16
General Questions and Answers / Re: Relative speed and accuracy of device algorithm, exchange correlation, basis set
« on: January 15, 2012, 06:39 »
So. No diffusive transport? Only Ballistic Transport. 
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17
General Questions and Answers / Re: Relative speed and accuracy of device algorithm, exchange correlation, basis set
« on: January 9, 2012, 00:19 »
What about the device algorithms? Can you make a relative comparison between Krylov, Direct and Recursion methods?
18
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
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
19
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.
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.
20
Installation and License Questions / Re: Cluster Network Setup
« on: December 10, 2011, 11:35 »
Thank you very much. It solved the problem. 
21
Installation and License Questions / Re: Cluster Network Setup
« on: December 9, 2011, 11:50 »
Thank you sir, MPICH2 was indeed installed successfully.
*When I compiled and ran a simple mpi program i got the following output
[root@vlsi112 ~]# mpiexec -n 4 /root/hello_world_mpi
Hello World from Node 0
Hello World from Node 1
Hello World from Node 2
Hello World from Node 3
*But when I tried to use two nodes (root@192.168.111.112 and root@192.168.111.116) it gave the following errors
[root@vlsi112 ~]# mpiexec -n 8 -machinefile /root/machines_mpi /root/hello_world_mpi
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(392)..............:
MPID_Init(139).....................: channel initialization failed
MPIDI_CH3_Init(38).................:
MPID_nem_init(234).................:
MPID_nem_tcp_init(108).............:
MPID_nem_tcp_get_business_card(346):
MPID_nem_tcp_init(305).............: gethostbyname failed, root@192.168.111.116 (errno 1)
*I have configured such that I can ssh one node from other without password.
I have also updated /etc/hosts in both nodes to include the hostnames and domainnames of the two nodes.
I have allowed 41000 to 41023 ports in the firewall and configured mpi to use them.
the file /root/machines_mpi contains only this line: root@192.168.111.116
*When I compiled and ran a simple mpi program i got the following output
[root@vlsi112 ~]# mpiexec -n 4 /root/hello_world_mpi
Hello World from Node 0
Hello World from Node 1
Hello World from Node 2
Hello World from Node 3
*But when I tried to use two nodes (root@192.168.111.112 and root@192.168.111.116) it gave the following errors
[root@vlsi112 ~]# mpiexec -n 8 -machinefile /root/machines_mpi /root/hello_world_mpi
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(392)..............:
MPID_Init(139).....................: channel initialization failed
MPIDI_CH3_Init(38).................:
MPID_nem_init(234).................:
MPID_nem_tcp_init(108).............:
MPID_nem_tcp_get_business_card(346):
MPID_nem_tcp_init(305).............: gethostbyname failed, root@192.168.111.116 (errno 1)
*I have configured such that I can ssh one node from other without password.
I have also updated /etc/hosts in both nodes to include the hostnames and domainnames of the two nodes.
I have allowed 41000 to 41023 ports in the firewall and configured mpi to use them.
the file /root/machines_mpi contains only this line: root@192.168.111.116
22
Installation and License Questions / Re: Cluster Network Setup
« on: December 1, 2011, 11:07 »
Thanks for the reply sir.
But currently we are facing some problem in accessing the gridmachine. However we would like to configure MPICH2 over network of 3 workstation we have in our lab. So I tried to install MPICH2 in linux I have followed the installation guide provided. I could configure and install MPICH2, but not without some errors which prevent it from functioning. I've attached the files generated from configure, make and make install alongwith the terminal commands and texts. I request you to help me find out the problem with it. I gave it some thought but I cant figure out what went wrong.
Thank you.
But currently we are facing some problem in accessing the gridmachine. However we would like to configure MPICH2 over network of 3 workstation we have in our lab. So I tried to install MPICH2 in linux I have followed the installation guide provided. I could configure and install MPICH2, but not without some errors which prevent it from functioning. I've attached the files generated from configure, make and make install alongwith the terminal commands and texts. I request you to help me find out the problem with it. I gave it some thought but I cant figure out what went wrong.
Thank you.
23
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.
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.
24
Installation and License Questions / Re: Efficiency of multiprocessing and multithreading
« on: September 6, 2011, 09:00 »
Thank you so much for making me understand the multiprocessing efficiency so well. 
However, we are in the process of quotation and we have encountered the term 'cluster' licence.
I want to know what does a cluster licence mean?
Is it a group of 1 master and several slave licences?
Or, its a single licence capable of multiprocessing?
(Then Does it contain MPICH2 feature? If so how many cores can it run?)
However, we are in the process of quotation and we have encountered the term 'cluster' licence.
I want to know what does a cluster licence mean?
Is it a group of 1 master and several slave licences?
Or, its a single licence capable of multiprocessing?
(Then Does it contain MPICH2 feature? If so how many cores can it run?)
25
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.
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.
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