configuration of the abinit 7.10.4 on Linux Redhat  [SOLVED]

option, parallelism,...

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Please have a look at ~abinit/doc/config/build-config.ac in the source package for detailed and up-to-date information about the configuration of Abinit 8 builds.
For a video explanation on how to build Abinit 7.x for Linux, please go to: http://www.youtube.com/watch?v=DppLQ-KQA68.
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noro
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Joined: Mon Sep 15, 2014 11:47 am

configuration of the abinit 7.10.4 on Linux Redhat

Post by noro » Wed Jul 08, 2015 2:45 am

Hi,
Dear users and developers, I have two questions :
1- is there a difference between Linux Ubunto and Redhat about the configuration of the ABINIT?
2- How to configure ABINIT 7.10.4 on Linux Redhat?
Thank you for your valuable guidance
Sincerely.

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pouillon
Posts: 651
Joined: Wed Aug 19, 2009 10:08 am
Location: Spain
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Re: configuration of the abinit 7.10.4 on Linux Redhat

Post by pouillon » Wed Jul 08, 2015 6:55 pm

For Abinit itself, there is no difference when configuring the build on Debian-based (e.g. Debian, Ubuntu, Mint) and RPM-based (e.g. Redhat, Fedora, CentOS).

The only difference is how you install the external dependencies, either from the package manager:

* apt-get on Debian-based distros;
* yum on RPM-based distros;

or by compiling them manually, since some packages may be available with one package manager and not the other.
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain

noro
Posts: 7
Joined: Mon Sep 15, 2014 11:47 am

Re: configuration of the abinit 7.10.4 on Linux Redhat

Post by noro » Wed Jul 08, 2015 8:48 pm

Thank you Mr. POUILLON for these Clarifications.
Best regards

noro
Posts: 7
Joined: Mon Sep 15, 2014 11:47 am

Site energy (or energy per site)

Post by noro » Thu Jul 30, 2015 12:11 pm

Hello to all,

I have a question about the site energy for a bicrystal of pure metal:
Well, the excess energy of the site (i) in alloy ΔE(Site i)= ΔEi(Exc (B))- ΔEi(Exc (A)), where :
the site excess energy i in a pure metal (A): ΔEi(Exc (A)) is defined as the difference between the energy of a site (i) intergranulaire (Ei (A)) and the energy of a site (M) in the bulk (EM(A)) for this metal :
ΔEi(Exc (A))=Ei(A)-EM(A)
My question is: how to calculate the energies of each site i (Ei (A)) for a bicrystal of a pure metal by ABINIT code (example : superlattice of bicrystal (02 grains separated by grain boundary) consisting of 50 atoms of Zr (ie 50 sites)?

Thank you very much and best regards.

noro
Posts: 7
Joined: Mon Sep 15, 2014 11:47 am

#BSUB -n 70, but the calculation is slow!!!

Post by noro » Mon Feb 08, 2016 12:23 am

Good morning ,
I do calculations on IBM Platform HPC 4.1.1.1 with OS RHEL 6.4 and PMPI module, with Linux RedHat 6.4 OS.
I have a question about the true number of cores that contribute in the calculation.
Well, I launched a calculating ABINIT and I put in the file script.sh : #BSUB -n 70 , #BSUB -R "span[ptile=10]".
I found that the calculation is slow (More than 10 days for a computation of 4 days), I don’t know is that the calculation is really done on what I requested in script file (n = 70), or he launches on only one or two nodes.

In (lsf2225.o) file, I received the following :
Job was executed on host(s) <10*compute028>.
<10*compute029>
<10*hpcadmin2>
<10*compute010>
<10*compute011>
<10*compute012>
<10*compute013>

But, at the end of this file (lsf2225.o) :
Resource usage summary:
CPU time : 16.00 sec.
Max Memory : 13 MB (??????????????)
Average Memory : 12.87 MB
Total Requested Memory : -
Delta Memory : -
(Delta: the difference between total requested memory and actual max usage.)
Max Swap : 514 MB

Max Processes : 13 (??????????????)
Max Threads : 14 (??????????????)
Please, let me know if my calculation is really launched on 70 cores and the max RAM, or it is launched on a minimum number of cores.
Thank you very much and best regards.

noro
Posts: 7
Joined: Mon Sep 15, 2014 11:47 am

How to read the files: *.DEN?

Post by noro » Thu Mar 31, 2016 12:00 am

Hello to all,
I would like to know how to read *.DEN files? if there is a software that reads these files, please, send me their address to download it.
Best regards.

Jordan
Posts: 282
Joined: Tue May 07, 2013 9:47 am

Re: configuration of the abinit 7.10.4 on Linux Redhat  [SOLVED]

Post by Jordan » Tue Apr 05, 2016 9:39 am

The cut3d utiliy of abinit provided in the bin directory of abinit can read the DEN file and produce files for post-processing

Cheers

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