Tutorial-v.1.0.0

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Prerequisites

In this guide, it is assumed that readers have a basic knowledge of Unix and its command line operations. For the installation of SALMON, following packages are required.

  • Fortran90/C compiler. Our package assumes users have one of the following compilers:
    • GCC (Gnu Compiler Collection)
    • Intel Fortran/C Compiler
    • Fujitsu Compiler (at FX100 / K-Computer)
  • One of the following library packages for linear algebra:
    • BLAS/LAPACK
    • Intel Math Kernel Library (MKL)
    • Fujitsu Scientific Subroutine Library 2 (SSL-II)
  • Build tools.
    • CMake

If you use other compilers, you may need to change build scripts (CMake). See Tutorial-v.1.0.0#Additional options in configure.py script If no numerical library is installed on your computer system, you may need to install BLAS/LAPACK by yourself. See Tips for Installation. See Troubleshooting of the Installation Process.

If there are any problem to use CMake tool in your environment by you can use the GNU make tools. See Troubleshooting of the Installation Process.

Download

The newest version of the SALMON can be downloaded from Download. To extract files from the downloaded file salmon-<VERSION>.tar.gz, type the following command in the command-line, 

$ tar –zxvf ./salmon-<VERSION>.tar.gz

After the extraction, the following directories will be created. 

SALMON
 |- src        Source codes
 |- example    Samples
 |- makefiles   GNU Makefiles for building
 |- cmakefiles   CMake related files
 |- makefiles   GNU Makefiles for building

Build

To compile SALMON to create executable binary files, two options are prepared, CMake and Gnu Make. If CMake works in your environment, we recommend to use it. If CMake fails in your environment, consider using Gnu Make Install_and_Run-v.1.0.0#Build_with_GNU_Makefile.

Installation of CMake

The CMake is a cross-platform build tool. In order to build the SALMON from the source code, the CMake of version 3.0.2 or later is required on your system.

You can get the binary distribution from the download page. First, move to the installation directory of salmon, 

cd <SALMON_INSTALLATION_DIRECTORY>

and download the binary distribution ( cmake-<VERSION>-<PLATFORM>.tar.gz) appropriate for your platform. You can do it by copy the URL of download link from the browser, and use wget command: 

wget https://cmake.org/files/v3.8/cmake-3.8.2-Linux-x86_64.tar.gz

In this document, we will use version 3.8.2 as an example. You can unpack the archive 

tar -zxvf cmake-3.8.2-Linux-x86_64.tar.gz

and you will have the binary make-3.8.2-Linux-x86_64/bin/cmake. To utilize the cmake command, the executable are settled inside the directory specified in your $PATH.

If you use the bash shell, you edit ~/.bashrc and append the line: 

export PATH=<SALMON_INSTALLATION_DIRECTORY>/cmake-3.8.2-Linux-x86_64/bin:$PATH

, and reload the configuration source ~/.bashrc.

Build using CMake

First, examine whether CMake is usable in your environment or not. Type the following in Unix command-line: 

$ cmake --version

If CMake is not installed in your system, an error message such as cmake: command not found will appear. If CMake is installed on your system, the version number will be shown. To build SALMON, CMake of version 3.0.2 or later is required. If CMake is not installed or CMake of the older version is installed in your system, you need to install the new version by yourself.

The installation of the CMake is simple. A detailed description of the installation is given in Installation of CMake. Here we describe a simple method to use the binary distribution of CMake. First, download the binary distribution file appropriate for your system from https://cmake.org/download/. The filename of the downloaded file will be cmake-<VERSION_PLATFORM>.tar.gz. In standard Unix environment, files for the platform of Linux x86_64 will be appropriate. Next extract the binary executable file of CMake, typing in the command-line as 

$ tar xvfz cmake-<VERSION_PLATFORM>.tar.gz

Then you will have the cmake binary file in bin directory. For the CMake binary file to be usable, you need to modify the Unix environmental variable $PATH appropriately.

Description how to modify the $PATH should come here

To confirm that CMake of the new version is usable in your environment, type cmake --version in the command-line.

Build using CMake specifying archtechture

Confirming that CMake of version 3.0.2 or later can be usable on your system, proceed the following steps. We assume that you are in the directory SALMON.

  • Create a new temporary directory build and move to the directory,
$ mkdir build
$ cd build
  • Execute the python script configure.py and then make,
$ python ../configure.py –arch=ARCHTECTURE
$ make

Here ARCHITECTURE specifies the architecture of the CPU in your computer system such as intel-avx. You need to choose ARCHTECUTRE from the following options:

arch Detail Compiler Numerical Library
intel-knl Intel Knights Landing Intel Compiler Intel MKL
intel-knc Intel Knights Corner Intel Compiler Intel MKL
intel-avx Intel Processer (Ivy-, Sandy-Bridge) Intel Compiler Intel MKL
intel-avx2 Intel Processer (Haswell, Broadwell ..) Intel Compiler Intel MKL
fujitsu-fx100 FX100 Supercomputer Fujitsu Compiler SSL-II
fujitsu-k Fujitsu FX100 / K-computer Fujitsu Compiler SSL-II

If the build is successful, you will get a file salmon.cpu at the directory salmon/bin. If you specify many-core archtechtures, intel-knl or intel-knc, you find a file salmon.mic or both files salmon.cpu and salmon.mic.


Files necessary to run SALMON

To run SALMON, at least two kinds of files are required for any calculations. One is an input file, with the filename extension of *.inp*, to be read from the standard input,　stdin. It should be prepared in the Fortran90 namelist format. Pseudopotential files of relevant elements are also required. Depending on your purpose, some other files may also be necessary. For example, coordinates of atomic positions of the target material may either be written in the input file or prepared as a separate file.

Pseudopotentials

SALMON utilizes norm-conserving pseudpotentials. You may find pseudopotentials of some elements in Samples. SALMON allows using several formats of pseudopotentials that can be easily obtained from websites listed below.


pseudopotential website
Ab-init FHI http://www.ab-init

In the input file, you need to write the filename of the pseudopotential. Use exactly the same filename as that downloaded from the website or that in the Samples.

input file

SALMON describes electron dynamics in systems with both isolated and periodic boundary conditions. The boundary condition is specified by the variable iperiodic in the namelist &system. Calculations are achieved in two steps; first, the ground state calculation is carried out and then electron dynamics calculations in real time are achieved. Choice of the calculation mode is specified by the variable calc_mode in the namelist &calculation. For isolated systems, the ground state and the electron dynamics calculations should be carried out in two steps. First the ground state calculation is achieved specifying calc_mode = 'GS' . Then the real-time electron dynamics calculation is achieved specifying calc_mode = 'RT' . For periodic systems, two calculations can also be carried out in one step specifying calc_mode = 'GS_RT' . For the isolated systems, ’GS-RT’ is not implemented. However, their calculations are done at once if users prepare appropriate shell scripts.

There are about 20 groups of main namelists listed below. A list of variables in each namelist is provided in the file ??? included in the source-file distribution.

name of namelist description
&calculation specify calculation modes
&control parameters related to general conditions for the calculation
&units specify units of input and output files
&parallel parameters related to parallelization
&system information related to the system
&pseudo information related to pseudopotentials
&functional specify density functional to be used
&rgrid parameters related to real space grid
&kgird parameters related to k-points for periodic systems
&tgrid parameters related to time evolution
&propagation specify a choice of the propagation method
&scf parameters related to ground state calculation
&emfield parameters of electric fields applied to the system
&linear_response magnitude of the distortion for linear response
&multiscale parameters related to coupled multiscale calculations of electron dynamics and light propagations
&analysis parameters related to output files
&hartree parameters related to Hartree potential calculation of isolated systems
&ewald parameters related to Ewald sum that appears in the ground state calculation of periodic systems
&atomic_coor Atomic coordinates can be written here

In Samples, we prepare six samples that cover typical calculations feasible by using SALMON. We prepare explanations for the input files that will help to prepare input files of your own interests.

Here we briefly explain the format of the namelist. 

&namelist1
  variable1 = int_value
  variable2 = 'char_value'
 /
&namelist2
  variable1 = real8_value
  variable2 = int_value1, int_value2, int_value3
/

A block of namelists starts with &namelist line and ends with / line. Between two lines, descriptions of variables and their values appear. Note that many variables have their default values so that it is not necessary to give values for all variables. The description of the variables may appear at any position if they are between &namelist and /. Input files constitute of several blocks of namelists. The blocks can appear in any order.

Run SALMON

To run SALMON, the executable file of salmon.cpu (and salmon.mic if your system is the many-core machine) should be built from the source file of SALMON as described above. An input file inputfile.inp and pseudopotential files should also be prepared as mentioned above. In order to execute the calculation, for the single process environment, type the following command: 

$ salmon.cpu < inputfile.inp > fileout.out

For the multiprocess environment, If the command to execute calculations using MPI is mpiexec', the calculation will start 

$ mpiexec -n NPROC salmon.cpu < inputfile.inp > fileout.out

where NPROC is the number of MPI processes you want to use. For the many-core processor (e.g. intel-knl) environment, the execution command is 

$ mpiexec.hydra -n NPROC salmon.mic < inputfile.inp > fileout.out

The execution command and the job submission procedure depends much on the local environment. We just summarize the general conditions to execute SALMON:

  • salmon runs in parallel environment using MPI.
  • executable files are prepared as /salmon/bin/salmon.cpu and/or /salmon/bin/salmon.mic in the standard build procedure.
  • to start calculations, inputfile.inp should be read through stdin.



Appendix

Additional options in configure.py script

In executing configure.py, you may manually specify compiler and environment variables instead of specifying the architecture, for example: 

$ python ../configure.py FC=mpiifort CC=mpiicc FFLAGS="-xAVX" CFLAGS="-restrict -xAVX"

The major options of configure.py is expressed as table below:

Commandline switch Detail
-a ARCH, --arch=ARCH Target architecture
--enable-mpi, --disable-mpi enable/disable MPI parallelization.
---enable-scalapack, --disable-scalapack enable/disable computations with ScaLAPACK library
---enable-scalapack, --disable-scalapack enable/disable computations with ScaLAPACK library
FC, FFLAGS User-defined Fortran Compiler, and the compiler options
CC, CFLAGS User-defined C Compiler, and the compiler options


Build for Single processor environment

If you want to build for the single process environment, please specify --disable-mpi. 

 $ python ../configure.py --arch=<ARCHITECTURE> --disable-mpi

Build for the GCC/GFortran environemnt

If you want to build by using GCC/GFortran compiler, you specify: 

$ python ../configure.py FC=gfortran CC=gcc FFLAG=-O3 CFLAG=-O3

Build by GNU Makefile

If CMake build fails in your environment, you can try Gnu Make for the build process.

First, enter to the makefile directory: 

$ cd SALMON/makefiles

and you need to choose Makefile appropriately according to your environment. The available makefiles are

  • fujitsu
  • gnu
  • gnu-without-mpi
  • intel
  • intel-avx
  • intel-avx2
  • intel-knc
  • intel-knl
  • intel-without-mpi

The -without-mpi specifies the build for the single process environment. Execute make command with the platform specified makefile: 

$ make -f Makefile.PLATFORM

The binary file is created in the directory SALMON/bin/.

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