Re: [AMBER] crashed run and time estimate

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 4 Nov 2011 22:49:25 -0700

Hi Yao,

> is there any way I can continue a crashed run and a flag for sander to
> estimate what time the job will be done?

To continue a crashed run in &cntrl set

irest=1, ntx=5

Then give the restart file as the input coordinates with -c.

$AMBERHOME/bin/sander -o -i mdin -o mdout -p prmtop -c inpcrd -x mdcrd -inf
mdinfo -r restart

<crash>

$AMBERHOME/bin/sander -O -i mdin.1 -o mdout.1 -c restart -x mdcrd.1 -inf
mdinfo.1 -r restart.1

To see how long a job is estimated to take let it run for about 3 or 4
minutes and then cat the file specified by the -inf command line option.
(default name is mdinfo).

E.g.


 NSTEP = 49924500 TIME(PS) = 100899.010 TEMP(K) = 293.55 PRESS =
0.0
 Etot = -296.0964 EKtot = 222.2512 EPtot =
-518.3476
 BOND = 46.4742 ANGLE = 156.2150 DIHED =
148.8680
 1-4 NB = 67.3502 1-4 EEL = 901.4083 VDWAALS =
-101.4540
 EELEC = -1388.9326 EGB = -348.2766 RESTRAINT =
0.0000
 
---------------------------------------------------------------------------- 
--
| Current Timing Info
| -------------------
| Total steps :  50000000 | Completed :  49924500 | Remaining :     75500
|
| Average timings for last   79250 steps:
|     Elapsed(s) =      59.84 Per Step(ms) =       0.76
|         ns/day =     228.86   seconds/ns =     377.53
|
| Average timings for all steps:
|     Elapsed(s) =   37739.59 Per Step(ms) =       0.76
|         ns/day =     228.59   seconds/ns =     377.97
|
|
| Estimated time remaining:      57.1 seconds.
 
----------------------------------------------------------------------------
--
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
|             Assistant Research Professor              |
|            San Diego Supercomputer Center             |
|             Adjunct Assistant Professor               |
|         Dept. of Chemistry and Biochemistry           |
|          University of California San Diego           |
|                     NVIDIA Fellow                     |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk  | 
---------------------------------------------------------
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Received on Fri Nov 04 2011 - 23:00:07 PDT
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