Project: 7020 (Run 1, Clone 304, Gen 1) LINCS Warning

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karlinhigh
Posts: 17
Joined: Tue Mar 01, 2011 4:03 am

Project: 7020 (Run 1, Clone 304, Gen 1) LINCS Warning

Post by karlinhigh »

My Linux client did something I haven't seen before: a LINCS warning that didn't crash the work unit. It's still running, at 90% or so now. Is there anything I need to do about this?

Code: Select all

# Linux Console Edition #######################################################
###############################################################################

                       Folding@Home Client Version 6.02

                          http://folding.stanford.edu

###############################################################################
###############################################################################

Launch directory: /home/karlin/FAH
Executable: ./fah6


[18:18:27] - Ask before connecting: No
[18:18:27] - User name: desktopsvcs.com (Team 35054)
[18:18:27] - User ID: 23F8368F4A5765C7
[18:18:27] - Machine ID: 1
[18:18:27]
[18:18:28] Loaded queue successfully.
[18:18:28]
[18:18:28] + Processing work unit
[18:18:28] Core required: FahCore_a4.exe
[18:18:28] Core found.
[18:18:28] Working on Unit 06 [July 4 18:18:28]
[18:18:28] + Working ...
[18:18:28]
[18:18:28] *------------------------------*
[18:18:28] Folding@Home Gromacs GB Core
[18:18:28] Version 2.27 (Dec. 15, 2010)
[18:18:28]
[18:18:28] Preparing to commence simulation
[18:18:28] - Looking at optimizations...
[18:18:28] - Files status OK
[18:18:28] - Expanded 51963 -> 197212 (decompressed 379.5 percent)
[18:18:28] Called DecompressByteArray: compressed_data_size=51963 data_size=1972                                                                                                 12, decompressed_data_size=197212 diff=0
[18:18:28] - Digital signature verified
[18:18:28]
[18:18:28] Project: 7020 (Run 1, Clone 304, Gen 1)
[18:18:28]
[18:18:28] Assembly optimizations on if available.
[18:18:28] Entering M.D.
                         :-)  G  R  O  M  A  C  S  (-:

                   Groningen Machine for Chemical Simulation

                            :-)  VERSION 4.5.3  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, P--r Bjelkmar, Rudi van Drunen, Anton Feenstra,
        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.


                               :-)  Gromacs  (-:

Reading file work/wudata_06.tpr, VERSION 4.5.2 (single precision)

Reading checkpoint file work/wudata_06.cpt generated: Sat Jul  2 23:20:12 2011


starting mdrun 'Protein'
20000000 steps, 100000.0 ps (continuing from step 14600001,  73000.0 ps).
[18:18:34] Using Gromacs checkpoints
[18:18:34] Mapping NT from 1 to 1
[18:18:34] Resuming from checkpoint
[18:18:34] Verified work/wudata_06.log
[18:18:34] Verified work/wudata_06.trr
[18:18:35] Verified work/wudata_06.xtc
[18:18:35] Verified work/wudata_06.edr
[18:18:35] Completed 4600001 out of 10000000 steps  (46%)
[18:50:57] Completed 4700000 out of 10000000 steps  (47%)
[19:22:52] Completed 4800000 out of 10000000 steps  (48%)
[19:54:35] Completed 4900000 out of 10000000 steps  (49%)
[20:26:43] Completed 5000000 out of 10000000 steps  (50%)
[20:58:31] Completed 5100000 out of 10000000 steps  (51%)
[21:31:00] Completed 5200000 out of 10000000 steps  (52%)
[22:02:45] Completed 5300000 out of 10000000 steps  (53%)
[22:34:57] Completed 5400000 out of 10000000 steps  (54%)
[23:06:51] Completed 5500000 out of 10000000 steps  (55%)
[23:38:46] Completed 5600000 out of 10000000 steps  (56%)
[00:10:19] Completed 5700000 out of 10000000 steps  (57%)
[00:42:25] Completed 5800000 out of 10000000 steps  (58%)
[01:14:13] Completed 5900000 out of 10000000 steps  (59%)
[01:46:23] Completed 6000000 out of 10000000 steps  (60%)
[02:18:17] Completed 6100000 out of 10000000 steps  (61%)
[02:50:13] Completed 6200000 out of 10000000 steps  (62%)
[03:21:48] Completed 6300000 out of 10000000 steps  (63%)
[03:53:39] Completed 6400000 out of 10000000 steps  (64%)
[04:25:22] Completed 6500000 out of 10000000 steps  (65%)
[04:57:11] Completed 6600000 out of 10000000 steps  (66%)
[05:29:06] Completed 6700000 out of 10000000 steps  (67%)

Step 16770937, time 83854.7 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000237, max 0.002110 (between atoms 399 and 408)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    407    408   32.4    0.0958   0.0960      0.0960

Step 16770937, time 83854.7 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000229, max 0.002549 (between atoms 399 and 408)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    407    408   32.7    0.0958   0.0958      0.0960

Step 16770938, time 83854.7 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000228, max 0.001257 (between atoms 399 and 408)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    407    408   31.9    0.0958   0.0961      0.0960

Step 16770938, time 83854.7 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000163, max 0.001672 (between atoms 399 and 408)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    407    408   32.0    0.0958   0.0960      0.0960

Step 16770955, time 83854.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000183, max 0.001835 (between atoms 312 and 314)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
[06:00:42] Completed 6800000 out of 10000000 steps  (68%)
[06:32:38] Completed 6900000 out of 10000000 steps  (69%)
[07:04:13] Completed 7000000 out of 10000000 steps  (70%)
[07:37:30] Completed 7100000 out of 10000000 steps  (71%)
[08:09:07] Completed 7200000 out of 10000000 steps  (72%)
[08:41:04] Completed 7300000 out of 10000000 steps  (73%)
[09:12:40] Completed 7400000 out of 10000000 steps  (74%)
[09:44:36] Completed 7500000 out of 10000000 steps  (75%)
[10:16:12] Completed 7600000 out of 10000000 steps  (76%)
[10:48:15] Completed 7700000 out of 10000000 steps  (77%)
[11:19:53] Completed 7800000 out of 10000000 steps  (78%)
[11:51:46] Completed 7900000 out of 10000000 steps  (79%)
[12:23:21] Completed 8000000 out of 10000000 steps  (80%)
[12:55:23] Completed 8100000 out of 10000000 steps  (81%)
[13:26:58] Completed 8200000 out of 10000000 steps  (82%)
[13:58:52] Completed 8300000 out of 10000000 steps  (83%)
[14:30:25] Completed 8400000 out of 10000000 steps  (84%)
[15:02:19] Completed 8500000 out of 10000000 steps  (85%)
[15:33:58] Completed 8600000 out of 10000000 steps  (86%)
[16:05:55] Completed 8700000 out of 10000000 steps  (87%)
[16:37:32] Completed 8800000 out of 10000000 steps  (88%)
[17:09:29] Completed 8900000 out of 10000000 steps  (89%)
[17:41:07] Completed 9000000 out of 10000000 steps  (90%)
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izaguirr
Pande Group Member
Posts: 30
Joined: Wed Sep 16, 2009 2:37 pm

Re: Project: 7020 (Run 1, Clone 304, Gen 1) LINCS Warning

Post by izaguirr »

Thanks for pointing it out. This is not a serious warning. LINCS is a method used to keep some distances in the molecule constrained. Some times the algorithm fails to converge. However, rarely does this cause a crash. Again, thank you for folding!
Prof. Jesus A. Izaguirre, Ph.D.
Department of Computer Science and Engineering
Interdisciplinary Center for Network Science and Applications
University of Notre Dame, IN, USA
Member, Folding@Home Consortium, Stanford University, CA, USA
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karlinhigh
Posts: 17
Joined: Tue Mar 01, 2011 4:03 am

Re: Project: 7020 (Run 1, Clone 304, Gen 1) LINCS Warning

Post by karlinhigh »

Thanks for the explanation. It just did it again now:

Code: Select all

[18:13:10] Completed 9100000 out of 10000000 steps  (91%)
[18:44:54] Completed 9200000 out of 10000000 steps  (92%)
[19:16:58] Completed 9300000 out of 10000000 steps  (93%)
[19:48:54] Completed 9400000 out of 10000000 steps  (94%)

Step 19483354, time 97416.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000254, max 0.002114 (between atoms 444 and 445)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    444    445   31.6    0.0960   0.0962      0.0960

Step 19483354, time 97416.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000095, max 0.000757 (between atoms 439 and 441)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    444    445   31.7    0.0960   0.0961      0.0960

Step 19483355, time 97416.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000228, max 0.001210 (between atoms 444 and 445)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    444    445   31.5    0.0961   0.0961      0.0960

Step 19483355, time 97416.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000097, max 0.000886 (between atoms 441 and 445)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    444    445   31.5    0.0961   0.0960      0.0960
[20:21:00] Completed 9500000 out of 10000000 steps  (95%)
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