Day1
DN-NSM2019 – 17th USPEX Workshop
TUTORIAL 1
Running USPEX at Library/BU
@Rennes 1 University
Artem R. Oganov & Gilles Frapper
In this 17th USPEX workshop, you will use UPSEX 10.3 version
(in order to get the license for your lab, you will have first to register online).
https://uspex-team.org/en/uspex/downloads
Here, USPEX is interfaced with GULP, VASP and MOPAC codes.
These codes are running on HPC Spin/THOR of Poitiers University.
From your local station - called BU thereafter-, follow these instructions once (DAY1 only !).
1) To open a terminal, click on the openSUSE icon located at the bottom left of the screen. Select « Emulateur de Terminal »
2) To generate an RSA key for local use, type :
ssh-keygen –t rsa
(press enter until the end of this command)
To run a USPEX@VASP job under THOR
- connect under your THOR account
ssh –oPort=86 yourlogin@thor.univ-poitiers.fr
LOGIN: uspexXX (with XX=10-32)
PWD: ?Ic2Mp;UsPeX!
- create your working directory
mkdir –p your_directory
- go to your_directory. Type :
cd your_directory
- copy your USPEX example1 (EX01, bulk Si) to that directory. Type
USPEX –c 1
(or copy the folder 3D_Si_vasp under /home/gfrapper/USPEX_workshop/Day1 )
cp –R /home/gfrapper/USPEX_workshop/Day1/3D_Si_vasp .
- copy under your_directory the submission script called runuspex.sh. Type :
cp /home/gfrapper/USPEX_workshop/runuspex.sh .
- edit the INPUT.txt using vieditor. Type :
vi INPUT.txt
- …
******************************************
* TYPE OF RUN AND SYSTEM *
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
300 : calculationType (dimension: 0-3; molecule: 0/1; varcomp: 0/1)
1 : AutoFrac
% optType
1
% EndOptType
% atomType
Si
% EndAtomType
% numSpecies
8
% EndNumSpecies
******************************************
* POPULATION *
******************************************
20 : populationSize (how many individuals per generation)
20 : initialPopSize
25 : numGenerations (how many generations shall be calculated)
8 : stopCrit
0 : reoptOld
0.6 : bestFrac
******************************************
* VARIATION OPERATORS *
******************************************
0.50 : fracGene (fraction of generation produced by heredity)
0.30 : fracRand (fraction of generation produced randomly from space groups)
0.20 : fracAtomsMut (fraction of the generation produced by softmutation)
0.00 : fracLatMut (fraction of the generation produced by softmutation)
0.00 : fracPerm
*****************************************
* DETAILS OF AB INITIO CALCULATIONS *
*****************************************
% abinitioCode
1 1 1 1 1 1
% ENDabinit
% KresolStart
0.13 0.11 0.09 0.07 0.05 0.04
% Kresolend
% commandExecutable
mpirun -np 20 /home/gfrapper/Software/vasp.5.4.4/bin/vasp_std >log
% EndExecutable
1 : whichCluster (0: no-job-script, 1: local submission, 2: remote submission)
2 : numParallelCalcs
0.00001: ExternalPressure
-------
- edit the Queue information in runuspex.sh and Submission/submitJob_local.py
R1067861 (500 cores) for uspex01~30 participants.
R1068123 (300 cores) for uspex31~55 participants.
- edit your user id in Submission/checkStatus_local.py
output = unicode(check_output(u'/sw/pbs/default/bin/qstat -u {}'.format('userid') , shell=True))
with userid = uspexXX
# In calculation node of Thor, 'qstat jobID' jobID will be followed with '.service0' automatically, error. But 'qstat -u username' works well.
- To run a USPEX job, type:
qsub runuspex.sh
A USPEX job is done when USPEX_IS_DONE file appears.
To download your USPEX results under LOCAL station (BU):
- under THOR in your_directory, type :
pwd
copy the output of this command, ie working_directory
- under BU station, in your local working directory, type:
scp –r login@thor.univ-poitiers.fr:working_directory .
check! ( ls command…)
To create a new USPEX@VASP job from EX01
- under THOR account, create a new your_directory
mkdir your_directory
- under your working directory, copy EXAMPLE 1. Type:
USPEX –c 1
- edit the INPUT.txt using vieditor. Type:
vi INPUT.txt
modify the parameters… save…
- go to Specific folder
cd Specific
- in Specific, copy the VASP pseudopotentials:
cp /home/gfrapper/POT_VASP/PAW_PBE/yourelement/POTCAR POTCAR_yourelement
To run a USPEX@GULP job under THOR
Here EX02 MgAl2O4under pressure
- create your working directory
mkdir –p your_directory
- go to your_directory. Type :
cd your_directory
- copy your USPEX example1 (EX02, bulk MgAl2O4) to that directory. Type
USPEX –c 2
- copy under your_directory the submission script called runuspex.sh. Type :
cp /home/gfrapper/USPEX_workshop/runuspex.sh .
(or copy the folder 3D_MgAl2O4_gulp under /home/gfrapper/USPEX_workshop/Day1 )
cp –R /home/gfrapper/USPEX_workshop/Day1/3D_MgAl2O4_gulp .
- edit the INPUT.txt using vieditor. Type :
vi INPUT.txt
- …
- To run a USPEX job, type:
qsub runuspex.sh