Updated 2021-05-17
Run Abinit on the Cluster¶
Overview¶
- This guide will focus on running Abinit - a software suite that calculates the optical, mechanical, vibrational, and other observable properties of materials.
- The example used in this guide comes from this link.
Tips¶
- There are many dependencies for this module including
intel/15.0
,openmpi/1.8
,hdf5/1.8.14
,netcdf/4.3.3
,mk1/11.2
,fftw/3.3.4
. Make sure to load them all before trying to loadabinit/8.4.2
in the order presented. - Here is a link to the Abinit new user help file.
- View a list of tutorials for using Abinit at this link. Note that these tutorials are expected to take up to two hours each.
Summary¶
- As an example, we will use abinit on an input file to create an output file that reports the point symmetry group and Bravais lattice and expected memory needs for each dataset.
Walkthrough: Run Abinit on the Cluster¶
- This walkthrough will use abinit on an input file containing a reference to the 01h.pspgth pseutopotential to create an output file that reports the point symmetry group and Bravais lattice and expected memory needs.
- The
tutorial
directory used in this example can be found here - PBS script can be found here
- You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.
Part 1: The PBS Script¶
#PBS -N testAbinit
#PBS -A [Account]
#PBS -l nodes=1:ppn=2
#PBS -l pmem=2gb
#PBS -l walltime=3:00
#PBS -q inferno
#PBS -j oe
#PBS -o testAbinit.out
cd $PBS_O_WORKDIR
module load intel/15.0
module load openmpi/1.8
module load hdf5/1.8.14
module load netcdf/4.3.3
module load mkl/11.2
module load fftw/3.3.4
module load abinit/8.4.2
abinit < tbase1_x.files
- The
#PBS
directives are standard, requesting just 3 minutes of walltime and 1 node with 2 cores. More on#PBS
directives can be found in the PBS guide $PBS_O_WORKDIR
is a variable that represents the directory you submit the PBS script from. Make sure the files you want to use (in this case, the abinit_tutorial directory) are in the same directory you put the PBS script in.- Output Files will also show up in this dir as well
module load abinit/8.4.2
loads the 8.4.2 version of Abinit. To see what Abinit versions are available, runmodule avail abinit
, and load the one you want. The other module are dependencies that must be loaded before Abinit is loaded.abinit < tbase1_x.files
makes files according to what is written in tbase1_x.files. Thetbase1_1.in
input file and01h.pspgth
pseudopotential are used bytbase1_x.files
to create thetbase1_1.out
file. Other files are also generated but they are not useful for the purposes of this tutorial.
Part 2: Submit Job and Check Status¶
- Make sure you're in the dir that contains the
PBS
Script as well as theabinit
program - Submit as normal, with
qsub <pbs script name>
. In this caseqsub testAbinit.pbs
- Check job status with
qstat -t 22182721
, replacing the number with the job id returned after running qsub - You can delete the job with
qdel 22182721
, again replacing the number with the jobid returned after running qsub
Part 3: Collecting Results¶
- In the directory where you submitted the
PBS
script, you should see atestAbinit.out
file, which contains the results of the job, atbase1_1.out
file which contains the report of the point symmetry group and Bravais lattice and expected memory needs, and other output files useful for tasks not covered in this tutorial. - Here is what a part of
testAbinit.out
looks like:
---------------------------------------
Begin PBS Prologue Mon Jun 24 15:53:59 EDT 2019
Job ID: 26165101.shared-sched.pace.gatech.edu
User ID: svemuri8
Job name: testAbinit
Queue: inferno
End PBS Prologue Mon Jun 24 15:53:59 EDT 2019
---------------------------------------
ABINIT 8.4.2
Give name for formatted input file:
tbase1_1.in
Give name for formatted output file:
tbase1_1.out
Give root name for generic input files:
tbase1_xi
Give root name for generic output files:
tbase1_xo
Give root name for generic temporary files:
tbase1_x
.Version 8.4.2 of ABINIT
.(MPI version, prepared for a x86_64_linux_intel15.0 computer)
.Copyright (C) 1998-2017 ABINIT group .
ABINIT comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).
ABINIT is a project of the Universite Catholique de Louvain,
Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt .
Please read ~abinit/doc/users/acknowledgments.html for suggested
acknowledgments of the ABINIT effort.
For more information, see http://www.abinit.org .
.Starting date : Mon 24 Jun 2019.
- ( at 15h54 )
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
=== Build Information ===
Version : 8.4.2
Build target : x86_64_linux_intel15.0
Build date : 20180329
=== Compiler Suite ===
C compiler : intel15.0
C++ compiler : intel15.0
Fortran compiler : intel15.0
CFLAGS : -O2 -Wno-missing-declarations
CXXFLAGS : -O2 -Wno-missing-declarations
FCFLAGS : -g -extend-source -noaltparam -nofpscomp
FC_LDFLAGS : -static-intel -static-libgcc
=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : intel_xeon
=== Multicore ===
Parallel build : yes
Parallel I/O : yes
openMP support : no
GPU support : no
=== Connectors / Fallbacks ===
Connectors on : yes
Fallbacks on : yes
DFT flavor : none
FFT flavor : fftw3
LINALG flavor : mkl
MATH flavor : none
TIMER flavor : abinit
TRIO flavor : none
- Here is what a part of
tbase1_1.out
looks like:
.Version 8.4.2 of ABINIT
.(MPI version, prepared for a x86_64_linux_intel15.0 computer)
.Copyright (C) 1998-2017 ABINIT group .
ABINIT comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).
ABINIT is a project of the Universite Catholique de Louvain,
Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt .
Please read ~abinit/doc/users/acknowledgments.html for suggested
acknowledgments of the ABINIT effort.
For more information, see http://www.abinit.org .
.Starting date : Mon 24 Jun 2019.
- ( at 15h54 )
- input file -> tbase1_1.in
- output file -> tbase1_1.out
- root for input files -> tbase1_xi
- root for output files -> tbase1_xo
Symmetries : space group P4/m m m (#123); Bravais tP (primitive tetrag.)
================================================================================
Values of the parameters that define the memory need of the present run
intxc = 0 ionmov = 0 iscf = 7 lmnmax = 1
lnmax = 1 mgfft = 30 mpssoang = 1 mqgrid = 3001
natom = 2 nloc_mem = 1 nspden = 1 nspinor = 1
nsppol = 1 nsym = 16 n1xccc = 0 ntypat = 1
occopt = 1 xclevel = 1
- mband = 2 mffmem = 1 mkmem = 1
mpw = 752 nfft = 27000 nkpt = 1
================================================================================
P This job should need less than 7.808 Mbytes of memory.
Rough estimation (10% accuracy) of disk space for files :
_ WF disk file : 0.025 Mbytes ; DEN or POT disk file : 0.208 Mbytes.
================================================================================
--------------------------------------------------------------------------------
------------- Echo of variables that govern the present computation ------------
--------------------------------------------------------------------------------
-
- outvars: echo of selected default values
- iomode0 = 0 , fftalg0 =312 , wfoptalg0 = 0
-
- outvars: echo of global parameters not present in the input file
- max_nthreads = 0
-
-outvars: echo values of preprocessed input variables --------
acell 1.0000000000E+01 1.0000000000E+01 1.0000000000E+01 Bohr
amu 1.00794000E+00
diemac 2.00000000E+00
ecut 1.00000000E+01 Hartree
- fftalg 312
istwfk 2
kptopt 0
P mkmem 1
natom 2
nband 2
ngfft 30 30 30
nkpt 1
nstep 10
nsym 16
ntypat 1
occ 2.000000 0.000000
spgroup 123
symrel 1 0 0 0 1 0 0 0 1 -1 0 0 0 -1 0 0 0 -1
-1 0 0 0 1 0 0 0 -1 1 0 0 0 -1 0 0 0 1
-1 0 0 0 -1 0 0 0 1 1 0 0 0 1 0 0 0 -1
1 0 0 0 -1 0 0 0 -1 -1 0 0 0 1 0 0 0 1
1 0 0 0 0 1 0 1 0 -1 0 0 0 0 -1 0 -1 0
-1 0 0 0 0 1 0 -1 0 1 0 0 0 0 -1 0 1 0
-1 0 0 0 0 -1 0 1 0 1 0 0 0 0 1 0 -1 0
1 0 0 0 0 -1 0 -1 0 -1 0 0 0 0 1 0 1 0
toldfe 1.00000000E-06 Hartree
typat 1 1
xangst -3.7042404601E-01 0.0000000000E+00 0.0000000000E+00
- After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
- Congratulations! You successfully ran Abinit on the cluster.