Messages

1

General Questions and Answers / Re: Devices and electrodes

« on: December 15, 2014, 14:06 »

Ok, this is scheme.



"Device" is central region, connected to electrodes with graphene nanoribbons. Nanoribbons itself is a part of device. The atomic structure and geometry of complete device is optimized separately (T=300K), peridodic in Z-direction, so that actaully the atoms of the left nanowire were connected to the atoms of the right nanowire during optimization.

Consequences:
1. There is no short-range periodicity in order of carbon atoms of nanoribbons.
2. Nanoribbons are non-flat, so that I can't extend them with ideal perfect nanoribbons. I can't even smoothly connect them to device.

2

General Questions and Answers / Re: Apploication bug

« on: December 15, 2014, 13:31 »

I requested to update video driver, I will notify will it solve issue or not.

3

General Questions and Answers / Devices and electrodes

« on: December 12, 2014, 18:52 »

1. I have atomic configuration of a "device", XYZ-file, already optimized from external source. There is no inherent periodicity in the structure.
2. I import XYZ-file into VNL, and start the construction of device.
3. If I will try to use "Device from bulk", I will have something completely wrong, because all interatomic distances are different.

The question is: how to declare part of the structure as electrode without repetions of device's atoms?

As an example, imagine that you have system similar to this http://quantumwise.com/documents/manuals/latest/VNLTutorial/index.html/chap.gnr.html#sect1.gnr.preface, but all atoms of the initial device (between red lines) were randomly displaced or missing.

4

General Questions and Answers / Re: Apploication bug

« on: December 12, 2014, 13:34 »

However, we offer you the possibility of using VNL to create your input files (both configurations from the Builder and scripts from the Scripter) and analyze your output files with all the dedicate plugins that the graphical interface offers you.
Unless you have a very good reason to do otherwise (do you?) you should do these operations from your local machine copying the files to and from your remote cluster.

Cluster has a license - I don't have, and I can't use cluster's license on my PC.

It seems you are an expert user so if you have to modify your input files it won't be a problem to do that directly from the server without going through VNL.

My area of expertise is a bit different, h-bar for me is mainly 0.

Also, if you do not care about graphics at all why do you run VNL?

I use VNL because it is convinient tools for the construction of nanodevoces. I like it.

1. How many CPUs VNL can use effectively? Why not all 64?

yes, of course. It seems you actually run in serial.
Please have a look to the Parallel Guide here http://quantumwise.com/support/manuals

What I saw in the guide: "MKL will detect the presence of a multi-core processor and enable OpenMP automatically. It is recommended to let the software figure out itself how many threads to use optimally."

So, I asume that when I run calculations from GUI ("locally"), all available processors should be used.

If not (this is what I see now), should I use

Code

mpiexec -localonly -n 64 ... 

to force usage of all 64 cores?

5

General Questions and Answers / Re: Apploication bug

« on: December 12, 2014, 11:34 »

Try to switch off shaders, in Preferences (in the menu) in the main VNL window, on the Graphics tab. You need to restart VNL after this.

This menu point is gray and unchecked. So, I assume it is off.

As a general note, your graphics driver is too old/simple to support high-performance graphics in VNL. If you want proper 3D graphics the machine should use vendor drivers (from NVidia or ATI or similar) rather than Mesa. That said, VNL should work anyway, we will look into why it fails - the shaders should have been automatically turned off.

In 99% scientists use remote servers for calculations, don't have physical access to them, and don't need high performance graphics. I don't care about graphics at ll. Actually, I have only two options: 1) ssh connection to hpc cluster (or dedicated server), or 2) VNC on request (VNC is more convenient). In the first case, I will construct system and run it from command line using batch system. In the second case, after constructions of the system I can either run it in VNC (using 1 server with 16-80 CPUs) or submit it using batch system (unlimited CPUs).

In my case, it is either dedicated HP DL585 with 4x16 cores, or HP SL230s with 2x8 cores. I even don't know what kind of graphics they have.

Moreover, why are you running VNL over VNC? Why not run it on your own computer, that way the graphics will probably be a lot faster (a lot!!!).

I don't need nice and fast graphics. I use VNL because it is convinient tools for the construction of nanodevoces. Running VNL locally on my laptop - is not a solution for many reasons.

Actually, I have more questions:
1. How many CPUs VNL can use effectively? When it was running on DL585 with 64 cores it was using 1, 10 or 32 CPUs in different moments of time. Why not all 64?
2. When running on cluster, I can specify as many CPUs as I want. But taking into account what I noticed about CPU usage on 1 server, it seems that running on cluster will just waste of computational time. So, can VNL run effectively on cluster?

6

General Questions and Answers / Re: Apploication bug

« on: December 11, 2014, 16:47 »

System information
Build: 2014.1.eefa9df
Platform: Linux
Python 2.7.2
Qt 4.8.5
PyQt 4.10.3
3D graphics - OpenGL
Vendor: Mesa project: www.mesa3d.org
GPU: Mesa GLX Indirect
Version: OpenGL 1.2 (1.5 Mesa 6.4.1)
Shading language version: Unknown

HP DL585, VNC server + VNC viewer.

It actually happens to all projects. Even when I tried to create new and just created nanoribbon: builder->add->plugin->nanoribbon. Immediatelly after "OK" VNL fails.

7

General Questions and Answers / Apploication bug

« on: December 11, 2014, 14:36 »

I have Ubuntu 12.04 LTS.

When I start VNL, and try to open Builder, application fails. Details:
non@non:~/ex/mp$ vnl
WARNING: Application calling GLX 1.3 function "glXCreatePbuffer" when GLX 1.3 is not supported!  This is an application bug!
X Error: GLXUnsupportedPrivateRequest 162
  Extension:    148 (Uknown extension)
  Minor opcode: 16 (Unknown request)
  Resource id:  0x10007
X Error: GLXUnsupportedPrivateRequest 162
  Extension:    148 (Uknown extension)
  Minor opcode: 17 (Unknown request)
  Resource id:  0x10008
X Error: GLXUnsupportedPrivateRequest 162
  Extension:    148 (Uknown extension)
  Minor opcode: 16 (Unknown request)
  Resource id:  0x10007
X Error: GLXBadDrawable 156
  Extension:    148 (Uknown extension)
  Minor opcode: 5 (Unknown request)
  Resource id:  0x4600212
Segmentation fault (core dumped)


It happens when I open existing project. When I'm trying to create "new project", builder doesn't crash.

8

Installation and License Questions / Licensing error

« on: November 4, 2014, 11:55 »

Hi!

I have Ubuntu and I'm trting to act as written in the installation guide of the user manual (http://quantumwise.com/documents/manuals/latest/InstallationGuide/index.html/chap.licensing.html).

After executing ./lmx_server -l licensefile.lic I got the following message:

[2014-11-04 11:40:48] Minimum user remove time set to 120 seconds.
[2014-11-04 11:40:48] LM-X License Server v4.6.5 build 60e4490c on ubuntu (Linux_x64)
[2014-11-04 11:40:48] Copyright (C) 2002-2014 X-Formation. All rights reserved.
[2014-11-04 11:40:48] Website: http://www.lm-x.com http://www.x-formation.com
[2014-11-04 11:40:48] License server has pid 3139.
[2014-11-04 11:40:48] Serving licenses for vendor QUANTUM.
[2014-11-04 11:40:48]
[2014-11-04 11:40:48] License server using TCP IPv4 port 6200.
[2014-11-04 11:40:48] License server using TCP IPv6 port 6200.
[2014-11-04 11:40:48] License server using UDP IPv4 port 6200.
[2014-11-04 11:40:48] Reading licenses...
[2014-11-04 11:40:48] License file(s):
[2014-11-04 11:40:48] qw_license.lic
[2014-11-04 11:40:48] WARNING: Feature atkclassical (v14.2) is ignored: (Err: 35) Unable to use local license as a network license.
[2014-11-04 11:40:48] WARNING: Feature atkdft (v14.2) is ignored: (Err: 35) Unable to use local license as a network license.
[2014-11-04 11:40:48] WARNING: Feature atkmaster (v14.2) is ignored: (Err: 35) Unable to use local license as a network license.
[2014-11-04 11:40:48] WARNING: Feature atkpython (v14.2) is ignored: (Err: 35) Unable to use local license as a network license.
[2014-11-04 11:40:48] WARNING: Feature atkse (v14.2) is ignored: (Err: 35) Unable to use local license as a network license.
[2014-11-04 11:40:48] WARNING: Feature atkslave (v14.2) is ignored: (Err: 35) Unable to use local license as a network license.
[2014-11-04 11:40:48] WARNING: Feature atkvasp (v14.2) is ignored: (Err: 35) Unable to use local license as a network license.
[2014-11-04 11:40:48] WARNING: Feature vnl (v14.2) is ignored: (Err: 35) Unable to use local license as a network license.
[2014-11-04 11:40:48] Log file path: Not set
[2014-11-04 11:40:48] Log to stdout: Yes
[2014-11-04 11:40:48] Log format: Normal
[2014-11-04 11:40:48] Configuration file path: Not set
[2014-11-04 11:40:48] WARNING: No licenses to serve.
[2014-11-04 11:40:48]
[2014-11-04 11:40:48] To administrate the license server go to page http://ubuntu:6200
[2014-11-04 11:40:48] Ready to serve...

I used demo license that I recieved on 31st of October.

What should I do?

9

Installation and License Questions / Built-in demo license

« on: October 30, 2014, 16:59 »

So, as I can reed in the readme: "Anyone who wants to try 12.2 - existing QuantumWise customer or not - can just download and install it without obtaining a license for it beforehand. This version will run using a built-in demo license which lasts for 14 days."

I installed Nanolab, and this is what I see:


What shall I do?