Difference between revisions of "Getting started"

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 +
=Getting started=
 
==User access==
 
==User access==
 
Go to [https://www.metacenter.no www.metacenter.no] > User Login (Passwords) > 1. Request a user account > HPC
 
Go to [https://www.metacenter.no www.metacenter.no] > User Login (Passwords) > 1. Request a user account > HPC
  
−
Fill in the form and choose the appropriate project. It is recommended to use your UiO username.
+
Fill in the form with your UiO username and choose the appropriate project. If you already have an account through for instance FYS-MENA41111, the project manager can in principle directly add you to the project without requesting a user account.
  
−
The project manager can give you access to the VASP license through the [https://www.vasp.at/ VASP portal] and thereafter informing [mailto:sigma2@uninett.no sigma2@uninett.no] to give your user the necessary group affiliations (xvasp and vasp5).
+
The project manager can give you access to the VASP license through the [https://www.vasp.at/ VASP portal] and thereafter informing [mailto:sigma@uninett.no sigma2@uninett.no] to give your user the necessary group affiliations (vasp5).
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 29: Line 30:
  
 
==Login==
 
==Login==
−
===ssh===
+
===ssh and scp===
−
ssh can be used to login using a terminal app on UNIX, macOS or Windows Subsystem for Linux
+
ssh can be used to login to the cluster with a terminal app on UNIX, macOS or Windows Subsystem for Linux
  
 
<code> ssh [username]@saga.sigma2.no </code>
 
<code> ssh [username]@saga.sigma2.no </code>
  
−
Hostnames and usernames can be defined by creating or editing the file <code> ~/.ssh/config </code>.
+
Hostnames and usernames can be saved by creating or editing the config file using for instance the vim text editor
−
 
 
−
This can be done using the text editor vim
 
  
 
<code> vim ~/.ssh/config </code>
 
<code> vim ~/.ssh/config </code>
Line 67: Line 66:
 
==Working in UNIX==
 
==Working in UNIX==
 
===Basic commands===
 
===Basic commands===
−
Use TAB to autocomplete commands, paths and filenames.
+
Learn to use the TAB key to autocomplete commands, paths and filenames.
  
−
Use <code> man [command] </code> to view the manual for any command.
+
Learn to view the manual for any command: <code> man [command] </code>  
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 83: Line 82:
 
|-
 
|-
 
|<code> cd [directoryname] </code>
 
|<code> cd [directoryname] </code>
−
|Change path to another directory
+
|Change current path to another directory
 
|-
 
|-
 
|<code> pwd </code>  
 
|<code> pwd </code>  
Line 104: Line 103:
 
|-
 
|-
 
|<code> cp -r  [directory] [path] </code>
 
|<code> cp -r  [directory] [path] </code>
−
|Copy directory to new location
+
|Copy directory and its contents to new location
 
|-
 
|-
 
|<code> rm [filename] </code>
 
|<code> rm [filename] </code>
Line 111: Line 110:
 
|<code> rm -r [directoryname] </code>
 
|<code> rm -r [directoryname] </code>
 
|Delete directory and its contents
 
|Delete directory and its contents
 +
|}
 +
 +
{| class="wikitable"
 +
|+Special paths and symbols
 +
!Symbol
 +
!Description
 +
|-
 +
|<code> . </code>
 +
|Current directory
 +
|-
 +
|<code> .. </code>
 +
|Parent directory
 +
|-
 +
|<code> ~ </code>
 +
|Home directory
 +
|-
 +
|<code> / </code>
 +
|Root directory
 +
|-
 +
|<code> * </code>
 +
|Any text pattern
 +
|-
 +
|<code> ? </code>
 +
|Any symbol
 
|}
 
|}
  
Line 119: Line 142:
 
|-
 
|-
 
|<code> less </code>
 
|<code> less </code>
−
|View text file. <code> Shift-F </code> to view live updates to file
+
|View text file. View live updates to end of file: <code> Shift-F </code>
 
|-
 
|-
 
|<code> head </code>
 
|<code> head </code>
−
|Display top 10 lines of text file. Options: <code> -n [count] </code> to specify number of lines
+
|Display top 10 lines of text file. Specify number of lines: <code> -n [count] </code>
 
|-
 
|-
 
|<code> tail </code>
 
|<code> tail </code>
−
|Display bottom 10 lines of text file. Options: <code> -n [count] </code> to specify number of lines
+
|Display bottom 10 lines of text file. Specify number of lines: <code> -n [count] </code>
 
|-
 
|-
 
|<code> grep [pattern] </code>
 
|<code> grep [pattern] </code>
−
|Display each line in text file containing text specific text/symbol pattern
+
|Display each line in text file containing text specific text/symbol pattern.
 +
|-
 +
|diff [file1] [file2]
 +
|Compare files line by line and display the difference between them.
 
|-
 
|-
 
|<code> cat </code>
 
|<code> cat </code>
−
|Concatenate text files sequentially. Use <code>> [filename] </code> to write to file.
+
|Concatenate text files sequentially. Write the output to a file: <code> > [filename] </code>
 
|}
 
|}
  
 
===Filesystem on Saga===
 
===Filesystem on Saga===
−
Home directory: personal files and scripts due to limited storage space
+
Home directory: mainly for personal files, scripts etc. due to limited storage space
  
 
<code> /cluster/home/[username] </code>
 
<code> /cluster/home/[username] </code>
  
−
Project folder: run jobs and store large output files
+
Project folder: Run jobs and store output files in a subfolder called your username
  
−
<code> /cluster/projects/[project number] </code>
+
<code> /cluster/projects/[project number]/[username] </code>
−
 
 
−
*NN4604K: create a subfolder [username]
 
  
 
Check disk usage and storage quota for home directory and project folder
 
Check disk usage and storage quota for home directory and project folder
Line 149: Line 173:
 
<code> dusage </code>
 
<code> dusage </code>
  
−
Find and remove files in current folder and subfolders
+
Check disk usage of current folder and subfolders
 +
 
 +
<code> du -hs </code>
 +
 
 +
Find and remove files matching [filename] in current folder and subfolders
  
 
<code> find . -name "[filename]" -exec rm {} \; </code>
 
<code> find . -name "[filename]" -exec rm {} \; </code>
  
−
===Jobscript===
+
===Logfile===
 +
Excel sheet for tracking jobs can be downloaded here: [[Media:Logfile.xlsx]]
 +
It also includes conversion between supercell size, number of atoms and k-point grid for a given k-point density.
 +
 
 +
===Job script===
 +
Sigma2 NRIS HPC clusters use Slurm as workload manager and job scheduler. Documentation is available on [https://documentation.sigma2.no/ documentation.sigma2.no/]
 +
 
 +
Computations are run by submitting a job script to the queue
 +
 
 +
<code> sbatch jobfile </code>
 +
 
 +
View the queue for a user or project
 +
 
 +
<code> squeue -u [username] </code>
 +
<code> squeue -p [project number] </code>
 +
 
 +
Job scripts for Saga are available in the project folder
 +
/cluster/projects/nn4604k/jobfile
 +
 
 +
The job script below contains several SBATCH options
 +
 
 +
Saga has 40 CPUs per node and it is recommended to use all CPUs on a node and a 1-2 nodes for optimal performance [https://documentation.sigma2.no/hpc_machines/saga.html documentation.sigma2.no/hpc_machines/saga]
  
 +
The module system is restored to avoid potential conflicts. There exist several compiled versions of VASP and specific versions are compiled for increased performance with gamma K-point grid
 +
module restore system
 +
module load VASPModules
 +
module load VASP/6.4.1-intel-2022b-std-wannier90-libxc-hdf5-beef-0a928426e459cf2aeab3d0bf8f441c74
 +
# module load VASP/6.4.1-intel-2022b-gam-wannier90-libxc-hdf5-beef-0a928426e459cf2aeab3d0bf8f441c74
  
−
#SBATCH --job-name=[jobname]
+
Available modules on the cluster can be listed with
−
#SBATCH --account=[project number]
+
  module avail
−
#SBATCH --time=hh:mm:ss
 
−
#SBATCH --mem-per-cpu=4600M
 
−
#SBATCH --nodes=2
 
−
  #SBATCH --ntasks-per-node=40
 
  
−
Copy files to temporary job folder
+
Files are copied to a temporary job folder ($SCRATCH). The WAVECAR file is copied if it is available.
 
  cp [filenames] $SCRATCH
 
  cp [filenames] $SCRATCH
 +
if [ -f WAVECAR ]
 +
then
 +
cp WAVECAR $SCRATCH
 +
fi
  
−
Copy files from job folder when job completes. Savefile will also copy files if the job crashes.
+
Output files are copied from the job folder to the submit folder when job completes. Savefile will also copy files if the job crashes.
 
  savefile [filenames]  
 
  savefile [filenames]  
  
−
The job folder can be accessed while the job is running
+
The job is started from the $SCRATCH folder and the elapsed time is recorded to slurm output
−
<code> /cluster/work/jobs/[slurm-id] </code>
+
cd $SCRATCH
 +
time srun vasp
  
−
<code> /cluster/projects/nn4604k/jobfile </code>
+
The progression of the job can be viewed in the slurm output file slurm-[slurm-id] in the submit folder once the job is running.
  
 +
The working folder can be accessed while the job is running
 +
<code> /cluster/work/jobs/[slurm-id] </code>
  
−
Submit job to queue
 
−
<code> sbatch jobfile </code>
 
  
−
View the queue
+
'''Example job script'''
−
<code> squeue -u [username] </code>
+
#!/bin/bash
 +
 +
#SBATCH --job-name=jobname
 +
#SBATCH --account=nn4604k
 +
#SBATCH --time=10:00:00
 +
#SBATCH --mem-per-cpu=4000M
 +
#SBATCH --nodes=1
 +
#SBATCH --ntasks-per-node=40
 +
 +
set -o errexit
 +
set -o nounset
 +
 +
module restore system
 +
module load VASPModules
 +
module load VASP/6.4.1-intel-2022b-std-wannier90-libxc-hdf5-beef-0a928426e459cf2aeab3d0bf8f441c74
 +
# module load VASP/6.4.1-intel-2022b-gam-wannier90-libxc-hdf5-beef-0a928426e459cf2aeab3d0bf8f441c74
 +
 +
cp INCAR POSCAR POTCAR KPOINTS $SCRATCH
 +
if [ -f WAVECAR ]
 +
then
 +
cp WAVECAR $SCRATCH
 +
fi
 +
 +
savefile CONTCAR OUTCAR DOSCAR CHGCAR WAVECAR
 +
 +
cd $SCRATCH
 +
time srun vasp
  
−
===Aliases and settings ===
+
===Aliases and settings===
−
Define shortcuts by adding aliases to <code> ~/.bash_profile </code>
+
Define useful shortcuts by adding aliases to <code> ~/.bash_profile </code>
  
 
  alias l='ls -l'
 
  alias l='ls -l'
Line 189: Line 270:
 
  alias nn='cd /cluster/projects/[project number]'
 
  alias nn='cd /cluster/projects/[project number]'
 
  alias q='squeue -u [username]'
 
  alias q='squeue -u [username]'
 +
 +
You can also add commands such as automatically changing directory to the project folder upon login.
  
 
Changes will take effect on next login or manually with <code> source ~/.bash_profile </code>.
 
Changes will take effect on next login or manually with <code> source ~/.bash_profile </code>.
  
  
−
vim can be configured in <code> ~/.vimrc </code>. Turn on line numbers to  
+
vim can be configured in <code> ~/.vimrc </code>. Turn on line numbers to easily jump to a specific line using <code> :[line number] </code>
 
  set number
 
  set number
  
−
===Bash scripting===
+
===Shell scripting===
 +
Shell scripting can be used to submit several jobs as exemplified below
 +
 
 +
#!/bin/bash
 +
 +
for i in $(seq 0.0 0.2 1.4); do
 +
    for j in $(seq 0.0 0.2 1.4); do
 +
      dir="$i-$j"
 +
      echo $dir
 +
      mkdir $dir
 +
      cp INCAR POTCAR KPOINTS jobfile $dir
 +
      cp "prefix_$dir.POSCAR.vasp" $dir/POSCAR
 +
      cd $dir
 +
      sbatch jobfile
 +
      cd ..
 +
    done
 +
done
 +
 
 +
==First VASP calculation==
 +
{| class="wikitable"
 +
|+ Five files required for a VASP simulation
 +
!File
 +
!Description
 +
|-
 +
|POSCAR
 +
|Structure file that specifies the unit cell vectors, types of atoms and their positions
 +
|-
 +
|POTCAR
 +
|Pseudopotentials for the atoms (same order as in POSCAR)
 +
|-
 +
|INCAR
 +
|Input parameters for the calculation including relaxation algorithms, functionals, convergence criteria, etc.
 +
|-
 +
|KPOINTS
 +
|k-point grid
 +
|-
 +
|jobfile
 +
|job script
 +
|}
 +
 
 +
'''Cell volume relaxation of BaZrO<sub>3</sub> unit cell'''
 +
 
 +
Go to the project folder: <code> cd /cluster/projects/nn4604k </code>
 +
 
 +
Or if you have defined an [[#Aliases and settings|alias]]:<code> nn </code>
 +
 
 +
Create a subfolder with your username (if you have not done so already)
 +
 
 +
<code> mkdir [username] </code>
 +
 
 +
<code> cd [username] </code>
 +
 
 +
<code> mkdir test </code>
 +
 
 +
<code> cd test </code>
 +
 
 +
Copy all the files from the 'vasptest' folder (POSCAR, KPOINTS and INCAR) to your current folder (remember to use TAB to autocomplete the path)
 +
 
 +
<code> cp ../../vasptest/* . </code>
 +
 
 +
Copy the necessary POTCAR files (press the UP arrow key to bring up your previous command)
 +
 
 +
<code> cp ../../potpaw_PBE.54/Ba_sv/POTCAR POTCAR_Ba_sv </code>
 +
 
 +
<code> cp ../../potpaw_PBE.54/Zr_sv/POTCAR POTCAR_Zr_sv </code>
 +
 
 +
<code> cp ../../potpaw_PBE.54/O/POTCAR POTCAR_O </code>
 +
 
 +
Check the order of the atoms in POSCAR file
 +
 
 +
<code> head POSCAR </code>
 +
 
 +
Concatenate the POTCAR files in the same order to a file named POTCAR
 +
 
 +
<code> cat POTCAR_Ba_sv POTCAR_Zr_sv POTCAR_O > POTCAR </code>
 +
 
 +
Check the order of the POTCAR
 +
 
 +
<code> grep TITEL POTCAR </code>
 +
 
 +
Copy job script to current folder
 +
 
 +
<code> cp ../../jobfile . </code>
 +
 
 +
Submit the job
 +
 
 +
<code> sbatch jobfile </code>
 +
 
 +
Check the queue
 +
 
 +
<code> squeue -u [username] </code>
 +
 
 +
Or if you have defined an [[#Aliases and settings|alias]]:<code> q </code>
 +
 
 +
When the job starts you can follow the progress in the slurm log file
 +
 
 +
<code> less slurm-[slurm-id] </code>
 +
 
 +
After three ionic relaxation steps, the required accuracy has been reached and the output files defined [[#Job script|job script]] are copied to the current folder.
 +
 
 +
3 F= -.41724097E+02 E0= -.41724097E+02  d E =-.431449E-02
 +
curvature:  -0.24 expect dE=-0.515E-06 dE for cont linesearch -0.515E-06
 +
trial: gam= 0.00000 g(F)=  0.940E-64 g(S)=  0.213E-05 ort =-0.198E-03 (trialstep = 0.895E+00)
 +
search vector abs. value=  0.213E-05
 +
reached required accuracy - stopping structural energy minimisation
 +
writing wavefunctions
 +
 
 +
Check the lattice parameter in the POSCAR (input) and output (CONTCAR)
 +
 
 +
<code> head POSCAR </code>
 +
 
 +
BaZrO3                         
 +
  1.00000000000000   
 +
    4.2200000000000000    0.0000000000000000    0.0000000000000000
 +
    0.0000000000000000    4.2200000000000000    0.0000000000000000
 +
    0.0000000000000000    0.0000000000000000    4.2200000000000000
 +
...
 +
<code> head CONTCAR </code>
 +
 
 +
BaZrO3                                 
 +
  1.00000000000000   
 +
    4.2353879522908331  -0.0000000000000000  -0.0000000000000000
 +
    0.0000000000000000    4.2353879522908331  -0.0000000000000000
 +
    0.0000000000000000  -0.0000000000000000    4.2353879522908331
 +
...
 +
The optimized cubic lattice parameter is 4.2354 Å.

Latest revision as of 13:38, 3 November 2023

Getting started

User access

Go to www.metacenter.no > User Login (Passwords) > 1. Request a user account > HPC

Fill in the form with your UiO username and choose the appropriate project. If you already have an account through for instance FYS-MENA41111, the project manager can in principle directly add you to the project without requesting a user account.

The project manager can give you access to the VASP license through the VASP portal and thereafter informing sigma2@uninett.no to give your user the necessary group affiliations (vasp5).

Project Manager Group Resources
NN4604K Jonathan M. Polfus Electrochemistry Saga
NN9136K Lasse Vines LENS Saga
NN9180K Clas Persson Structure Physics Saga

Login

ssh and scp

ssh can be used to login to the cluster with a terminal app on UNIX, macOS or Windows Subsystem for Linux

ssh [username]@saga.sigma2.no

Hostnames and usernames can be saved by creating or editing the config file using for instance the vim text editor

vim ~/.ssh/config

Press i to insert text 

Host saga
   HostName = saga.sigma2.no
   user [username]

Press escape to exit insert mode, and then :wq to 'write' and 'quit'.

Login is then simplified

ssh saga

Copy files from cluster to current folder (.)

scp saga:[path]/[filename] .

Copy files to the home directory on the cluster

scp [filename] saga:

PuTTY and WinSCP

PuTTY is an ssh client for Windows that can be downloaded from www.putty.org.

WinSCP is an scp client for Windows that can be downloaded from winscp.net.

Working in UNIX

Basic commands

Learn to use the TAB key to autocomplete commands, paths and filenames.

Learn to view the manual for any command: man [command]

Navigating the filesystem
Command Description
ls List files and directories in current directory
mkdir [directoryname] Make a directory
cd [directoryname] Change current path to another directory
pwd Display current path
cd .. Change path to parent directory
cp [path]/[filename] . Copy file to current directory
cp [filename] [directoryname] Copy file to another directory
mv [filename] [path] Move file to another directory
mv [filename] [newfilename] Change the name of a file
cp -r [directory] [path] Copy directory and its contents to new location
rm [filename] Delete file
rm -r [directoryname] Delete directory and its contents
Special paths and symbols
Symbol Description
. Current directory
.. Parent directory
~ Home directory
/ Root directory
* Any text pattern
 ? Any symbol
Reading text files
Command Description
less View text file. View live updates to end of file: Shift-F
head Display top 10 lines of text file. Specify number of lines: -n [count]
tail Display bottom 10 lines of text file. Specify number of lines: -n [count]
grep [pattern] Display each line in text file containing text specific text/symbol pattern.
diff [file1] [file2] Compare files line by line and display the difference between them.
cat Concatenate text files sequentially. Write the output to a file: > [filename]

Filesystem on Saga

Home directory: mainly for personal files, scripts etc. due to limited storage space

/cluster/home/[username]

Project folder: Run jobs and store output files in a subfolder called your username

/cluster/projects/[project number]/[username]

Check disk usage and storage quota for home directory and project folder

dusage

Check disk usage of current folder and subfolders

du -hs

Find and remove files matching [filename] in current folder and subfolders

find . -name "[filename]" -exec rm {} \;

Logfile

Excel sheet for tracking jobs can be downloaded here: Media:Logfile.xlsx It also includes conversion between supercell size, number of atoms and k-point grid for a given k-point density.

Job script

Sigma2 NRIS HPC clusters use Slurm as workload manager and job scheduler. Documentation is available on documentation.sigma2.no/

Computations are run by submitting a job script to the queue

sbatch jobfile

View the queue for a user or project

squeue -u [username] squeue -p [project number]

Job scripts for Saga are available in the project folder 

/cluster/projects/nn4604k/jobfile

The job script below contains several SBATCH options

Saga has 40 CPUs per node and it is recommended to use all CPUs on a node and a 1-2 nodes for optimal performance documentation.sigma2.no/hpc_machines/saga

The module system is restored to avoid potential conflicts. There exist several compiled versions of VASP and specific versions are compiled for increased performance with gamma K-point grid 

module restore system
module load VASPModules
module load VASP/6.4.1-intel-2022b-std-wannier90-libxc-hdf5-beef-0a928426e459cf2aeab3d0bf8f441c74
# module load VASP/6.4.1-intel-2022b-gam-wannier90-libxc-hdf5-beef-0a928426e459cf2aeab3d0bf8f441c74

Available modules on the cluster can be listed with 

module avail

Files are copied to a temporary job folder ($SCRATCH). The WAVECAR file is copied if it is available. 

cp [filenames] $SCRATCH
if [ -f WAVECAR ]
then
cp WAVECAR $SCRATCH
fi

Output files are copied from the job folder to the submit folder when job completes. Savefile will also copy files if the job crashes. 

savefile [filenames]

The job is started from the $SCRATCH folder and the elapsed time is recorded to slurm output 

cd $SCRATCH
time srun vasp

The progression of the job can be viewed in the slurm output file slurm-[slurm-id] in the submit folder once the job is running.

The working folder can be accessed while the job is running /cluster/work/jobs/[slurm-id]


Example job script 

#!/bin/bash

#SBATCH --job-name=jobname
#SBATCH --account=nn4604k
#SBATCH --time=10:00:00
#SBATCH --mem-per-cpu=4000M
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40

set -o errexit 
set -o nounset

module restore system module load VASPModules module load VASP/6.4.1-intel-2022b-std-wannier90-libxc-hdf5-beef-0a928426e459cf2aeab3d0bf8f441c74

  1. module load VASP/6.4.1-intel-2022b-gam-wannier90-libxc-hdf5-beef-0a928426e459cf2aeab3d0bf8f441c74
cp INCAR POSCAR POTCAR KPOINTS $SCRATCH
if [ -f WAVECAR ]
then
cp WAVECAR $SCRATCH
fi

savefile CONTCAR OUTCAR DOSCAR CHGCAR WAVECAR 

cd $SCRATCH
time srun vasp

Aliases and settings

Define useful shortcuts by adding aliases to ~/.bash_profile 

alias l='ls -l'
alias la='ls -l -a'
alias ..='cd ..'
alias nn='cd /cluster/projects/[project number]'
alias q='squeue -u [username]'

You can also add commands such as automatically changing directory to the project folder upon login.

Changes will take effect on next login or manually with source ~/.bash_profile .


vim can be configured in ~/.vimrc . Turn on line numbers to easily jump to a specific line using  :[line number] 

set number

Shell scripting

Shell scripting can be used to submit several jobs as exemplified below 

#!/bin/bash

for i in $(seq 0.0 0.2 1.4); do
   for j in $(seq 0.0 0.2 1.4); do
      dir="$i-$j"
      echo $dir
      mkdir $dir
      cp INCAR POTCAR KPOINTS jobfile $dir
      cp "prefix_$dir.POSCAR.vasp" $dir/POSCAR
      cd $dir
      sbatch jobfile
      cd ..
   done
done

First VASP calculation

Five files required for a VASP simulation
File Description
POSCAR Structure file that specifies the unit cell vectors, types of atoms and their positions
POTCAR Pseudopotentials for the atoms (same order as in POSCAR)
INCAR Input parameters for the calculation including relaxation algorithms, functionals, convergence criteria, etc.
KPOINTS k-point grid
jobfile job script

Cell volume relaxation of BaZrO3 unit cell

Go to the project folder: cd /cluster/projects/nn4604k

Or if you have defined an alias: nn

Create a subfolder with your username (if you have not done so already)

mkdir [username]

cd [username]

mkdir test

cd test

Copy all the files from the 'vasptest' folder (POSCAR, KPOINTS and INCAR) to your current folder (remember to use TAB to autocomplete the path)

cp ../../vasptest/* .

Copy the necessary POTCAR files (press the UP arrow key to bring up your previous command)

cp ../../potpaw_PBE.54/Ba_sv/POTCAR POTCAR_Ba_sv

cp ../../potpaw_PBE.54/Zr_sv/POTCAR POTCAR_Zr_sv

cp ../../potpaw_PBE.54/O/POTCAR POTCAR_O

Check the order of the atoms in POSCAR file

head POSCAR

Concatenate the POTCAR files in the same order to a file named POTCAR

cat POTCAR_Ba_sv POTCAR_Zr_sv POTCAR_O > POTCAR

Check the order of the POTCAR

grep TITEL POTCAR

Copy job script to current folder

cp ../../jobfile .

Submit the job

sbatch jobfile

Check the queue

squeue -u [username]

Or if you have defined an alias: q

When the job starts you can follow the progress in the slurm log file

less slurm-[slurm-id]

After three ionic relaxation steps, the required accuracy has been reached and the output files defined job script are copied to the current folder. 

3 F= -.41724097E+02 E0= -.41724097E+02  d E =-.431449E-02
curvature:  -0.24 expect dE=-0.515E-06 dE for cont linesearch -0.515E-06
trial: gam= 0.00000 g(F)=  0.940E-64 g(S)=  0.213E-05 ort =-0.198E-03 (trialstep = 0.895E+00)
search vector abs. value=  0.213E-05
reached required accuracy - stopping structural energy minimisation
writing wavefunctions

Check the lattice parameter in the POSCAR (input) and output (CONTCAR)

head POSCAR 

BaZrO3                           
  1.00000000000000     
    4.2200000000000000    0.0000000000000000    0.0000000000000000
    0.0000000000000000    4.2200000000000000    0.0000000000000000
    0.0000000000000000    0.0000000000000000    4.2200000000000000
...

head CONTCAR 

BaZrO3                                  
  1.00000000000000     
    4.2353879522908331   -0.0000000000000000   -0.0000000000000000
    0.0000000000000000    4.2353879522908331   -0.0000000000000000
    0.0000000000000000   -0.0000000000000000    4.2353879522908331
...

The optimized cubic lattice parameter is 4.2354 Å.

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