Messages

16

General Questions and Answers / Re: Extra output when running parallel calculations

« on: May 24, 2013, 02:20 »

Thanks for all the replies!

The case was like your last suggestion, Anders. Everything was printed twice, including all "starting" messages and the atom positions etc.
I was using OpenMPI, so I'm trying now using MPICH2. According to the log file, so far it's writing only once.

I'll get back once the calculation is over.

17

General Questions and Answers / Extra output when running parallel calculations

« on: May 23, 2013, 04:48 »

Dear all,

I recently tried my luck with running parallel calculations. Taking up 2 full 8-core nodes with one process per node (as per suggested by Parallel Guide) I got a massive speed up from more than a week on my local computer to less than 8 hours !

Now my question is; it seems that the output files - both the log file and the .nc file - get twice the output written to them when running the calculation as I described. I have a hunch that output gets n-fold written for n processes? This is not a major problem, but a minor nuisance since the log file gets a bit more messy and the size of the .nc file, which is already sizeable, is increased.

Is there a way to avoid this or is it an inherent feature of parallel calculations?

Thank you all!
Kaspar

18

General Questions and Answers / Re: Question about nlread usage

« on: May 3, 2013, 18:41 »

Thank you both!

Still I would like to see if there is a list of all the types of objects that can be called with nlread. Like 'TotalEnergy', 'DeviceConfiguration' etc. Or are they all just that intuitive, ie. the name without spaces?

As a reference to other people who might have questions about the negative index, I realized that the negative index is a property of Python and found this link which explains it: http://docs.python.org/2/tutorial/introduction.html#lists


Edit: Minor typos

19

General Questions and Answers / Question about nlread usage

« on: May 3, 2013, 05:07 »

Dear Forum,

I am a little confused about how to properly use the nlread function.
I have done a major calculation on a quite big system (120 atoms) which took days on my computer , but I would like to redo the DOS and transmission.
I got this example of how to load the "device configuration" from the .nc file that was saved to along the way

Code

device_configuration = nlread('file.nc', DeviceConfiguration)[-1]

I am not quite sure why the object type/name is DeviceConfiguration. Where can I see a list of suitable names usable for nlread?
I would expect it to be 'device_configuration' since that is how it got saved in the original script (the standard when doing the script out the the Script Generator), or otherwise 'Device Configuration' as shown in the the VNL window when clicking on my .nc file.
Otherwise, I can refer to the object handle eg. 'gID000', right?

Lastly I do not know what the [-1] means. I learned that nlread gets a list (array?) and so you need to specify the element that you want to use, but how can that be [-1] ? In the VNL window I have two objects, 'Device Configuration' and 'Density of States'  (the one I wish to redo). I would expect that the device configuration would be [ 0 ] and DOS would be [1]. Is this correct/wrong?

Thank you a lot!

Kaspar