Topics

1

Installation and License Questions / Assymetrical core distribution (in Parallel)

« on: May 4, 2012, 14:53 »

Hi,

           If I have two 12 core machine and one 80 core SUN machine, can I some how define which node has how many cores and make the program run such that each 12+12+80 cores are utilized? I tried to simply include the ip of SUN machine and increase the number to 12+12+80, and mpich2 just roughly divided it by 3 and allocated it symmetrically.

Thanks

2

Installation and License Questions / Pause/Restore simulation after network failure (in Parallel)

« on: May 4, 2012, 14:48 »

Hi,

           I have two 12 core machine in our lab and a 80 core SUN server in other lab. The license server is one of the two machine in our lab. I am trying to run a simulation over the SUN machine. But we have some power failures and the simulation gets killed without the license. Is there any way to pause the simulation automatically (when network fails/no license) and resume it again automatically (when power comes back)? The simulation will be waiting for the license to become available again and not get killed (like Synopsys TCAD Sentaurus).

Thanks

3

General Questions and Answers / Obtaining Energy band diagram

« on: April 3, 2012, 12:31 »

Hello,

        How to obtain Energy band diagram (E vs. x) to visualize band bending of conduction and valence band?
        I have a guess that I have to find an effective potential profile w.r.t. fermi energy and adjust the band minima w.r.t that value.
        Am I right?

Thanks

4

Scripts, Tutorials and Applications / 1d DOS script port

« on: January 16, 2012, 10:15 »

Anders,

Will you please port the 1ddos script to newest ATK version? (with example script)

Thank You

5

General Questions and Answers / Relative speed and accuracy of device algorithm, exchange correlation, basis set

« on: January 7, 2012, 08:43 »

Hi,

        I want to know the relative speed and accuracy of device algorithm (maybe like Recursion > Direct > Krylov), exchange Correlation, basis set for ATK-DFT (device). (especially in the case of I-V characteristics of CNT with various metal contacts). Accuracy is very important.

I'd also like to know whether ATK-device calculates both ballistic transport and diffusive transport. Does not ATK calculate scattering probability from scattering potentials in diffusive transport?

Thank You

6

Scripts, Tutorials and Applications / Negative Current obtained from positive bias Voltage

« on: December 10, 2011, 12:16 »

Hi,

       Recently I've tried to simulate I-V characteristics of Platinum contacted (10, 0) Zigzag CNT. I've used Huckel calculator with cedra basis sets and (3, 3, 100) k-point sampling. And the attached pictures show my result. The transmission spectra for each bias did not have any negative value (but gaps where the curves did not appear above Tr=0). The I-V analyzer interpolated those to some negative value. So why do I get negative current for some positive bias voltages?

Thank you.

7

Installation and License Questions / Cluster Network Setup

« on: November 24, 2011, 11:14 »

Hi,

          We have a Sun server in our campus and we have access to that server using remote login. The detailed description of the server is as below:
system:       Sun Gridengine
processors: 20 quad-cores
proc-arch:   X86_64
memory:      3.4GB per core
OS:              CentOS 4.5
Kernel:         2.6.9-55.0.2.Elsmp

           Currently I am working on a Red Hat Linux workstation with four quad core proc and 8 GB RAM.
Red Hat Enterprise Linux Client release 5.3 (Tikanga)
Linux version 2.6.18-128.el5 (mockbuild@hs20-bc1-7.build.redhat.com) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed Dec 17 11:41:38 EST 2008

I would like to make a cluster setup with my workstation as master and the server nodes as slaves. Please, tell me which software do I need to set up this cluster network over LAN and also tell me how to do it with that software.


Thank You.

8

Installation and License Questions / Efficiency of multiprocessing and multithreading

« on: August 30, 2011, 07:53 »

Hi,

        We are planning to buy QuantumWise SE and DFT licenses and need help with selection of workstations. We plan to buy 2 work stations. After reading the manuals and numerous posts here I gathered some ideas about parallelization of ATK calculations. However, I want to clarify about some questions regarding efficient use of OpenMP threading on multicore processors. Say I want to use one single node with 12 core processors (like two dell hex core processors each with 12MB L3 cache, 2.4-3.3GHz clock, 1333-1033MHz RAM speed) and 24-36MB of DDR3 system RAM.

For system A using 60-100 atoms (usually carbon) with doublezetapolaroid and system B using nearly 3000 atoms (consists of various types of atoms) with doublezetapolaroid ->

(1) Can OpenMP effectively use all the cores so that when the parallelized part of the calculation runs all 12 cores are opened for threading and used with highest efficiency? (please consider the limited bandwidth of cpu cache)

(2) If 1 above was not good enough, can using MPICH2 multiprocessing improve the picture? How many MPI processes are to be opened here for optimum performance?

(3) If 1 above was not good enough, can reducing the number of cores and running only OpenMP significantly improve the efficency of processor usage? (like two quad core processors or one hex core processors)

Expecting your most helpful reply and thank you in advance.