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Atomsk is designed to run in Unix/Linux and Microsoft® Windows® environments.
It is recommended to download Atomsk from this page. You may, at your convenience, download the executable binary for your platform, or download the source code and compile it for your system.
The easiest way to start with Atomsk is to download the executable version for your platform from this page. This static binary version should run out-of-the-box, without any additional requirement.
The GNU/Linux versions of Atomsk come with an install script called "install.sh". If you choose to run this script, run it as root (or with sudo). The program will be installed in /usr/local/bin/ by default.
If you do not wish to use the static binary version of Atomsk, you can download the source code and compile it yourself. The compilation requires the LAPACK library to be present on your system.
The source code of the program comes with a Makefile. For a summary of available targets, enter the
src directory and type "
make" or "
make help". To compile the program, type:
If your machine has multiple CPUs or a multi-core CPU then it is possible to speed up the process with parallel compilation thanks to the
-j) trigger. For instance, to compile the program using five threads:
make -j5 atomsk
Note that if the number of threads is higher than the actual number of CPUs on your machine then the compilation will not be faster.
If the command above does not work straightforwardly check the following points. First you need the GNU Make program installed on your computer. Second, by default the Makefile uses the GNU Fortran Compiler (
gfortran), so it is recommended that you have it installed.
Then, check that the LAPACK library is installed on your system. The path to the library must be defined in the
LAPACK variable. On UNIX/Linux systems, if LAPACK is installed system-wide then using "
LAPACK=-llapack" should work. Otherwise (e.g. if you compiled LAPACK in your home directory), enter the full path to the library with the format: "
LAPACK=-L/path/to/library -llapack". The users of Intel® MKL may refer to the Intel® documentation. On Microsoft® Windows® systems, a version of the LAPACK library properly compiled is also required (the
Makefile.windows gives some hints on how to achieve that, see also here and/or here). Please note that the author of Atomsk will not provide any support for LAPACK. If you experience problems with getting or compiling LAPACK on your machine,
please turn to the LAPACK community.
In order to customize the compilation for your machine, please do not edit the main Makefile (i.e. the file
Makefile). Instead, it is recommended to create a separate file named
Makefile.something that you can re-use each time you compile Atomsk. This custom
Makefile.something may contain some or all of the following variables:
export(this keyword is mandatory)
FORTRAN=mycompilerindicates to use the compiler "
MPATHcan be specified. If only
INSTPATHis given then the other paths will be defined relatively to it.
include Makefile" is mandatory and must appear at the end.
You may take example on the provided alternatives
Makefile.local. Then, to compile the code using your custom Makefile type:
make -f Makefile.something atomsk
Note that the program uses some procedures that are available only in Fortran 95, so make sure to use a F95-compiler. So far the program was tested and compiles successfully with the following compilers:
In order to optimize the program you may also change the compilation flags, depending on your machine's architecture, by modifying the
FFLAGS variable. Note that
-O3 can introduce very aggressive optimizations that can compromise the behavior of the code, a maximum optimization level
-O2 is recommended. When compiling on Microsoft® Windows® systems the compilation flag
-DWINDOWS is required.
If compilation results in errors, first have a look at the FAQ, and second ask your local system administrator to help you. If you believe that the problem is directpilatiog> 0Notue> gilaat ong> ometsecomp bugt t>not