Folding@Home

ddrueding · Feb 10, 2014

timwhit said:
Dave, reminder: you are not folding again.

Thanks! I haven't been to my office in nearly two weeks. Most of my time has been at a facility 20 miles the other direction from my house. I do run into the building that contains my office to put out fires, but never long enough to sit down at my computer. I'll get it going again now.

P5-133XL · Feb 24, 2014

Intoducing a new folding Web app for Chrome (Win, Lin, OSx) using Native mode i.e. NaCl

Official anounancement + Info thread

Very easy to install and run (especially if you configure chrome to auto load the web-page http://folding.stanford.edu/nacl/ after installing the app)
Gives very good PPD (My observation is that it is significantly better than standard SMP)
Very small WU's that take very little time each. So It works well for part-timers, and low-end HW.

There are some significant limitations:

Currently open beta -- there may be undiscovered issues.
Only uses CPU (No GPU WU's).
No monitoring capability because of sandboxing/security limitations.
Runs only from within Chrome.
Doesn't run non-x86 yet, but that may be possible at some time in the future.

timwhit · Feb 24, 2014

Nice. It crashed the first time I tried to install it, but I restarted Chrome and tried again and it worked on the second try. I have it folding now.

CougTek · Feb 25, 2014

Buggy as Hell. NaCL module keeps crashing. The few times it worked, just playing with my favorites in the favorites bar was enough to crash it. I'll wait for a future version.

timwhit · Feb 25, 2014

I'm running it on 3 different computers and I haven't had a single crash after the issue I had installing. These are all Linux machines if that makes any difference.

P5-133XL · Feb 25, 2014

I've run the client on 5 different machines using 4 different Windows OS's over two weeks and not had a single crash and none of the other Alpha testers reported issues such as you are describing.

I did have one instance of the App failing to install the first time but it worked later after I found the flag that reset the app-cache.

timwhit · Feb 25, 2014

Mark, I'd really like to be able to see the estimated points for the current WU and PPD. Any idea if this will make it into a future version?

P5-133XL · Feb 25, 2014

I can't commit PG on time-line for a prospective feature, but I'd be very surprised if it doesn't eventually get there much sooner than later. If for no other reason than this is totally open-source with the source code available to all. If Stanford doesn't add that feature, then someone else will.

If you want, I'll look up the points got on your installs:

CPUId	WU	Points

08B70B53E05E2080	2981( 0, 1, 1599)	83.875
12EE0B535271D400	2981( 0, 25, 120)	116.269
2C230C53BC053200	2981( 0, 14, 727)	133.342

PPD is harder for me to calculate because the site I use is giving obviously wrong information about received times (all identical). However, you can probably estimate how long each machine is using for a WU and manually calculate PPD

CougTek · Feb 28, 2014

We have a new contributing member. Welcome to whs.

Howell · Feb 28, 2014

It's not much but with the chrome app the barrier to entry was very low.

timwhit · Feb 28, 2014

Howell said:
It's not much but with the chrome app the barrier to entry was very low.

Did you register for a passkey?

Howell · Feb 28, 2014

Yes, and installed I'm pretty sure.

P5-133XL · Feb 28, 2014

You are proving the whole purpose of the Chrome NaCl app is a valid premise.

CougTek · Mar 2, 2014

P5-133XL said:
Intoducing a new folding Web app for Chrome (Win, Lin, OSx) using Native mode i.e. NaCl

I've configured it in a VM under Lubuntu, but I always get the message : "Waiting to retry ID request". I'm sure my username, team and passkey are correct. WTF?

P5-133XL · Mar 2, 2014

I don't know but you can use F12 key to open the debug log and the click refresh in the browser to see what is going on under the hood. I'd look at it if you copy& paste it then post it but you should edit it to remove the passkey from any references before posting because it will be readable (assuming you care).

CougTek · Mar 3, 2014

P5-133XL said:
I don't know but you can use F12 key to open the debug log and the click refresh in the browser to see what is going on under the hood. I'd look at it if you copy& paste it then post it but you should edit it to remove the passkey from any references before posting because it will be readable (assuming you care).

In the debugging console, this is the error I get :

Code:

DEBUG: Status: downloading: Requesting ID. main.js:72OPTIONS http://assign5.stanford.edu/api/id?0.7155914502218366 No 'Access-Control-Allow-Origin' header is present on the requested resource. Origin 'http://folding.stanford.edu' is therefore not allowed access. jquery-1.10.2.min.js:4XMLHttpRequest cannot load http://assign5.stanford.edu/api/id?0.7155914502218366. No 'Access-Control-Allow-Origin' header is present on the requested resource. Origin 'http://folding.stanford.edu' is therefore not allowed access. folding.stanford.edu/:1DEBUG: Warning: ID request failed, retrying main.js:72DEBUG: Status: waiting: Waiting to retry ID request main.js:72

I don't know what to make of it. This is on a Lubuntu installation with the latest available version of Chrome for Linux.

P5-133XL · Mar 3, 2014

Do you have a something (Firewall, router, proxy server, security suite) preventing internet access?

P5-133XL · Mar 3, 2014

This is what I get as normal

Code:

DEBUG: NaCl module loading main.js:72DEBUG: Status: downloading: Downloading the Folding@home software in your Web browser.  On your first visit this can take awhile. main.js:72
DEBUG: load progress: 0.0% (0 of 18000000 bytes) main.js:72
DEBUG: load progress: 0.0% (0 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (509799 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (3815392 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (4815616 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (5939417 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (6887834 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (7699200 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (8590574 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (9272064 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (10320640 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (11369216 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (12626574 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (13466368 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (14252800 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (15276164 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (16344888 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 100.0% (17125192 of 17125192 bytes) main.js:72
DEBUG: NaCl module loaded main.js:72
DEBUG: NaCl module responded main.js:72
DEBUG: Status: downloading: Requesting a work server assignment. main.js:72
DEBUG: Status: downloading: Requesting a work server assignment. main.js:72
DEBUG: WS: {"client_id":"0x4d7c7df053046bf5","threads":4,"version":"8.0.0","type":"NACL","os":"NACL","user":"P5_133XL","team":"10047","passkey":"Redacted","ts":"2014-03-03T17:41:38Z","ws":"143.89.28.86","project":2981} main.js:72
DEBUG: Status: downloading: Downloading a work unit. main.js:72
DEBUG: Status: downloading: Downloading a work unit. main.js:72
DEBUG: WU: {"client_id":"0x4d7c7df053046bf5","threads":4,"version":"8.0.0","type":"NACL","os":"NACL","user":"P5_133XL","team":"10047","passkey":"Redacted","ts":"2014-03-03T17:41:38Z","ws":"143.89.28.86","project":2981,"server_version":703,"core":176,"core_version":227,"unit_id":"0x000002950893a18a52e6da8a855b44b3","run":0,"clone":36,"gen":632,"wu_ts":"2014-03-03T17:41:39Z","deadline":"2014-03-04T17:41:39Z","timeout":"2014-03-03T20:05:39Z","credit":10,"compression":"bzip2","checksum":"ZoLsq8yM3aVZDgWPYZTRAqYHidcDp5Bs87P43TXJz+E="} main.js:72
DEBUG: Status: running: Starting work unit. main.js:72
DEBUG: core: checksum verified main.js:72
DEBUG: core: unpacking: frame632.tpr main.js:72
DEBUG:                 :-)  G  R  O  M  A  C  S  (-: main.js:72
DEBUG:                 Groningen Machine for Chemical Simulation main.js:72
DEBUG:                 :-)  VERSION 4.6.5  (-: main.js:72
DEBUG:         Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,            Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,       Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,         Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,                 Michael Shirts, Alfons Sijbers, Peter Tieleman, main.js:72
DEBUG:                Berk Hess, David van der Spoel, and Erik Lindahl. main.js:72
DEBUG:        Copyright (c) 1991-2000, University of Groningen, The Netherlands.         Copyright (c) 2001-2012,2013, The GROMACS development team at        Uppsala University & The Royal Institute of Technology, Sweden.            check out http://www.gromacs.org for more information. main.js:72
DEBUG:  main.js:72
DEBUG:                 :-)  Gromacs  (-: main.js:72
DEBUG: Option------------------------------------------------------------ main.js:72
DEBUG:   -s   frame632.tpr  Input        Run input file: tpr tpb tpa  -o       traj.trr  Output       Full precision trajectory: trr trj cpt  -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)-cpi      state.cpt  Input, Opt.  Checkpoint file-cpo      state.cpt  Output, Opt. Checkpoint file  -c    confout.gro  Output       Structure file: gro g96 pdb etc.  -e       ener.edr  Output       Energy file  -g         md.log  Output       Log file-dhdl      dhdl.xvg  Output, Opt. xvgr/xmgr file-field    field.xvg  Output, Opt. xvgr/xmgr file-table    table.xvg  Input, Opt.  xvgr/xmgr file-tabletf    tabletf.xvg  Input, Opt.  xvgr/xmgr file-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file-tableb   table.xvg  Input, Opt.  xvgr/xmgr file-rerun    rerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt-tpi        tpi.xvg  Output, Opt. xvgr/xmgr file-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file -ei        sam.edi  Input, Opt.  ED sampling input -eo      edsam.xvg  Output, Opt. xvgr/xmgr file  -j       wham.gct  Input, Opt.  General coupling stuff -jo        bam.gct  Output, Opt. General coupling stuff-ffout      gct.xvg  Output, Opt. xvgr/xmgr file-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file-runav  runaver.xvg  Output, Opt. xvgr/xmgr file -px      pullx.xvg  Output, Opt. xvgr/xmgr file -pf      pullf.xvg  Output, Opt. xvgr/xmgr file -ro   rotation.xvg  Output, Opt. xvgr/xmgr file -ra  rotangles.log  Output, Opt. Log file -rs   rotslabs.log  Output, Opt. Log file -rt  rottorque.log  Output, Opt. Log file-mtx         nm.mtx  Output, Opt. Hessian matrix -dn     dipole.ndx  Output, Opt. Index file-multidir    rundir  Input, Opt., Mult. Run directory-membed  membed.dat  Input, Opt.  Generic data file -mp     membed.top  Input, Opt.  Topology file -mn     membed.ndx  Input, Opt.  Index file main.js:72
DEBUG: Option------------------------------------------------------ main.js:72
DEBUG: -[no]h       bool   no      Print help info and quit main.js:72
DEBUG: -[no]version bool   no      Print version info and quit main.js:72
DEBUG: -nice        int    0       Set the nicelevel main.js:72
DEBUG: -deffnm      string         Set the default filename for all file options main.js:72
DEBUG: -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none main.js:72
DEBUG: -[no]pd      bool   no      Use particle decompostion main.js:72
DEBUG: -dd          vector 0 0 0   Domain decomposition grid, 0 is optimize main.js:72
DEBUG: -ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian main.js:72
DEBUG: -npme        int    -1      Number of separate nodes to be used for PME, -1 main.js:72
DEBUG:                             is guess
 main.js:72
DEBUG: -nt          int    4       Total number of threads to start (0 is guess) main.js:72
DEBUG: -ntmpi       int    0       Number of thread-MPI threads to start (0 is guess) main.js:72
DEBUG: -ntomp       int    0       Number of OpenMP threads per MPI process/thread main.js:72
DEBUG:                             to start (0 is guess)
 main.js:72
DEBUG: -ntomp_pme   int    0       Number of OpenMP threads per MPI process/thread main.js:72
DEBUG:                             to start (0 is -ntomp)
 main.js:72
DEBUG: -pin         enum   auto    Fix threads (or processes) to specific cores: main.js:72
DEBUG:                             auto, on or off
 main.js:72
DEBUG: -pinoffset   int    0       The starting logical core number for pinning to main.js:72
DEBUG:                             cores; used to avoid pinning threads from
                            different mdrun instances to the same core
 main.js:72
DEBUG:                             different mdrun instances to the same core
 main.js:72
DEBUG: -pinstride   int    0       Pinning distance in logical cores for threads, main.js:72
DEBUG:                             use 0 to minimize the number of threads per
                            physical core
 main.js:72
DEBUG:                             physical core
 main.js:72
DEBUG: -gpu_id      string         List of GPU device id-s to use, specifies the main.js:72
DEBUG:                             per-node PP rank to GPU mapping
 main.js:72
DEBUG: -[no]ddcheck bool   yes     Check for all bonded interactions with DD main.js:72
DEBUG: -rdd         real   0       The maximum distance for bonded interactions with main.js:72
DEBUG:                             DD (nm), 0 is determine from initial coordinates
 main.js:72
DEBUG: -rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate main.js:72
DEBUG: -dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes main.js:72
DEBUG: -dds         real   0.8     Minimum allowed dlb scaling of the DD cell size main.js:72
DEBUG: -gcom        int    -1      Global communication frequency main.js:72
DEBUG: -nb          enum   auto    Calculate non-bonded interactions on: auto, cpu, main.js:72
DEBUG:                             gpu or gpu_cpu
 main.js:72
DEBUG: -[no]tunepme bool   yes     Optimize PME load between PP/PME nodes or GPU/CPU main.js:72
DEBUG: -[no]testverlet bool   no      Test the Verlet non-bonded scheme main.js:72
DEBUG: -[no]v       bool   no      Be loud and noisy main.js:72
DEBUG: -[no]compact bool   yes     Write a compact log file main.js:72
DEBUG: -[no]seppot  bool   no      Write separate V and dVdl terms for each main.js:72
DEBUG:                             interaction type and node to the log file(s)
 main.js:72
DEBUG: -pforce      real   -1      Print all forces larger than this (kJ/mol nm) main.js:72
DEBUG: -[no]reprod  bool   no      Try to avoid optimizations that affect binary main.js:72
DEBUG:                             reproducibility
 main.js:72
DEBUG: -cpt         real   -1      Checkpoint interval (minutes) main.js:72
DEBUG: -[no]cpnum   bool   no      Keep and number checkpoint files main.js:72
DEBUG: -[no]append  bool   yes     Append to previous output files when continuing main.js:72
DEBUG:                             from checkpoint instead of adding the simulation
                            part number to all file names
 main.js:72
DEBUG:                             part number to all file names
 main.js:72
DEBUG: -nsteps      step   -2      Run this number of steps, overrides .mdp file main.js:72
DEBUG:                             option
 main.js:72
DEBUG: -maxh        real   -1      Terminate after 0.99 times this time (hours) main.js:72
DEBUG: -multi       int    0       Do multiple simulations in parallel main.js:72
DEBUG: -replex      int    0       Attempt replica exchange periodically with this main.js:72
DEBUG:                             period (steps)
 main.js:72
DEBUG: -nex         int    0       Number of random exchanges to carry out each main.js:72
DEBUG:                             exchange interval (N^3 is one suggestion).  -nex
                            zero or not specified gives neighbor replica main.js:72
DEBUG:                             zero or not specified gives neighbor replica
                            exchange.
 main.js:72
DEBUG:                             exchange.
 main.js:72
DEBUG: -reseed      int    -1      Seed for replica exchange, -1 is generate a seed main.js:72
DEBUG: -[no]ionize  bool   no      Do a simulation including the effect of an X-Ray main.js:72
DEBUG:                             bombardment on your system
 main.js:72
DEBUG:  main.js:72
DEBUG: core: steps: 15168000 -> 15192000 main.js:72
DEBUG: Reading file Using Compiled acceleration:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
2
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG: Status: running: Calculations underway. main.js:72
DEBUG: starting mdrun '15192000 main.js:72
DEBUG:  main.js:72
DEBUG: Writing final coordinates.
 main.js:72
DEBUG:  main.js:72
DEBUG:  Average load imbalance: 3.8 % main.js:72
DEBUG:  Part of the total run time spent waiting due to load imbalance: 1.3 % main.js:72
DEBUG:  Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % main.js:72
2
DEBUG:  main.js:72
DEBUG:                                Performance: main.js:72
DEBUG: core: Packaging results: main.js:72
DEBUG: core:   md.log 20719 main.js:72
DEBUG: core:   traj.trr 806448 main.js:72
DEBUG: Status: uploading: Uploading results. main.js:72
DEBUG: Status: uploading: Uploading results. main.js:72
DEBUG: stats: {"team_rank":112,"earned":127293124,"url":"http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userpage&username=P5_133XL","contributed":127292037,"team_url":"http://www.storageforum.net","team_urllogo":"http://www.storageforum.net/forum/images/misc/storageforum_logo.png","team_name":"StorageForum_net","team_total":460699303} main.js:72
NativeClient: NaCl module crashed folding.stanford.edu/:1
DEBUG: Module exit main.js:72
DEBUG: NaCl module loading main.js:72
DEBUG: Status: downloading: Downloading the Folding@home software in your Web browser.  On your first visit this can take awhile. main.js:72
DEBUG: load progress: 0.0% (0 of 18000000 bytes) main.js:72
DEBUG: load progress: 0.0% (0 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (360448 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (852604 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (1671168 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (2780266 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (3736104 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (4800702 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (5864192 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (6887834 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (7699200 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (8685073 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (9657950 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (10557951 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (11535536 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (12553707 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (13552169 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (14756839 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (15772151 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (16656655 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 100.0% (17125192 of 17125192 bytes) main.js:72
DEBUG: NaCl module loaded main.js:72
DEBUG: NaCl module responded main.js:72
DEBUG: Status: downloading: Requesting a work server assignment. main.js:72
DEBUG: Status: downloading: Requesting a work server assignment. main.js:72
DEBUG: WS: {"client_id":"0x4d7c7df053046bf5","threads":4,"version":"8.0.0","type":"NACL","os":"NACL","user":"P5_133XL","team":"10047","passkey":"Redacted","ts":"2014-03-03T18:01:30Z","ws":"143.89.28.86","project":2981} main.js:72
DEBUG: Status: downloading: Downloading a work unit. main.js:72
DEBUG: Status: downloading: Downloading a work unit. main.js:72
DEBUG: WU: {"client_id":"0x4d7c7df053046bf5","threads":4,"version":"8.0.0","type":"NACL","os":"NACL","user":"P5_133XL","team":"10047","passkey":"Redacted","ts":"2014-03-03T18:01:30Z","ws":"143.89.28.86","project":2981,"server_version":703,"core":176,"core_version":227,"unit_id":"0x0000026a0893a18a52e6da887c0af25a","run":0,"clone":33,"gen":585,"wu_ts":"2014-03-03T18:01:31Z","deadline":"2014-03-04T18:01:31Z","timeout":"2014-03-03T20:25:31Z","credit":10,"compression":"bzip2","checksum":"3s2KDnzLUC+H69BqiJBTYaq2bEBxopjyljo42xbPtdE="} main.js:72
DEBUG: Status: running: Starting work unit. main.js:72
DEBUG: core: checksum verified main.js:72
DEBUG: core: unpacking: frame585.tpr main.js:72
DEBUG:                 :-)  G  R  O  M  A  C  S  (-: main.js:72
DEBUG:                 Groningen Machine for Chemical Simulation main.js:72
DEBUG:                 :-)  VERSION 4.6.5  (-: main.js:72
DEBUG:         Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,            Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,       Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,         Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,                 Michael Shirts, Alfons Sijbers, Peter Tieleman, main.js:72
DEBUG:                Berk Hess, David van der Spoel, and Erik Lindahl. main.js:72
DEBUG:        Copyright (c) 1991-2000, University of Groningen, The Netherlands.         Copyright (c) 2001-2012,2013, The GROMACS development team at        Uppsala University & The Royal Institute of Technology, Sweden.            check out http://www.gromacs.org for more information. main.js:72
DEBUG:  main.js:72
DEBUG:                 :-)  Gromacs  (-: main.js:72
DEBUG: Option------------------------------------------------------------ main.js:72
DEBUG:   -s   frame585.tpr  Input        Run input file: tpr tpb tpa  -o       traj.trr  Output       Full precision trajectory: trr trj cpt  -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)-cpi      state.cpt  Input, Opt.  Checkpoint file-cpo      state.cpt  Output, Opt. Checkpoint file  -c    confout.gro  Output       Structure file: gro g96 pdb etc.  -e       ener.edr  Output       Energy file  -g         md.log  Output       Log file-dhdl      dhdl.xvg  Output, Opt. xvgr/xmgr file-field    field.xvg  Output, Opt. xvgr/xmgr file-table    table.xvg  Input, Opt.  xvgr/xmgr file-tabletf    tabletf.xvg  Input, Opt.  xvgr/xmgr file-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file-tableb   table.xvg  Input, Opt.  xvgr/xmgr file-rerun    rerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt-tpi        tpi.xvg  Output, Opt. xvgr/xmgr file-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file -ei        sam.edi  Input, Opt.  ED sampling input -eo      edsam.xvg  Output, Opt. xvgr/xmgr file  -j       wham.gct  Input, Opt.  General coupling stuff -jo        bam.gct  Output, Opt. General coupling stuff-ffout      gct.xvg  Output, Opt. xvgr/xmgr file-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file-runav  runaver.xvg  Output, Opt. xvgr/xmgr file -px      pullx.xvg  Output, Opt. xvgr/xmgr file -pf      pullf.xvg  Output, Opt. xvgr/xmgr file -ro   rotation.xvg  Output, Opt. xvgr/xmgr file -ra  rotangles.log  Output, Opt. Log file -rs   rotslabs.log  Output, Opt. Log file -rt  rottorque.log  Output, Opt. Log file-mtx         nm.mtx  Output, Opt. Hessian matrix -dn     dipole.ndx  Output, Opt. Index file-multidir    rundir  Input, Opt., Mult. Run directory-membed  membed.dat  Input, Opt.  Generic data file -mp     membed.top  Input, Opt.  Topology file -mn     membed.ndx  Input, Opt.  Index file main.js:72
DEBUG: Option------------------------------------------------------ main.js:72
DEBUG: -[no]h       bool   no      Print help info and quit main.js:72
DEBUG: -[no]version bool   no      Print version info and quit main.js:72
DEBUG: -nice        int    0       Set the nicelevel main.js:72
DEBUG: -deffnm      string         Set the default filename for all file options main.js:72
DEBUG: -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none main.js:72
DEBUG: -[no]pd      bool   no      Use particle decompostion main.js:72
DEBUG: -dd          vector 0 0 0   Domain decomposition grid, 0 is optimize main.js:72
DEBUG: -ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian main.js:72
DEBUG: -npme        int    -1      Number of separate nodes to be used for PME, -1 main.js:72
DEBUG:                             is guess
 main.js:72
DEBUG: -nt          int    4       Total number of threads to start (0 is guess) main.js:72
DEBUG: -ntmpi       int    0       Number of thread-MPI threads to start (0 is guess) main.js:72
DEBUG: -ntomp       int    0       Number of OpenMP threads per MPI process/thread main.js:72
DEBUG:                             to start (0 is guess)
 main.js:72
DEBUG: -ntomp_pme   int    0       Number of OpenMP threads per MPI process/thread main.js:72
DEBUG:                             to start (0 is -ntomp)
 main.js:72
DEBUG: -pin         enum   auto    Fix threads (or processes) to specific cores: main.js:72
DEBUG:                             auto, on or off
 main.js:72
DEBUG: -pinoffset   int    0       The starting logical core number for pinning to main.js:72
DEBUG:                             cores; used to avoid pinning threads from
                            different mdrun instances to the same core
 main.js:72
DEBUG:                             different mdrun instances to the same core
 main.js:72
DEBUG: -pinstride   int    0       Pinning distance in logical cores for threads, main.js:72
DEBUG:                             use 0 to minimize the number of threads per
                            physical core
 main.js:72
DEBUG:                             physical core
 main.js:72
DEBUG: -gpu_id      string         List of GPU device id-s to use, specifies the main.js:72
DEBUG:                             per-node PP rank to GPU mapping
 main.js:72
DEBUG: -[no]ddcheck bool   yes     Check for all bonded interactions with DD main.js:72
DEBUG: -rdd         real   0       The maximum distance for bonded interactions with main.js:72
DEBUG:                             DD (nm), 0 is determine from initial coordinates
 main.js:72
DEBUG: -rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate main.js:72
DEBUG: -dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes main.js:72
DEBUG: -dds         real   0.8     Minimum allowed dlb scaling of the DD cell size main.js:72
DEBUG: -gcom        int    -1      Global communication frequency main.js:72
DEBUG: -nb          enum   auto    Calculate non-bonded interactions on: auto, cpu, main.js:72
DEBUG:                             gpu or gpu_cpu
 main.js:72
DEBUG: -[no]tunepme bool   yes     Optimize PME load between PP/PME nodes or GPU/CPU main.js:72
DEBUG: -[no]testverlet bool   no      Test the Verlet non-bonded scheme main.js:72
DEBUG: -[no]v       bool   no      Be loud and noisy main.js:72
DEBUG: -[no]compact bool   yes     Write a compact log file main.js:72
DEBUG: -[no]seppot  bool   no      Write separate V and dVdl terms for each main.js:72
DEBUG:                             interaction type and node to the log file(s)
 main.js:72
DEBUG: -pforce      real   -1      Print all forces larger than this (kJ/mol nm) main.js:72
DEBUG: -[no]reprod  bool   no      Try to avoid optimizations that affect binary main.js:72
DEBUG:                             reproducibility
 main.js:72
DEBUG: -cpt         real   -1      Checkpoint interval (minutes) main.js:72
DEBUG: -[no]cpnum   bool   no      Keep and number checkpoint files main.js:72
DEBUG: -[no]append  bool   yes     Append to previous output files when continuing main.js:72
DEBUG:                             from checkpoint instead of adding the simulation
                            part number to all file names
 main.js:72
DEBUG:                             part number to all file names
 main.js:72
DEBUG: -nsteps      step   -2      Run this number of steps, overrides .mdp file main.js:72
DEBUG:                             option
 main.js:72
DEBUG: -maxh        real   -1      Terminate after 0.99 times this time (hours) main.js:72
DEBUG: -multi       int    0       Do multiple simulations in parallel main.js:72
DEBUG: -replex      int    0       Attempt replica exchange periodically with this main.js:72
DEBUG:                             period (steps)
 main.js:72
DEBUG: -nex         int    0       Number of random exchanges to carry out each main.js:72
DEBUG:                             exchange interval (N^3 is one suggestion).  -nex
                            zero or not specified gives neighbor replica main.js:72
DEBUG:                             zero or not specified gives neighbor replica
                            exchange.
 main.js:72
DEBUG:                             exchange.
 main.js:72
DEBUG: -reseed      int    -1      Seed for replica exchange, -1 is generate a seed main.js:72
DEBUG: -[no]ionize  bool   no      Do a simulation including the effect of an X-Ray main.js:72
DEBUG:                             bombardment on your system
 main.js:72
DEBUG:  main.js:72
DEBUG: core: steps: 14040000 -> 14064000 main.js:72
DEBUG: Reading file Using Compiled acceleration:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG: Status: running: Calculations underway. main.js:72
DEBUG: starting mdrun '14064000 main.js:72
DEBUG: Writing final coordinates.
 main.js:72
DEBUG:  main.js:72
DEBUG:  Average load imbalance: 14.1 % main.js:72
DEBUG:  Part of the total run time spent waiting due to load imbalance: 4.7 % main.js:72
2
DEBUG:  main.js:72
DEBUG:                                Performance: main.js:72
DEBUG: core: Packaging results: main.js:72
DEBUG: core:   md.log 20422 main.js:72
DEBUG: core:   traj.trr 806448 main.js:72
DEBUG: Status: uploading: Uploading results. main.js:72
DEBUG: Status: uploading: Uploading results. main.js:72
DEBUG: stats: {"team_rank":112,"earned":127293462,"url":"http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userpage&username=P5_133XL","contributed":127292375,"team_url":"http://www.storageforum.net","team_urllogo":"http://www.storageforum.net/forum/images/misc/storageforum_logo.png","team_name":"StorageForum_net","team_total":461109049} main.js:72
NativeClient: NaCl module crashed folding.stanford.edu/:1
DEBUG: Module exit main.js:72
DEBUG: NaCl module loading main.js:72
DEBUG: Status: downloading: Downloading the Folding@home software in your Web browser.  On your first visit this can take awhile. main.js:72
DEBUG: load progress: 0.0% (0 of 18000000 bytes) main.js:72
DEBUG: load progress: 0.0% (0 of 18446744073709552000 bytes) main.js:72
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DEBUG: load progress: 100.0% (17125192 of 17125192 bytes) main.js:72
DEBUG: NaCl module loaded main.js:72
DEBUG: NaCl module responded main.js:72
DEBUG: Status: downloading: Requesting a work server assignment. main.js:72
DEBUG: Status: downloading: Requesting a work server assignment. main.js:72
DEBUG: WS: {"client_id":"0x4d7c7df053046bf5","threads":4,"version":"8.0.0","type":"NACL","os":"NACL","user":"P5_133XL","team":"10047","passkey":"Redacted","ts":"2014-03-03T18:21:41Z","ws":"143.89.28.86","project":2981} main.js:72
DEBUG: Status: downloading: Downloading a work unit. main.js:72
DEBUG: Status: downloading: Downloading a work unit. main.js:72
DEBUG: WU: {"client_id":"0x4d7c7df053046bf5","threads":4,"version":"8.0.0","type":"NACL","os":"NACL","user":"P5_133XL","team":"10047","passkey":"Redacted","ts":"2014-03-03T18:21:41Z","ws":"143.89.28.86","project":2981,"server_version":703,"core":176,"core_version":227,"unit_id":"0x0000026b0893a18a52e6da887c0af25a","run":0,"clone":33,"gen":586,"wu_ts":"2014-03-03T18:21:42Z","deadline":"2014-03-04T18:21:42Z","timeout":"2014-03-03T20:45:42Z","credit":10,"compression":"bzip2","checksum":"ZI/M9Dzj0ne9Iz/FV3nolixmnYGKmpzgFwnbR1978K4="} main.js:72
DEBUG: Status: running: Starting work unit. main.js:72
DEBUG: core: checksum verified main.js:72
DEBUG: core: unpacking: frame586.tpr main.js:72
DEBUG:                 :-)  G  R  O  M  A  C  S  (-: main.js:72
DEBUG:                 Groningen Machine for Chemical Simulation main.js:72
DEBUG:                 :-)  VERSION 4.6.5  (-: main.js:72
DEBUG:         Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,            Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,       Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,         Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,                 Michael Shirts, Alfons Sijbers, Peter Tieleman, main.js:72
DEBUG:                Berk Hess, David van der Spoel, and Erik Lindahl. main.js:72
DEBUG:        Copyright (c) 1991-2000, University of Groningen, The Netherlands.         Copyright (c) 2001-2012,2013, The GROMACS development team at        Uppsala University & The Royal Institute of Technology, Sweden.            check out http://www.gromacs.org for more information. main.js:72
DEBUG:  main.js:72
DEBUG:                 :-)  Gromacs  (-: main.js:72
DEBUG: Option------------------------------------------------------------ main.js:72
DEBUG:   -s   frame586.tpr  Input        Run input file: tpr tpb tpa  -o       traj.trr  Output       Full precision trajectory: trr trj cpt  -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)-cpi      state.cpt  Input, Opt.  Checkpoint file-cpo      state.cpt  Output, Opt. Checkpoint file  -c    confout.gro  Output       Structure file: gro g96 pdb etc.  -e       ener.edr  Output       Energy file  -g         md.log  Output       Log file-dhdl      dhdl.xvg  Output, Opt. xvgr/xmgr file-field    field.xvg  Output, Opt. xvgr/xmgr file-table    table.xvg  Input, Opt.  xvgr/xmgr file-tabletf    tabletf.xvg  Input, Opt.  xvgr/xmgr file-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file-tableb   table.xvg  Input, Opt.  xvgr/xmgr file-rerun    rerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt-tpi        tpi.xvg  Output, Opt. xvgr/xmgr file-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file -ei        sam.edi  Input, Opt.  ED sampling input -eo      edsam.xvg  Output, Opt. xvgr/xmgr file  -j       wham.gct  Input, Opt.  General coupling stuff -jo        bam.gct  Output, Opt. General coupling stuff-ffout      gct.xvg  Output, Opt. xvgr/xmgr file-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file-runav  runaver.xvg  Output, Opt. xvgr/xmgr file -px      pullx.xvg  Output, Opt. xvgr/xmgr file -pf      pullf.xvg  Output, Opt. xvgr/xmgr file -ro   rotation.xvg  Output, Opt. xvgr/xmgr file -ra  rotangles.log  Output, Opt. Log file -rs   rotslabs.log  Output, Opt. Log file -rt  rottorque.log  Output, Opt. Log file-mtx         nm.mtx  Output, Opt. Hessian matrix -dn     dipole.ndx  Output, Opt. Index file-multidir    rundir  Input, Opt., Mult. Run directory-membed  membed.dat  Input, Opt.  Generic data file -mp     membed.top  Input, Opt.  Topology file -mn     membed.ndx  Input, Opt.  Index file main.js:72
DEBUG: Option------------------------------------------------------ main.js:72
DEBUG: -[no]h       bool   no      Print help info and quit main.js:72
DEBUG: -[no]version bool   no      Print version info and quit main.js:72
DEBUG: -nice        int    0       Set the nicelevel main.js:72
DEBUG: -deffnm      string         Set the default filename for all file options main.js:72
DEBUG: -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none main.js:72
DEBUG: -[no]pd      bool   no      Use particle decompostion main.js:72
DEBUG: -dd          vector 0 0 0   Domain decomposition grid, 0 is optimize main.js:72
DEBUG: -ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian main.js:72
DEBUG: -npme        int    -1      Number of separate nodes to be used for PME, -1 main.js:72
DEBUG:                             is guess
 main.js:72
DEBUG: -nt          int    4       Total number of threads to start (0 is guess) main.js:72
DEBUG: -ntmpi       int    0       Number of thread-MPI threads to start (0 is guess) main.js:72
DEBUG: -ntomp       int    0       Number of OpenMP threads per MPI process/thread main.js:72
DEBUG:                             to start (0 is guess)
 main.js:72
DEBUG: -ntomp_pme   int    0       Number of OpenMP threads per MPI process/thread main.js:72
DEBUG:                             to start (0 is -ntomp)
 main.js:72
DEBUG: -pin         enum   auto    Fix threads (or processes) to specific cores: main.js:72
DEBUG:                             auto, on or off
 main.js:72
DEBUG: -pinoffset   int    0       The starting logical core number for pinning to main.js:72
DEBUG:                             cores; used to avoid pinning threads from
                            different mdrun instances to the same core
 main.js:72
DEBUG:                             different mdrun instances to the same core
 main.js:72
DEBUG: -pinstride   int    0       Pinning distance in logical cores for threads, main.js:72
DEBUG:                             use 0 to minimize the number of threads per
                            physical core
 main.js:72
DEBUG:                             physical core
 main.js:72
DEBUG: -gpu_id      string         List of GPU device id-s to use, specifies the main.js:72
DEBUG:                             per-node PP rank to GPU mapping
 main.js:72
DEBUG: -[no]ddcheck bool   yes     Check for all bonded interactions with DD main.js:72
DEBUG: -rdd         real   0       The maximum distance for bonded interactions with main.js:72
DEBUG:                             DD (nm), 0 is determine from initial coordinates
 main.js:72
DEBUG: -rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate main.js:72
DEBUG: -dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes main.js:72
DEBUG: -dds         real   0.8     Minimum allowed dlb scaling of the DD cell size main.js:72
DEBUG: -gcom        int    -1      Global communication frequency main.js:72
DEBUG: -nb          enum   auto    Calculate non-bonded interactions on: auto, cpu, main.js:72
DEBUG:                             gpu or gpu_cpu
 main.js:72
DEBUG: -[no]tunepme bool   yes     Optimize PME load between PP/PME nodes or GPU/CPU main.js:72
DEBUG: -[no]testverlet bool   no      Test the Verlet non-bonded scheme main.js:72
DEBUG: -[no]v       bool   no      Be loud and noisy main.js:72
DEBUG: -[no]compact bool   yes     Write a compact log file main.js:72
DEBUG: -[no]seppot  bool   no      Write separate V and dVdl terms for each main.js:72
DEBUG:                             interaction type and node to the log file(s)
 main.js:72
DEBUG: -pforce      real   -1      Print all forces larger than this (kJ/mol nm) main.js:72
DEBUG: -[no]reprod  bool   no      Try to avoid optimizations that affect binary main.js:72
DEBUG:                             reproducibility
 main.js:72
DEBUG: -cpt         real   -1      Checkpoint interval (minutes) main.js:72
DEBUG: -[no]cpnum   bool   no      Keep and number checkpoint files main.js:72
DEBUG: -[no]append  bool   yes     Append to previous output files when continuing main.js:72
DEBUG:                             from checkpoint instead of adding the simulation
                            part number to all file names
 main.js:72
DEBUG:                             part number to all file names
 main.js:72
DEBUG: -nsteps      step   -2      Run this number of steps, overrides .mdp file main.js:72
DEBUG:                             option
 main.js:72
DEBUG: -maxh        real   -1      Terminate after 0.99 times this time (hours) main.js:72
DEBUG: -multi       int    0       Do multiple simulations in parallel main.js:72
DEBUG: -replex      int    0       Attempt replica exchange periodically with this main.js:72
DEBUG:                             period (steps)
 main.js:72
DEBUG: -nex         int    0       Number of random exchanges to carry out each main.js:72
DEBUG:                             exchange interval (N^3 is one suggestion).  -nex
                            zero or not specified gives neighbor replica main.js:72
DEBUG:                             zero or not specified gives neighbor replica
                            exchange.
 main.js:72
DEBUG:                             exchange.
 main.js:72
DEBUG: -reseed      int    -1      Seed for replica exchange, -1 is generate a seed main.js:72
DEBUG: -[no]ionize  bool   no      Do a simulation including the effect of an X-Ray main.js:72
DEBUG:                             bombardment on your system
 main.js:72
DEBUG:  main.js:72
DEBUG: core: steps: 14064000 -> 14088000 main.js:72
DEBUG: Reading file Using Compiled acceleration:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG: Status: running: Calculations underway. main.js:72
DEBUG: starting mdrun '14088000 main.js:72
DEBUG:  main.js:72
DEBUG: Writing final coordinates.
 main.js:72
DEBUG:  main.js:72
DEBUG:  Average load imbalance: 3.3 % main.js:72
DEBUG:  Part of the total run time spent waiting due to load imbalance: 1.2 % main.js:72
DEBUG:  Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % main.js:72
2
DEBUG:  main.js:72
DEBUG:                                Performance: main.js:72
DEBUG: core: Packaging results: main.js:72
DEBUG: core:   md.log 20718 main.js:72
DEBUG: core:   traj.trr 806448 main.js:72
DEBUG: Status: uploading: Uploading results. main.js:72
DEBUG: Status: uploading: Uploading results. main.js:72
DEBUG: stats: {"team_rank":112,"earned":127293462,"url":"http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userpage&username=P5_133XL","contributed":127292375,"team_url":"http://www.storageforum.net","team_urllogo":"http://www.storageforum.net/forum/images/misc/storageforum_logo.png","team_name":"StorageForum_net","team_total":461109049} main.js:72
NativeClient: NaCl module crashed folding.stanford.edu/:1
DEBUG: Module exit main.js:72
DEBUG: NaCl module loading main.js:72
DEBUG: Status: downloading: Downloading the Folding@home software in your Web browser.  On your first visit this can take awhile. main.js:72
DEBUG: load progress: 0.0% (0 of 18000000 bytes) main.js:72
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DEBUG: load progress: 0.0% (16017217 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 0.0% (16859226 of 18446744073709552000 bytes) main.js:72
DEBUG: load progress: 100.0% (17125192 of 17125192 bytes) main.js:72
DEBUG: NaCl module loaded main.js:72
DEBUG: NaCl module responded main.js:72
DEBUG: Status: downloading: Requesting a work server assignment. main.js:72
DEBUG: Status: downloading: Requesting a work server assignment. main.js:72
DEBUG: WS: {"client_id":"0x4d7c7df053046bf5","threads":4,"version":"8.0.0","type":"NACL","os":"NACL","user":"P5_133XL","team":"10047","passkey":"Redacted","ts":"2014-03-03T18:41:18Z","ws":"143.89.28.86","project":2981} main.js:72
DEBUG: Status: downloading: Downloading a work unit. main.js:72
DEBUG: Status: downloading: Downloading a work unit. main.js:72
DEBUG: WU: {"client_id":"0x4d7c7df053046bf5","threads":4,"version":"8.0.0","type":"NACL","os":"NACL","user":"P5_133XL","team":"10047","passkey":"Redacted","ts":"2014-03-03T18:41:18Z","ws":"143.89.28.86","project":2981,"server_version":703,"core":176,"core_version":227,"unit_id":"0x0000026c0893a18a52e6da887c0af25a","run":0,"clone":33,"gen":587,"wu_ts":"2014-03-03T18:41:19Z","deadline":"2014-03-04T18:41:19Z","timeout":"2014-03-03T21:05:19Z","credit":10,"compression":"bzip2","checksum":"sNtLZlAE82g4LVD2zUgE49RKiAy07rgNC3KiRK0/0a0="} main.js:72
DEBUG: Status: running: Starting work unit. main.js:72
DEBUG: core: checksum verified main.js:72
DEBUG: core: unpacking: frame587.tpr main.js:72
DEBUG:                 :-)  G  R  O  M  A  C  S  (-: main.js:72
DEBUG:                 Groningen Machine for Chemical Simulation main.js:72
DEBUG:                 :-)  VERSION 4.6.5  (-: main.js:72
DEBUG:         Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,            Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,       Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,         Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,                 Michael Shirts, Alfons Sijbers, Peter Tieleman, main.js:72
DEBUG:                Berk Hess, David van der Spoel, and Erik Lindahl. main.js:72
DEBUG:        Copyright (c) 1991-2000, University of Groningen, The Netherlands.         Copyright (c) 2001-2012,2013, The GROMACS development team at        Uppsala University & The Royal Institute of Technology, Sweden.            check out http://www.gromacs.org for more information. main.js:72
DEBUG:  main.js:72
DEBUG:                 :-)  Gromacs  (-: main.js:72
DEBUG: Option------------------------------------------------------------ main.js:72
DEBUG:   -s   frame587.tpr  Input        Run input file: tpr tpb tpa  -o       traj.trr  Output       Full precision trajectory: trr trj cpt  -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)-cpi      state.cpt  Input, Opt.  Checkpoint file-cpo      state.cpt  Output, Opt. Checkpoint file  -c    confout.gro  Output       Structure file: gro g96 pdb etc.  -e       ener.edr  Output       Energy file  -g         md.log  Output       Log file-dhdl      dhdl.xvg  Output, Opt. xvgr/xmgr file-field    field.xvg  Output, Opt. xvgr/xmgr file-table    table.xvg  Input, Opt.  xvgr/xmgr file-tabletf    tabletf.xvg  Input, Opt.  xvgr/xmgr file-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file-tableb   table.xvg  Input, Opt.  xvgr/xmgr file-rerun    rerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt-tpi        tpi.xvg  Output, Opt. xvgr/xmgr file-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file -ei        sam.edi  Input, Opt.  ED sampling input -eo      edsam.xvg  Output, Opt. xvgr/xmgr file  -j       wham.gct  Input, Opt.  General coupling stuff -jo        bam.gct  Output, Opt. General coupling stuff-ffout      gct.xvg  Output, Opt. xvgr/xmgr file-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file-runav  runaver.xvg  Output, Opt. xvgr/xmgr file -px      pullx.xvg  Output, Opt. xvgr/xmgr file -pf      pullf.xvg  Output, Opt. xvgr/xmgr file -ro   rotation.xvg  Output, Opt. xvgr/xmgr file -ra  rotangles.log  Output, Opt. Log file -rs   rotslabs.log  Output, Opt. Log file -rt  rottorque.log  Output, Opt. Log file-mtx         nm.mtx  Output, Opt. Hessian matrix -dn     dipole.ndx  Output, Opt. Index file-multidir    rundir  Input, Opt., Mult. Run directory-membed  membed.dat  Input, Opt.  Generic data file -mp     membed.top  Input, Opt.  Topology file -mn     membed.ndx  Input, Opt.  Index file main.js:72
DEBUG: Option------------------------------------------------------ main.js:72
DEBUG: -[no]h       bool   no      Print help info and quit main.js:72
DEBUG: -[no]version bool   no      Print version info and quit main.js:72
DEBUG: -nice        int    0       Set the nicelevel main.js:72
DEBUG: -deffnm      string         Set the default filename for all file options main.js:72
DEBUG: -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none main.js:72
DEBUG: -[no]pd      bool   no      Use particle decompostion main.js:72
DEBUG: -dd          vector 0 0 0   Domain decomposition grid, 0 is optimize main.js:72
DEBUG: -ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian main.js:72
DEBUG: -npme        int    -1      Number of separate nodes to be used for PME, -1 main.js:72
DEBUG:                             is guess
 main.js:72
DEBUG: -nt          int    4       Total number of threads to start (0 is guess) main.js:72
DEBUG: -ntmpi       int    0       Number of thread-MPI threads to start (0 is guess) main.js:72
DEBUG: -ntomp       int    0       Number of OpenMP threads per MPI process/thread main.js:72
DEBUG:                             to start (0 is guess)
 main.js:72
DEBUG: -ntomp_pme   int    0       Number of OpenMP threads per MPI process/thread main.js:72
DEBUG:                             to start (0 is -ntomp)
 main.js:72
DEBUG: -pin         enum   auto    Fix threads (or processes) to specific cores: main.js:72
DEBUG:                             auto, on or off
 main.js:72
DEBUG: -pinoffset   int    0       The starting logical core number for pinning to main.js:72
DEBUG:                             cores; used to avoid pinning threads from
                            different mdrun instances to the same core
 main.js:72
DEBUG:                             different mdrun instances to the same core
 main.js:72
DEBUG: -pinstride   int    0       Pinning distance in logical cores for threads, main.js:72
DEBUG:                             use 0 to minimize the number of threads per
                            physical core
 main.js:72
DEBUG:                             physical core
 main.js:72
DEBUG: -gpu_id      string         List of GPU device id-s to use, specifies the main.js:72
DEBUG:                             per-node PP rank to GPU mapping
 main.js:72
DEBUG: -[no]ddcheck bool   yes     Check for all bonded interactions with DD main.js:72
DEBUG: -rdd         real   0       The maximum distance for bonded interactions with main.js:72
DEBUG:                             DD (nm), 0 is determine from initial coordinates
 main.js:72
DEBUG: -rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate main.js:72
DEBUG: -dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes main.js:72
DEBUG: -dds         real   0.8     Minimum allowed dlb scaling of the DD cell size main.js:72
DEBUG: -gcom        int    -1      Global communication frequency main.js:72
DEBUG: -nb          enum   auto    Calculate non-bonded interactions on: auto, cpu, main.js:72
DEBUG:                             gpu or gpu_cpu
 main.js:72
DEBUG: -[no]tunepme bool   yes     Optimize PME load between PP/PME nodes or GPU/CPU main.js:72
DEBUG: -[no]testverlet bool   no      Test the Verlet non-bonded scheme main.js:72
DEBUG: -[no]v       bool   no      Be loud and noisy main.js:72
DEBUG: -[no]compact bool   yes     Write a compact log file main.js:72
DEBUG: -[no]seppot  bool   no      Write separate V and dVdl terms for each main.js:72
DEBUG:                             interaction type and node to the log file(s)
 main.js:72
DEBUG: -pforce      real   -1      Print all forces larger than this (kJ/mol nm) main.js:72
DEBUG: -[no]reprod  bool   no      Try to avoid optimizations that affect binary main.js:72
DEBUG:                             reproducibility
 main.js:72
DEBUG: -cpt         real   -1      Checkpoint interval (minutes) main.js:72
DEBUG: -[no]cpnum   bool   no      Keep and number checkpoint files main.js:72
DEBUG: -[no]append  bool   yes     Append to previous output files when continuing main.js:72
DEBUG:                             from checkpoint instead of adding the simulation
                            part number to all file names
 main.js:72
DEBUG:                             part number to all file names
 main.js:72
DEBUG: -nsteps      step   -2      Run this number of steps, overrides .mdp file main.js:72
DEBUG:                             option
 main.js:72
DEBUG: -maxh        real   -1      Terminate after 0.99 times this time (hours) main.js:72
DEBUG: -multi       int    0       Do multiple simulations in parallel main.js:72
DEBUG: -replex      int    0       Attempt replica exchange periodically with this main.js:72
DEBUG:                             period (steps)
 main.js:72
DEBUG: -nex         int    0       Number of random exchanges to carry out each main.js:72
DEBUG:                             exchange interval (N^3 is one suggestion).  -nex
                            zero or not specified gives neighbor replica main.js:72
DEBUG:                             zero or not specified gives neighbor replica
                            exchange.
 main.js:72
DEBUG:                             exchange.
 main.js:72
DEBUG: -reseed      int    -1      Seed for replica exchange, -1 is generate a seed main.js:72
DEBUG: -[no]ionize  bool   no      Do a simulation including the effect of an X-Ray main.js:72
DEBUG:                             bombardment on your system
 main.js:72
DEBUG:  main.js:72
DEBUG: core: steps: 14088000 -> 14112000 main.js:72
DEBUG: Reading file Using Compiled acceleration:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG:  main.js:72
DEBUG: Can not set thread affinities on the current platform. On NUMA systems this main.js:72
DEBUG: can cause performance degradation. If you think your platform should support
setting affinities, contact the GROMACS developers. main.js:72
DEBUG: setting affinities, contact the GROMACS developers. main.js:72
DEBUG: Status: running: Calculations underway. main.js:72

timwhit · Mar 3, 2014

Coug, what kind of WUs are you getting that give you 150k points?

Howell · Mar 3, 2014

Any word on the efficiency of the Chrome NaCl app vs the desktop app?

timwhit · Mar 3, 2014

Howell said:
Any word on the efficiency of the Chrome NaCl app vs the desktop app?

From what I've read NaCl can achieve about 95% of the performance of a native application. However, in this case, I don't think that matters as the number of PPD I can get from the Chrome app is far more than I could with the desktop app.

CougTek · Mar 3, 2014

timwhit said:
Coug, what kind of WUs are you getting that give you 150k points?

Those are from the project 8105 and 8104, I think. I ran two instances of the FAH client on VM on our new server setup, configured to receive big units (since the Google app didn't work). I might run those on occasion until our electrical circuit is up and that I have to move to the production setup. In the meanwhile, I'm stuck waiting, so some of our machines (2) might as well do something useful.

We have a dedicated firewall at the office and it must be it that blocks the communication from Stanford's servers. It doesn't block the regular client's communication though. I'm not about to edit the security settings for something non-essential like the NaCl FAH module.

Handruin · Mar 5, 2014

I noticed a large spike in your PPD. Is that from the two instances of FAH?

My coworker who is on our team (StarBlazer) said he picked up a GTX 780 that he's going to add to the folding. He has the GPU now, but I don't know when he'll bring it online to fold. This should help the team a bit more.

timwhit · Mar 5, 2014

Handruin said:
My coworker who is on our team (StarBlazer) said he picked up a GTX 780 that he's going to add to the folding. He has the GPU now, but I don't know when he'll bring it online to fold. This should help the team a bit more.

I will never catch him now.

Handruin · Mar 5, 2014

Did your production increase from the Chrome plugin? Your production rate is good none the less.

timwhit · Mar 5, 2014

Yes, the NaCl version produces far more PPD than the desktop client right now.

CougTek · Mar 5, 2014

Handruin said:
I noticed a large spike in your PPD. Is that from the two instances of FAH?

That would be the two virtual machines running the FAH client part time. It is only a matter of days before I shut them down permanently in order to replace them with production machines.

Handruin · Mar 6, 2014

My team's new setup came in today with the 16 UCS blades and we got a VXN 7600 storage array with 377 drives (of which are 50 SSDs and the rest are 10K SAS!). It's a massive 6'4 display of blinking blue LEDs as it was initializing the drives this afternoon. It's almost ready for me to get my paws on it to test it out. I wish it was a viable option to run FAH to stress them in over a weekend. My plan for now is to use Prime95 with a local stress test otherwise I'd do like you've done and burn it in with some FAH.

CougTek · Mar 6, 2014

Handruin said:
My team's new setup came in today with the 16 UCS blades and we got a VXN 7600 storage array with 377 drives (of which are 50 SSDs and the rest are 10K SAS!).

You had me searching a little before I've found that it's a VNX7600. Nice storage unit. Your company officially has more IT budget than mine.

What's preventing you from stressing the systems with the FAH client is the need to get Internet access, isn't it?

On unrelated news, I've finally been able to configure one of my home system to run the NaCl Google app. I run it together with the desktop application configured for the GPU client. I need to find the motivation to configure my last functional home system that's been shut down for the last month and a half.

P5-133XL · Mar 6, 2014

Do not use the beta version of Chrome, unless you have a desperate need to keep the folding app tab primary focus and never shrink chrome to the desktop. Seems Google added a new "feature" with NaCl where it will not restart unless Chrome and the specific app has primary focus. I am keeping an instance of Chrome with only the folding tab constantly running but with the window shrunk down to the size of an icon to prevent it from pausing between WU's.

With the non-beta Chrome, there is a 500 WU limit before requiring a restart of chrome and the temp folder gets filled with files. They fixed both of these with the beta version but they added the above very annoying bug.

So there are issues ...

P5-133XL · Mar 6, 2014

You effectively can't run folding without internet access. However, you can run FAHBench for GPU stress testing but it won't give out any points.

CougTek · Mar 6, 2014

I'm using the latest stable build of Chrome under Lubuntu 3.10. Thanks for the warning about the beta version, but I've had so many problems setting up a functional NaCl client that I won't try to run it under a beta version anytime soon.

timwhit · Mar 6, 2014

Anyone know what's up with ExtremeOverclocking's stats?

Howell · Mar 6, 2014

How about a liveboot cd or other temporary install and chrome nacl?

timwhit · Mar 6, 2014

Howell said:
How about a liveboot cd or other temporary install and chrome nacl?

You could try this? http://chromeos.hexxeh.net/

P5-133XL · Mar 6, 2014

timwhit said:
Anyone know what's up with ExtremeOverclocking's stats?

According to the message they put on their web site they are pruning old historical data from their database. It takes a Long time and the stats won't be up till it is done.

Service Temporarily Unavailable

The server is temporarily unable to service your request due to maintenance downtime.

I'm pruning old historical data which is taking a VERY LONG TIME.
It will go faster without people querying data, which is why you are seeing this page!

CougTek · Mar 6, 2014

timwhit said:
You could try this? http://chromeos.hexxeh.net/

It looks outdated. I can't believe there's been no new nightly build in 11 months.

P5-133XL · Mar 6, 2014

The Native client a is very new (and relatively buggy) feature in Chrome. The open-source Chrome(ium) look-a-likes are much less likely to be up to date and work properly than current Google versions.

timwhit · Mar 6, 2014

CougTek said:
It looks outdated. I can't believe there's been no new nightly build in 11 months.

I didn't notice it was that old. Doesn't look like it's getting updated anymore.

P5-133XL · Mar 6, 2014

Coug,

One thing I'd be interested in is what kind of PPD one of your super-servers get on the Chrome-app as opposed to bigadv.

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