Hi,
I am trying to run NPT simulations using pmemd.cuda using TITAN graphics
cards. The equilibration & steps were completed with the CPU version of
sander.
I have 2x EVGA superclocked TITAN cards.There have been problems with the
TITAN graphics cards and I RMA'd one. I have benchmarked both the cards
after the RMA and determined that they have no obvious problems that would
warrant them being RMA'd again. Though there is an issue with the AMBER
cuda code and TITANs in general as discussed in the following thread:
< sorry, can't find it, but it's a ~200 posts long and titled: experiences
with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? >
As I'm not sure whether this is the same issue, I'm posting this in a new
thread.
I began running 12 100ns production run using TITAN-a. There were no
problems. After waiting for and testing the replacement card (TITAN-b), I
put that into the machine as well. So both cards were working on finishing
the total of 300 segments.
Very shortly, all the segments had failed, though the cards still showed a
100% utilisation and I did not realise until I checked the outfiles which
showed "ERROR: nfft1 must be in the range of blah, blah, blah" (error
posted below). This was pretty weird as I am used to the jobs visibly
failing and not carrying on eating resources, whilst doing nothing.
So I pulled the TITAN-a out and restarted the calculations with TITAN-b
from the last good rst. Usually 2 back. There have been no problems at all
and all the simulations have completed.
My hardware specs are:
Gigabyte GA-X58-UD7 mobo
i7-930 processor
6GB RAM
1200 Watt Bequiet power supply
Does anyone have any idea as to what's going on?
br,
g
############################################################
############################################################
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 12
| Run on 06/09/2013 at 16:26:10
[-O]verwriting output
File Assignments:
| MDIN: prod.in
| MDOUT: md_4.out
| INPCRD: md_3.rst
| PARM: ../leap/TMC_I54V-V82S_Complex_25.parm
| RESTRT: md_4.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md_4.ncdf
| MDINFO: mdinfo
Here is the input file:
Constant pressure constant temperature production run
&cntrl
nstlim=2000000, dt=0.002, ntx=5, irest=1, ntpr=250, ntwr=1000, ntwx=500,
temp0=300.0, ntt=1, tautp=2.0, ioutfm=1, ig=-1, ntxo=2,
ntb=2, ntp=1,
ntc=2, ntf=2,
nrespa=1,
&end
Note: ig = -1. Setting random seed based on wallclock time in microseconds.
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.3
|
| 04/24/2013
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
| Duncan Poole (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2012, (In review).
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX TITAN
| CUDA Device Global Mem Size: 6143 MB
| CUDA Device Num Multiprocessors: 14
| CUDA Device Core Freq: 0.93 GHz
|
|--------------------------------------------------------
| ERROR: nfft1 must be in the range of 6 to 512!
| ERROR: nfft2 must be in the range of 6 to 512!
| ERROR: nfft3 must be in the range of 6 to 512!
| ERROR: a must be in the range of 0.10000E+01 to 0.10000E+04!
| ERROR: b must be in the range of 0.10000E+01 to 0.10000E+04!
| ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
Input errors occurred. Terminating execution.
############################################################
############################################################
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 17 2013 - 22:30:02 PDT
