Difference between revisions of "Install and Run"

Revision as of 10:08, 19 July 2018

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. SALMON 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 #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 Troubleshooting of the Installation Process.

For the installation of SALMON, we adopt the CMake tools as the first option. If there were any problems to use CMake tools in your environment, you may use the GNU make tools. See Troubleshooting of the Installation Process.

Download

The newest version of 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
 |- cmakefiles   CMake related files
 |- gnumakefiles   GNU Makefiles for building

Build

To compile SALMON to create executable the binary files, we adopt to use CMake tools as the first option. In case you fail to build SALMON using CMake in your environment, we may use Gnu Make. See #Build using GNU Makefile.

Checking CMake availability

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 you confirm that CMake of version 3.0.2 or later is installed in your system, proceed to #Build using CMake. However, we realize that old versions of CMake are installed in many systems. If CMake is not installed or CMake of older versions is installed in your system, you need to install the new version by yourself. It is a simple procedure and explained below.

Installation of CMake

CMake is a cross-platform build tool. The simplest way to make CMake usable in your environment is to get the binary distribution of CMake from the download page. The file name of the binary distribution will be cmake-<VERSION>-<PLATFORM>.tar.gz). In standard Unix environment, a file for the platform of Linux x86_64 will be appropriate.

To download the file, proceed as follows: We assume that you are in the directory that you extracted files from the downloaded file of SALMON, and that you will use the version 3.8.2. First get the URL of the download link from your browser, and use wget command in your Unix command-line.

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

Next, unpack the archive by

$ 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 in your directory.

To make the cmake command usable in your command-line, you need to modify the environment variable $PATH so that the executable of CMake are settled inside the directory specified in your $PATH. If you use the bash shell, you need to modify the file ~/.bashrc that specifies the $PATH variable. It can be done by typing the following command in your login directory,

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

and then reload the configuration by typing:

$ source ~/.bashrc

Build using CMake

Confirming that CMake of version 3.0.2 or later can be usable in your environment, 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=ARCHITECTURE --prefix=../
$ make
$ make install

In executing the python script, you need to specify ARCHITECTURE that indicates the architecture of the CPU in your computer system such as intel-avx. The options of the ARCHITECUTRE are as follows:

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

Build for single process calculations

In default, the python script assumes parallel execution. If you use a single processor machine, specify --disable-mpi in executing the python script:

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

Build with Libxc

You can build with Libxc library by adding the configure script are as below:

• --enable-libxc: link the Libxc library (by automatic detection in CMake)
• --with-libxc=INSTALL/PATH/OF/LIBXC: manually specify the Libxc prefix directory.

To use Libxc

If you want to use Libxc mode, you must do adittional preparation. Download the source-list and install by the website(http://www.tddft.org/programs/libxc/installation/):

wget http://www.tddft.org/programs/octopus/down.php?file=libxc/4.2.1/libxc-4.2.1.tar.gz
tar -zxvf libxc-4.2.1.tar.gz

Enter to the libxc source directory:

./configure --prefix=INSTALL/PATH/OF/LIBXC
make; make install

Finally, you can execute configure.py script of SALMON with specifying the Libxc directory.

Enter to SALMON directory

configure.py --arch=ARCHITECTURE --prefix=PREFIX --with-libxc=INSTALL/PATH/OF/LIBXC
make; make install

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 *.inp* that should be read from the standard input stdin. This file 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 be either 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 the samples prepared in Exercises. In SALMON, several formats of pseudopotentials may be usable. Pseudopotentials with an extension .fhi can be obtained from the website listed below. (This is a part of previous atomic data files for the ABINIT code.)

Filenames of the pseudopotentials should be written in the input file.

input file

Input files are composed of several blocks of namelists,

&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. The blocks may appear in any order.

Between two lines of &namelist and /, 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. Descriptions of the variables may appear at any position if they are between &namelist and /.

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 usually achieved in two steps; first, the ground state calculation is carried out and then electron dynamics calculations in real time is carried out. A 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 as two separate executions. First the ground state calculation is carried out specifying calc_mode = 'GS' . Then the real-time electron dynamics calculation is carried out specifying calc_mode = 'RT' . For periodic systems, two calculations should be carried out as a single execution specifying calc_mode = 'GS_RT' .

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

There are more than 20 groups of namelists. A complete list of namelist variables is given in the file SALMON/manual/input_variables.md. Namelist variables that are used in our exercises are explained at Input variables.

Run SALMON

Before running SALMON, the following preparations are required as described above: 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. An input file inputfile.inp and pseudopotential files should also be prepared.

The execution of the calculation can be done as follows: In single process environment, type the following command:

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

In multiprocess environment in which the command to execute parallel calculations using MPI is mpiexec, type the following command:

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

where NPROC is the number of MPI processes that you will use. In 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 local environment. We summarize general conditions to execute SALMON:

• SALMON runs in both single-process and multi-process environments 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

Manual specifications of compiler and environment variables

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 are as follows:

Build for single process calculations

If you use a single processor machine, specify --disable-mpi in executing the python script:

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

Build in GCC/GFortran environemnt

If you use GCC/GFortran compiler, specify the following flags in executing the python script:

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

Build using GNU Makefile

If CMake build fails in your environment, we recommend you to try to use Gnu Make for the build process. First, enter the directory makefiles:

$ cd SALMON/makefiles

In the directory, Makefile files are prepared for several architectures:

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

Makefile files with -without-mpi indicate that they are for single processor environment. Choose Makefile appropriate for your environment, and execute the make command:

$ make -f Makefile.PLATFORM

If the make proceeds successful, a binary file is created in the directory SALMON/bin/.