SALMON TUTORIAL, TSUKUBA, 2018

Installation
Quick start of SALMON

Shunsuke Yamada
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, TSUKUBA, 20182

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, TSUKUBA, 20183

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/bin:$PATH
export PATH
module load intel intelmpi mkl Setting of compiler (if needed)

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 2018

4

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, TSUKUBA, 20185Build of SALMON
Installation example for “intel-avx” architecture$ cd ~/work/$ wget http://salmon-tddft.jp/download/SALMON-v.1.2.0.tar.gz$ tar xvfz SALMON-v.1.2.0.tar.gz$ cd SALMON-v.1.2.0$ mkdir build$ cd build$ ../configure.py --arch=intel-avx --prefix=~/work/SALMON$ make && make install$ which salmon.cpu> ~/work/SALMON/bin/salmon.cpu → success!
* Specify an appropriate --arch (architecture of the CPU in your computer)
Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/SALMON TUTORIAL, TSUKUBA, 20186

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, TSUKUBA, 2018

7

Run SALMON
Copy example input files & job.sh$ cd ~/work$ mkdir tmp$ cd tmp$ cp ~/work/SALMON-v.1.2.0/examples/C2H2/* .
Run$ salmon.cpu < C2H2_gs.inp > out.log* Ground state calculation of acetylene

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20188

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 -1à OK

otherwise à error

Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience
http://salmon-tddft.jp/
SALMON TUTORIAL, TSUKUBA, 20189