvg
>> 
>> Any idea of what goes wrong? 
>> 
>> Best regards /
>> 
>> Magnus
>> 
> 
> -- 
> ---------------------------------------------------
> Dr. Jochen Hub
> Computational Molecular Biophysics Group
> Institute for Microbiology and Genetics
> Georg-August-University of Göttingen
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
> Phone: +49-551-39-14189
> http://cmb.bio.uni-goettingen.de/
> ---------------------------------------------------

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