Difference between revisions of "SALMON Manual for Beginners"
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== Prerequisites == | == Prerequisites == | ||
| − | In this guide, it is assumed that readers have a basic knowledge | + | In this guide, it is assumed that readers have a basic knowledge of Unix. In the following, most works will be done in the command-line interface of Unix. For the installation of SALMON, following packages are required. |
| − | In the following, most works will be done in the command-line interface of Unix. | ||
| − | For the installation of SALMON, following packages are required. | ||
* Fortran90/C compiler with MPI support. Our package assumes users have one of the following compilers: | * Fortran90/C compiler with MPI support. Our package assumes users have one of the following compilers: | ||
| Line 19: | Line 17: | ||
** Gnu Make | ** Gnu Make | ||
| − | If you use other compilers, you may need to change build scripts (CMake, Makefile). | + | If you use other compilers, you may need to change build scripts (CMake, Makefile). If no numerical library is installed on your computer system, you may need to install BLAS/LAPACK by yourself. See Tips for Installation. |
| − | If no numerical library is installed | + | See [[Troubleshooting of the Installation Process]]. |
| − | See [[ | ||
| − | |||
== Download == | == 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, | To extract files from the downloaded file ''salmon-<VERSION>.tar.gz'', type the following command in the command-line, | ||
| Line 40: | Line 36: | ||
|- example Samples | |- example Samples | ||
|- Makefile Files related to building | |- Makefile Files related to building | ||
| − | |||
== Build == | == Build == | ||
| Line 46: | Line 41: | ||
To compile SALMON to create executable binary files, two options are prepared, CMake and Gnu Make. | 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 works in your environment, we recommend to use it. | ||
| − | If CMake fails in your environment, consider | + | If CMake fails in your environment, consider using Gnu Make. |
=== Build using CMake === | === Build using CMake === | ||
| − | First examine whether CMake is usable in your environment or not. | + | First, examine whether CMake is usable in your environment or not. |
Type the following in Unix command-line: | Type the following in Unix command-line: | ||
$ cmake --version | $ cmake --version | ||
| − | If CMake is not installed in your system, error message such as <code>cmake: command not found</code> will appear. | + | If CMake is not installed in your system, an error message such as <code>cmake: command not found</code> will appear. |
| − | If CMake is installed | + | 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. | To build SALMON, CMake of version 3.0.2 or later is required. | ||
| − | If CMake is not installed or CMake of older version is installed in your system, you need to install the new version by yourself. | + | 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. | The installation of the CMake is simple. | ||
| − | A detailed description of the installation is given in [[Installation of CMake]]. | + | A detailed description of the installation is given in [[Tips_for_Installation#Installation_of_CMake | Installation of CMake]]. |
Here we describe a simple method to use the binary distribution 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/. | + | 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''. | 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. | In standard Unix environment, files for the platform of Linux x86_64 will be appropriate. | ||
| Line 79: | Line 74: | ||
==== Build using CMake specifying archtechture ==== | ==== Build using CMake specifying archtechture ==== | ||
| − | Confirming that CMake of version 3.0.2 or later can be usable | + | 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. | We assume that you are in the directory SALMON. | ||
* Create a new temporary directory ''build'' and move to the directory, | * Create a new temporary directory ''build'' and move to the directory, | ||
| Line 91: | Line 86: | ||
$ make | $ make | ||
| − | Here '' | + | 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: | You need to choose ''ARCHTECUTRE'' from the following options: | ||
| Line 128: | Line 123: | ||
If CMake build fails in your environment, try Gnu Make for the build process. | If CMake build fails in your environment, try Gnu Make for the build process. | ||
Gnu Make utilize a file, ''Makefile'', which you can find at the directory ''SALMON/Makefile''. | Gnu Make utilize a file, ''Makefile'', which you can find at the directory ''SALMON/Makefile''. | ||
| − | First you need to modify ''Makefile'' appropriately according to your environment. | + | First, you need to modify ''Makefile'' appropriately according to your environment. |
Edit the ''Makefile'' using a text editor. | Edit the ''Makefile'' using a text editor. | ||
| − | At least you need to change the line that choose the architecture of the system, from line | + | At least you need to change the line that choose the architecture of the system, from line 4 to 10 |
# This is a makefile for SALMON program. | # This is a makefile for SALMON program. | ||
# please select architecture by deleting “#” | # please select architecture by deleting “#” | ||
| + | |||
#ARCH = gnu | #ARCH = gnu | ||
ARCH = intel | ARCH = intel | ||
| + | #ARCH = intel-avx | ||
| + | #ARCH = intel-avx2 | ||
#ARCH = fujitsu | #ARCH = fujitsu | ||
#ARCH = intel-knl | #ARCH = intel-knl | ||
| + | #ARCH = intel-knc | ||
Then use ''make'' command in the command-line to build the executable file. | Then use ''make'' command in the command-line to build the executable file. | ||
| Line 146: | Line 145: | ||
To run SALMON, at least two kinds of files are required for any calculations. | 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 | + | 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. | It should be prepared in the Fortran90 namelist format. | ||
Pseudopotential files of relevant elements are also required. | Pseudopotential files of relevant elements are also required. | ||
| Line 156: | Line 155: | ||
SALMON utilizes norm-conserving pseudpotentials. | SALMON utilizes norm-conserving pseudpotentials. | ||
You may find pseudopotentials of some elements in [[Samples]]. | You may find pseudopotentials of some elements in [[Samples]]. | ||
| − | SALMON allows | + | SALMON allows using several formats of pseudopotentials that can be easily obtained from websites listed below. |
| + | |||
{| class="wikitable" | {| class="wikitable" | ||
| Line 171: | Line 171: | ||
SALMON describes electron dynamics in systems with both isolated and periodic boundary conditions. | 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''. | 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. | + | 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''. | 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. | For isolated systems, the ground state and the electron dynamics calculations should be carried out in two steps. | ||
| Line 221: | Line 221: | ||
|- | |- | ||
| &atomic_coor || Atomic coordinates can be written here | | &atomic_coor || Atomic coordinates can be written here | ||
| − | |||
| − | |||
| − | |||
| − | |||
|} | |} | ||
| Line 251: | Line 247: | ||
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. | 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. | ||
| − | If the command to execute calculations using MPI is '' | + | 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. | The execution command and the job submission procedure depends much on the local environment. | ||
Latest revision as of 09:12, 30 July 2017
Contents
Prerequisites
In this guide, it is assumed that readers have a basic knowledge of Unix. In the following, most works will be done in the command-line interface of Unix. For the installation of SALMON, following packages are required.
- Fortran90/C compiler with MPI support. 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)
- One of the following build tools.
- CMake
- Gnu Make
If you use other compilers, you may need to change build scripts (CMake, Makefile). 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.
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 |- ARTED Source codes related to periodic systems |- GCEED Source codes related to isolated systems |- src Source codes of core modules |- main Source codes of the main routines |- example Samples |- Makefile Files related to 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.
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 Su | 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.
Build using Gnu Make
If CMake build fails in your environment, try Gnu Make for the build process. Gnu Make utilize a file, Makefile, which you can find at the directory SALMON/Makefile. First, you need to modify Makefile appropriately according to your environment. Edit the Makefile using a text editor. At least you need to change the line that choose the architecture of the system, from line 4 to 10
# This is a makefile for SALMON program. # please select architecture by deleting “#”
#ARCH = gnu ARCH = intel #ARCH = intel-avx #ARCH = intel-avx2 #ARCH = fujitsu #ARCH = intel-knl #ARCH = intel-knc
Then use make command in the command-line to build the executable file.
$ make
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 should be carried out in one step specifying calc_mode = 'GS_RT' .
There are about 20 groups of 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 |
| ¶llel | 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.
Output files
See Samples.
