Folding Forum

Posted: **Thu Aug 13, 2009 10:13 pm**

Hello,

I have a C2D machine that has been running very reliably with A2 core SMP WU's, and generally performing at something under 10 minutes per frame. But today, this WU downloaded and I noticed it's going to miss the deadline, since it is taking approximately 63 minutes per frame.

When I noticed it, logged onto the machine, checked to see if anything peculiar was going on (it's running notfred's ISO straight from a CD), but didn't find anything at first. It's running at the same CPU speed as ever.

I killed the client and restarted it manually, but after waiting over 20 minutes it still hadn't progressed, so I knew it hadn't made any difference. After waiting for a backup, I restarted the machine. It's still running the same as ever, but with less than 1/6 the normal speed.

The only thing I've discovered that is different is that the 2 cores of this CPU seem to very in temperature more than I've seen with other WU's, with one being 8-9C warmer than the other, and the temperatures switch between cores. That is to say, for example, the first core will run at, say, 70C, and the other at 78C, and then after a period the first core will run at 79C, and the other at 71C. Normally the temp diffs are 2C or less.

Does anyone have any ideas?

Posted: **Thu Aug 13, 2009 10:31 pm**

I think pasting relevant console/FAHlog.txt excerpt is more likely to trigger ideas

tear

Posted: **Thu Aug 13, 2009 10:35 pm**

The problem with that is, it doesn't show anything. It just shows slower progress compared to the normal rate. There's no console available, since it's not running in a VM as most do. It's sitting in text mode, but there's no output since all error messages are > /dev/null anyway.

Posted: **Thu Aug 13, 2009 10:39 pm**

Ok, let me rephrase.

I thought it might be one of these but hey, you're the one with the log.

tear

Posted: **Fri Aug 14, 2009 3:58 am**

Thanks for replying again. I was a bit hurried and hadn't built up enough since the reboot to show much, but I will post the FAHlog.txt, the unitinfo.txt, and the wudate_06.log and see if that gives any useful information. I think the link that you kindly provided may be something similar to what I'm seeing, except that my progress would appear to be quite a bit faster than the one discussed on the first page of that thread, at least.

FAHlog.txt:

Code: Select all


--- Opening Log file [August 13 15:36:50] 


# SMP Client ##################################################################
###############################################################################

                       Folding@Home Client Version 6.02

                          http://folding.stanford.edu

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

Launch directory: /etc/folding/1
Executable: ./fah6
Arguments: -local -forceasm -smp 2 

Warning:
 By using the -forceasm flag, you are overriding
 safeguards in the program. If you did not intend to
 do this, please restart the program without -forceasm.
 If work units are not completing fully (and particularly
 if your machine is overclocked), then please discontinue
 use of the flag.

[15:36:50] - Ask before connecting: No
[15:36:50] - User name: Ragnar_Dan (Team 2630)
[15:36:50] - User ID: [edited out]
[15:36:50] - Machine ID: 1
[15:36:50] 
[15:36:50] Loaded queue successfully.
[15:36:50] 
[15:36:50] + Processing work unit
[15:36:50] At least 4 processors must be requested.Core required: FahCore_a2.exe
[15:36:50] Core not found.
[15:36:50] - Core is not present or corrupted.
[15:36:50] - Attempting to download new core...
[15:36:50] + Downloading new core: FahCore_a2.exe
[15:36:51] + 10240 bytes downloaded
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[15:36:52] Verifying core Core_a2.fah...
[15:36:53] Signature is VALID
[15:36:53] 
[15:36:53] Trying to unzip core FahCore_a2.exe
[15:36:53] Decompressed FahCore_a2.exe (4382312 bytes) successfully
[15:36:53] + Core successfully engaged
[19:36:59] 
[19:36:59] + Processing work unit
[19:36:59] At least 4 processors must be requested.Core required: FahCore_a2.exe
[19:36:59] Core found.
[19:36:59] Working on Unit 06 [August 13 19:36:59]
[19:36:59] + Working ...
[19:36:59] 
[19:36:59] *------------------------------*
[19:36:59] Folding@Home Gromacs SMP Core
[19:36:59] Version 2.08 (Mon May 18 14:47:42 PDT 2009)
[19:36:59] 
[19:36:59] Preparing to commence simulation
[19:36:59] - Ensuring status. Please wait.
[19:37:08] - Assembly optimizations manually forced on.
[19:37:08] - Not checking prior termination.
[19:37:09] - Expanded 1531002 -> 23999905 (decompressed 1567.5 percent)
[19:37:09] Called DecompressByteArray: compressed_data_size=1531002 data_size=23999905, decompressed_data_size=23999905 diff=0
[19:37:09] - Digital signature verified
[19:37:09] 
[19:37:09] Project: 2675 (Run 1, Clone 261, Gen 133)
[19:37:09] 
[19:37:09] Assembly optimizations on if available.
[19:37:09] Entering M.D.
[19:37:15] Using Gromacs checkpoints
[19:37:17] Multi-core optimizations on
[19:37:18] Resuming from checkpoint
[19:37:18] Verified work/wudata_06.log
[19:37:18] Verified work/wudata_06.trr
[19:37:18] Verified work/wudata_06.xtc
[19:37:18] Verified work/wudata_06.edr
[19:37:31] Completed 5818 out of 250000 steps  (2%)
[20:19:32] Completed 7500 out of 250000 steps  (3%)
[21:22:14] Completed 10000 out of 250000 steps  (4%)
[22:24:57] Completed 12500 out of 250000 steps  (5%)
[23:27:40] Completed 15000 out of 250000 steps  (6%)
[00:30:23] Completed 17500 out of 250000 steps  (7%)
[01:33:06] Completed 20000 out of 250000 steps  (8%)
[02:35:49] Completed 22500 out of 250000 steps  (9%)
[03:38:32] Completed 25000 out of 250000 steps  (10%)

unitinfo.txt:

Code: Select all

Current Work Unit
-----------------
Name: Gromacs
Tag: P2675R1C261G133
Download time: August 13 16:59:14
Due time: August 16 16:59:14
Progress: 10%  [|_________]

And here's the wudata_06.log file:

Code: Select all

Log file opened on Thu Aug 13 16:59:31 2009
Host: fold-875A  pid: 5280  nodeid: 0  nnodes:  4
The Gromacs distribution was built Mon May 18 11:23:14 PDT 2009 by
server@vspmf93 (Linux 2.6.16.13-4-default x86_64)


                         :-)  G  R  O  M  A  C  S  (-:

                   Groningen Machine for Chemical Simulation

                 :-)  VERSION 4.0.99_development_20090425  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, The GROMACS development team,
            check out http://www.gromacs.org for more information.


                                :-)  mdrun  (-:


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------

parameters of the run:
   integrator           = md
   nsteps               = 250000
   init_step            = 33250002
   ns_type              = Grid
   nstlist              = 10
   ndelta               = 2
   nstcomm              = 1
   comm_mode            = Linear
   nstlog               = 1000
   nstxout              = 50000
   nstvout              = 50000
   nstfout              = 0
   nstenergy            = 1000
   nstxtcout            = 5000
   init_t               = 0
   delta_t              = 0.002
   xtcprec              = 1000
   nkx                  = 10
   nky                  = 10
   nkz                  = 10
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = FALSE
   ePBC                 = xyz
   bPeriodicMols        = FALSE
   bContinuation        = TRUE
   bShakeSOR            = FALSE
   etc                  = Berendsen
   epc                  = No
   epctype              = Isotropic
   tau_p                = 10
   ref_p (3x3):
      ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   compress (3x3):
      compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   refcoord_scaling     = No
   posres_com (3):
      posres_com[0]= 0.00000e+00
      posres_com[1]= 0.00000e+00
      posres_com[2]= 0.00000e+00
   posres_comB (3):
      posres_comB[0]= 0.00000e+00
      posres_comB[1]= 0.00000e+00
      posres_comB[2]= 0.00000e+00
   andersen_seed        = 815131
   rlist                = 1.2
   rtpi                 = 0.05
   coulombtype          = Reaction-Field
   rcoulomb_switch      = 0.9
   rcoulomb             = 1.2
   vdwtype              = Shift
   rvdw_switch          = 0.9
   rvdw                 = 1.2
   epsilon_r            = 1
   epsilon_rf           = 60
   tabext               = 1
   implicit_solvent     = No
   gb_algorithm         = Still
   gb_epsilon_solvent   = 80
   nstgbradii           = 1
   rgbradii             = 2
   gb_saltconc          = 0
   gb_obc_alpha         = 1
   gb_obc_beta          = 0.8
   gb_obc_gamma         = 4.85
   gb_dielectric_offset = 0
   sa_algorithm         = No
   sa_surface_tension   = 2.092
   DispCorr             = EnerPres
   free_energy          = no
   init_lambda          = 0
   delta_lambda         = 0
   n_foreign_lambda     = 0
   sc_alpha             = 0
   sc_power             = 0
   sc_sigma             = 0.3
   nstdhdl              = 1
   nwall                = 0
   wall_type            = 9-3
   wall_atomtype[0]     = -1
   wall_atomtype[1]     = -1
   wall_density[0]      = 0
   wall_density[1]      = 0
   wall_ewald_zfac      = 3
   pull                 = no
   disre                = No
   disre_weighting      = Equal
   disre_mixed          = FALSE
   dr_fc                = 1000
   dr_tau               = 1.25
   nstdisreout          = 100
   orires_fc            = 418.4
   orires_tau           = 10
   nstorireout          = 100
   dihre-fc             = 1000
   em_stepsize          = 0.01
   em_tol               = 10
   niter                = 20
   fc_stepsize          = 0
   nstcgsteep           = 1000
   nbfgscorr            = 10
   ConstAlg             = Lincs
   shake_tol            = 0.0001
   lincs_order          = 4
   lincs_warnangle      = 90
   lincs_iter           = 1
   bd_fric              = 0
   ld_seed              = 1993
   cos_accel            = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   userint1             = 0
   userint2             = 0
   userint3             = 0
   userint4             = 0
   userreal1            = 0
   userreal2            = 0
   userreal3            = 0
   userreal4            = 0
grpopts:
   nrdf:     57431.4     614.994      247699
   ref_t:         300         300         300
   tau_t:           1           1           1
anneal:          No          No          No
ann_npoints:           0           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp_flags[  0]: 0
   efield-x:
      n = 0
   efield-xt:
      n = 0
   efield-y:
      n = 0
   efield-yt:
      n = 0
   efield-z:
      n = 0
   efield-zt:
      n = 0
   bQMMM                = FALSE
   QMconstraints        = 0
   QMMMscheme           = 0
   scalefactor          = 1
qm_opts:
   ngQM                 = 0

Initializing Domain Decomposition on 4 nodes
Dynamic load balancing: yes
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 0.000 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.219 nm
Estimated maximum distance required for P-LINCS: 0.219 nm
This distance will limit the DD cell size, you can override this with -rcon
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 4 cells with a minimum initial size of 0.274 nm
The maximum allowed number of cells is: X 36 Y 36 Z 54
Domain decomposition grid 1 x 1 x 4, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0

Table routines are used for coulomb: FALSE
Table routines are used for vdw:     TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Reaction-Field:
epsRF = 60, rc = 1.2, krf = 0.282178, crf = 1.23967, epsfac = 138.935
The electrostatics potential has its minimum at r = 1.21008
System total charge: 0.000
Generated table with 1100 data points for RF.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Enabling SPC water optimization for 41132 molecules.

Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE support... present.



Initializing Parallel LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------

The number of constraints is 11352
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


Linking all bonded interactions to atoms

NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp

There are 126480 inter charge-group exclusions,
will use an extra communication step for exclusion forces for Reaction-Field

The maximum number of communication pulses is: Z 1
The minimum size for domain decomposition cells is 1.200 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: Z 0.32
The maximum allowed distance for charge groups involved in interactions is:
                 non-bonded interactions           1.200 nm
            two-body bonded interactions  (-rdd)   1.200 nm
          multi-body bonded interactions  (-rdd)   1.200 nm
  atoms separated by up to 5 constraints  (-rcon)  1.200 nm


Making 1D domain decomposition grid 1 x 1 x 4, home cell index 0 0 0

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------

There are: 146832 Atoms
Charge group distribution at step 33250002: 64568 0 0 0
Grid: 26 x 26 x 14 cells
Initial temperature: nan K

Started mdrun on node 0 Thu Aug 13 16:59:33 2009

           Step           Time         Lambda
       33250002    66500.00716        0.00000

Long Range LJ corr.: <C6> 3.5483e-04
Long Range LJ corr.: Epot   -17044.2, Pres:   -188.874, Vir:    8530.67
   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan    0.00000e+00

DD  step 33250009  vol min/aver 1.000  load imb.: force 288.6%

Writing checkpoint, step 33250010 at Thu Aug 13 16:59:59 2009

Writing checkpoint, step 33250810 at Thu Aug 13 17:19:57 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33250999  vol min/aver 0.320! load imb.: force 290.5%

           Step           Time         Lambda
       33251000    66502.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33251210 at Thu Aug 13 17:29:59 2009

Writing checkpoint, step 33251610 at Thu Aug 13 17:40:01 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33251999  vol min/aver 0.320! load imb.: force 290.6%

           Step           Time         Lambda
       33252000    66504.00316        0.00000

Writing checkpoint, step 33252000 at Thu Aug 13 17:49:48 2009

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33252400 at Thu Aug 13 17:59:51 2009

Writing checkpoint, step 33252510 at Thu Aug 13 18:02:36 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33252999  vol min/aver 0.320! load imb.: force 290.7%

           Step           Time         Lambda
       33253000    66506.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33253200 at Thu Aug 13 18:19:55 2009

Writing checkpoint, step 33253600 at Thu Aug 13 18:29:57 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33253999  vol min/aver 0.320! load imb.: force 290.7%

           Step           Time         Lambda
       33254000    66508.00316        0.00000

Writing checkpoint, step 33254000 at Thu Aug 13 18:39:59 2009

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33254400 at Thu Aug 13 18:50:02 2009

Writing checkpoint, step 33254790 at Thu Aug 13 18:59:49 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33254999  vol min/aver 0.320! load imb.: force 290.6%

           Step           Time         Lambda
       33255000    66510.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33255010 at Thu Aug 13 19:05:20 2009

           Step           Time         Lambda
       33255010    66510.02316        0.00000

Long Range LJ corr.: <C6> 3.5483e-04
Long Range LJ corr.: Epot   -17044.2, Pres:   -188.874, Vir:    8530.67
   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan    0.00000e+00

DD  step 33255019  vol min/aver 1.000  load imb.: force 282.6%

Writing checkpoint, step 33255020 at Thu Aug 13 19:14:20 2009

Writing checkpoint, step 33255820 at Thu Aug 13 19:34:19 2009

           Step           Time         Lambda
       33255820    66511.64316        0.00000

Long Range LJ corr.: <C6> 3.5483e-04
Long Range LJ corr.: Epot   -17044.2, Pres:   -188.874, Vir:    8530.67
   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan    0.00000e+00

DD  step 33255829  vol min/aver 1.000  load imb.: force 288.5%

Writing checkpoint, step 33255830 at Thu Aug 13 19:37:45 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33255999  vol min/aver 0.320! load imb.: force 290.3%

           Step           Time         Lambda
       33256000    66512.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33256630 at Thu Aug 13 19:57:42 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33256999  vol min/aver 0.320! load imb.: force 290.3%

           Step           Time         Lambda
       33257000    66514.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33257030 at Thu Aug 13 20:07:44 2009

Writing checkpoint, step 33257430 at Thu Aug 13 20:17:46 2009

Writing checkpoint, step 33257510 at Thu Aug 13 20:19:47 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33257999  vol min/aver 0.320! load imb.: force 290.2%

           Step           Time         Lambda
       33258000    66516.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33258220 at Thu Aug 13 20:37:35 2009

Writing checkpoint, step 33258620 at Thu Aug 13 20:47:37 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33258999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33259000    66518.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33259020 at Thu Aug 13 20:57:39 2009

Writing checkpoint, step 33259420 at Thu Aug 13 21:07:41 2009

Writing checkpoint, step 33259820 at Thu Aug 13 21:17:43 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33259999  vol min/aver 0.320! load imb.: force 290.5%

           Step           Time         Lambda
       33260000    66520.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33260010 at Thu Aug 13 21:22:29 2009

Writing checkpoint, step 33260610 at Thu Aug 13 21:37:32 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33260999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33261000    66522.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33261010 at Thu Aug 13 21:47:34 2009

Writing checkpoint, step 33261410 at Thu Aug 13 21:57:36 2009

Writing checkpoint, step 33261810 at Thu Aug 13 22:07:38 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33261999  vol min/aver 0.320! load imb.: force 290.5%

           Step           Time         Lambda
       33262000    66524.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33262210 at Thu Aug 13 22:17:41 2009

Writing checkpoint, step 33262510 at Thu Aug 13 22:25:12 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33262999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33263000    66526.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33263010 at Thu Aug 13 22:37:45 2009

Writing checkpoint, step 33263410 at Thu Aug 13 22:47:47 2009

Writing checkpoint, step 33263800 at Thu Aug 13 22:57:34 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33263999  vol min/aver 0.320! load imb.: force 290.5%

           Step           Time         Lambda
       33264000    66528.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33264200 at Thu Aug 13 23:07:36 2009

Writing checkpoint, step 33264600 at Thu Aug 13 23:17:38 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33264999  vol min/aver 0.320! load imb.: force 290.5%

           Step           Time         Lambda
       33265000    66530.00316        0.00000

Writing checkpoint, step 33265000 at Thu Aug 13 23:27:40 2009

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33265010 at Thu Aug 13 23:27:55 2009

Writing checkpoint, step 33265800 at Thu Aug 13 23:47:44 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33265999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33266000    66532.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33266200 at Thu Aug 13 23:57:46 2009

Writing checkpoint, step 33266590 at Fri Aug 14 00:07:33 2009

Writing checkpoint, step 33266990 at Fri Aug 14 00:17:35 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33266999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33267000    66534.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33267390 at Fri Aug 14 00:27:37 2009

Writing checkpoint, step 33267510 at Fri Aug 14 00:30:38 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33267999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33268000    66536.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33268190 at Fri Aug 14 00:47:41 2009

Writing checkpoint, step 33268590 at Fri Aug 14 00:57:43 2009

Writing checkpoint, step 33268990 at Fri Aug 14 01:07:45 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33268999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33269000    66538.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33269380 at Fri Aug 14 01:17:32 2009

Writing checkpoint, step 33269780 at Fri Aug 14 01:27:34 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33269999  vol min/aver 0.320! load imb.: force 290.3%

           Step           Time         Lambda
       33270000    66540.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33270010 at Fri Aug 14 01:33:21 2009

Writing checkpoint, step 33270580 at Fri Aug 14 01:47:39 2009

Writing checkpoint, step 33270980 at Fri Aug 14 01:57:41 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33270999  vol min/aver 0.320! load imb.: force 290.3%

           Step           Time         Lambda
       33271000    66542.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33271380 at Fri Aug 14 02:07:43 2009

Writing checkpoint, step 33271780 at Fri Aug 14 02:17:45 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33271999  vol min/aver 0.320! load imb.: force 290.1%

           Step           Time         Lambda
       33272000    66544.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33272180 at Fri Aug 14 02:27:47 2009

Writing checkpoint, step 33272510 at Fri Aug 14 02:36:04 2009

Writing checkpoint, step 33272970 at Fri Aug 14 02:47:36 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33272999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33273000    66546.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33273370 at Fri Aug 14 02:57:38 2009

Writing checkpoint, step 33273770 at Fri Aug 14 03:07:40 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33273999  vol min/aver 0.320! load imb.: force 290.3%

           Step           Time         Lambda
       33274000    66548.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33274170 at Fri Aug 14 03:17:42 2009

Writing checkpoint, step 33274570 at Fri Aug 14 03:27:44 2009

Writing checkpoint, step 33274970 at Fri Aug 14 03:37:46 2009

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 33274999  vol min/aver 0.320! load imb.: force 290.4%

           Step           Time         Lambda
       33275000    66550.00316        0.00000

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
            nan    3.72501e+07    8.93014e+04            nan            nan
        LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.      Potential
    0.00000e+00   -1.70442e+04    0.00000e+00            nan            nan
    Kinetic En.   Total Energy    Temperature Pressure (bar)   Constr. rmsd
            nan            nan            nan            nan            nan

Writing checkpoint, step 33275010 at Fri Aug 14 03:38:47 2009

Posted: **Fri Aug 14, 2009 4:03 am**

BTW the machine is running at 3120 MHz. And it appears all 4 a2 cores were getting plenty of CPU time, the "ps" list showing 194, 134, 134, and 147 minutes for the respective FahCore_a2.exe processes in the last ~9 hours.

For whatever it's worth, I'm going to delete the WU since it will be discarded by Stanford anyway.

Posted: **Fri Aug 14, 2009 4:59 am**

Reported as bad.

Posted: **Fri Aug 14, 2009 6:21 pm**

Thanks.

Folding Forum

Project: 2675 (Run 1, Clone 261, Gen 133) going slowly

Project: 2675 (Run 1, Clone 261, Gen 133) going slowly

Re: Project: 2675 (Run 1, Clone 261, Gen 133) going slowly

Re: Project: 2675 (Run 1, Clone 261, Gen 133) going slowly

Re: Project: 2675 (Run 1, Clone 261, Gen 133) going slowly

Re: Project: 2675 (Run 1, Clone 261, Gen 133) going slowly

Re: Project: 2675 (Run 1, Clone 261, Gen 133) going slowly

Re: Project: 2675 (Run 1, Clone 261, Gen 133) going slowly

Re: Project: 2675 (Run 1, Clone 261, Gen 133) going slowly