Messages

1

Scripts, Tutorials and Applications / Error

« on: November 7, 2016, 16:00 »

I am using VNL-ATK 2016.2 trial version for NEB calculation I used 24 cores. I am getting following errors.

Traceback (most recent call last):
  File "N.py", line 5818, in <module>
    climbing_image=False,
  File "./zipdir/NL/Dynamics/Optimization/OptimizeNudgedElasticBand.py", line 581, in OptimizeNudgedElasticBand
  File "./zipdir/NL/Dynamics/Optimization/OptimizeNudgedElasticBand.py", line 276, in projectedForces
  File "./zipdir/NL/Dynamics/Optimization/OptimizeNudgedElasticBand.py", line 232, in _update
  File "./zipdir/NL/CommonConcepts/Configurations/NudgedElasticBand.py", line 815, in update
  File "./zipdir/NL/ComputerScienceUtilities/ParallelTools/ParallelTools.py", line 897, in ParallelEnergyAndForces
  File "./zipdir/NL/ComputerScienceUtilities/ParallelTools/StaticTaskScheduler.py", line 212, in run
  File "./zipdir/NL/ComputerScienceUtilities/ParallelTools/StaticTaskScheduler.py", line 269, in __runInParallelMode
  File "./zipdir/NL/ComputerScienceUtilities/ParallelTools/ParallelTools.py", line 887, in calculateEnergiesAndForces
  File "./zipdir/NL/Analysis/TotalEnergy.py", line 32, in __init__
  File "./zipdir/NL/ComputerScienceUtilities/Timer.py", line 45, in __call__
  File "./zipdir/NL/Analysis/TotalEnergy.py", line 31, in <lambda>
  File "./zipdir/NL/Calculators/Interfaces/CachedCalculator.py", line 26, in totalEnergyWrapper
  File "./zipdir/NL/Calculators/SemiEmpirical/HuckelCalculator/Analysis/TotalEnergy.py", line 19, in calculateHuckelTotalEnergy
  File "./zipdir/NL/Calculators/SemiEmpirical/HuckelCalculator/Analysis/EnergyForcesStressUtilities.py", line 141, in setupEnergyForcesStress
  File "./zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 1491, in update
  File "./zipdir/NL/Calculators/Interfaces/BulkCalculatorInterface.py", line 266, in _update
  File "./zipdir/NL/Calculators/SemiEmpirical/HuckelCalculator/HuckelCalculator.py", line 629, in scfLoop
  File "./zipdir/NL/Calculators/GenericParameters/CheckpointHandler.py", line 156, in _storeIfNecessary
  File "./zipdir/NL/IO/IOUtilityFunctions.py", line 1147, in createNetCDFFile
  File "./zipdir/NL/IO/MetaCDFFile.py", line 251, in __init__
  File "./zipdir/NL/IO/MetaCDFFile.py", line 893, in _read
NL.ComputerScienceUtilities.Exceptions.NLIOError: Error: /home/abhijeet/ncl/*_checkpoint.nc is not a valid NetCDF 3 file
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5

2

Scripts, Tutorials and Applications / Restarting script after certain fixed period

« on: October 18, 2016, 06:04 »

On my clusters there is hard time limit of 24 hr. I want to restart the script after that period automatically. If it not converged how should I do it. I am using VNL 2016.2.

3

Scripts, Tutorials and Applications / Re: how to run a earlier scripts in latest version

« on: October 18, 2016, 05:59 »

Sir I wont get any error it simply get hang.
And I also want to know if I have 2016.0 license I updated it to 2016.2 does it work.

4

Scripts, Tutorials and Applications / how to run a earlier scripts in latest version

« on: October 17, 2016, 11:49 »

I have a scripts made in version 13.2 and I want to run it on 16 so how should I do it??

5

General Questions and Answers / Re: Restarting script

« on: October 14, 2016, 10:05 »

So is there any way to restart the script in 13 version??

6

General Questions and Answers / Restarting script

« on: October 3, 2016, 14:28 »

Hello
I was restarting my NEB calculation. I won't find device_configuration.update() instead I found neb_configuration.update() so I changed it to neb_configuration.update(force_restart=true) and before that I added a checkpoint file. So the part of script looks like below

neb_configuration.setCalculator(calculator)

device_configuration = nlread("/tmp/checkpoint07605367.nc")[0]
neb_configuration.update(force_restart=True)
nlsave('/home/NEB/analysis.nc', neb_configuration)


After I run the script I got the following error

Traceback (most recent call last):
  File "W.py", line 13577, in <module>
    neb_configuration.update(force_restart=True)
TypeError: update() got an unexpected keyword argument 'force_restart'



I am using VNL-ATK 13.8.0

7

Scripts, Tutorials and Applications / How to make LAMMPS scripts in VNL Builder

« on: October 3, 2016, 08:17 »

Is it possible to make LAMMPS scripts in VNL Builder?

8

General Questions and Answers / Re: Rerun the script

« on: October 1, 2016, 11:07 »

Thank You!!

9

General Questions and Answers / Rerun the script

« on: September 30, 2016, 06:49 »

I run the script with max. 200 steps. But due to light fluctuation it stopped in middle. I gave it on the 20 parallel processors with mpich. How do I restart it from where it has been stopped??
(In command line).
Or does it need to run from the beginning??