SALMON Tutorial, Osaka, 2019

Installation in
CMD environment
Quick start of SALMON

Shunsuke Yamada (and Mitsuharu Uemoto)Center for Computational Sciences, University of Tsukuba
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/1Prerequisites• Fortran90/C compiler with MPI• GCC (Gnu Compiler Collection)• Intel Fortran/C Compiler• Fujitsu Compiler (at FX100 / K-Computer)• Library packages for linear algebra• BLAS/LAPACK• Intel Math Kernel Library (MKL)• Fujitsu Scientific Subroutine Library 2 (SSL-II)• Build tool• CMake• Gnu Make

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON Tutorial, Osaka, 20192

Installation plan for CMD environment~stud??/ ß Your home directory in “rl.phys.sci.osaka-u.ac.jp”└── work├── SALMON-v.1.2.1.tar.gz├── SALMONß SALMON installation directory│├── build ß Temporally files for buildßBinary│├── bin│└── ...
├── cmake-3.9.6-Linux-x86_64.tar.gz├── cmake ß cmake installation directory│├── bin│└── ...
ß Excercises samples└── cmd35•

Create your working directory$ cd ~$ mkdir work

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON Tutorial, Osaka, 20193

CMake: version check & install
Version check$ cmake --version
CMake of version 3.0.2 or later is required.
Installation example of CMake version 3.9.6$ cd ~/work$ wget https://cmake.org/files/v3.9/cmake-3.9.6-Linux-x86_64.tar.gz$ tar xvzf cmake-3.9.6-Linux-x86_64.tar.gz$ mv cmake-3.9.6-Linux-x86_64 cmake$ cmake --version> cmake version 3.9.6→ success!

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON Tutorial, Osaka, 20194

Path setting
Modify ~/.bash_profile* In this example, all programs will
be installed in ~/work directory

Add $PATH settings as follows# User specific environment and startup programs
PATH=$HOME/work/cmake/bin:$PATH Location of executable files
PATH=$HOME/work/SALMON-v.1.2.1/bin:$PATH
export PATH
Update your configulation$ source ~/.bashrc
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON Tutorial, Osaka, 20195

Build of SALMON
Installation example for “intel-avx” architecture$ cd ~/work/$ wget http://salmon-tddft.jp/download/SALMON-v.1.2.1.tar.gz$ tar xvfz SALMON-v.1.2.1.tar.gz$ mv SALMON-v.1.2.1 SALMON$ cd SALMON$ mkdir build$ cd build$ ../configure.py CC=mpicc FC=mpifort --prefix=..
$ make && make install$ which salmon.cpu> ~/work/SALMON/bin/salmon.cpu → success!
* Specify the compiler by CC and FC option (or use “arch” option)
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON Tutorial, Osaka, 20196

Build of SALMON: Compile options
View help$ ../configure.py --help
For more information → Install and Run (SALMON web page)
Explicit specification of compile options (example: gnu compilers)$ ../configure.py FC=gfortran CC=gcc FFLAGS=-O3 …
Optional: Gnu Make
$ cd ~/work/SALMON-v.1.2.0/makefiles$ make -f Makefile.<PLATFORM>

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON Tutorial, Osaka, 20197

Run SALMON
Copy example input files & job.sh$ cp -r ~teac23/work/cmd35 ~/work$ cd ~/work/cmd35/test

Execute in PC cluster system$ qsub ./job.sh* Ground state calculation of acetylene

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON Tutorial, Osaka, 20198

Quick check of output

1. Standard output (out.log)
Syntax error à “error(s) in input”
2. variables.log
For check of input variables (including default)#namelist: <Namelist>, status= 0 or -1

à OKotherwise à error

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON Tutorial, Osaka, 20199