GALAMOST
GPU-Accelerated Large-Scale Molecular Simulation Toolkit
Station: Documentation

1 Compiling and installation

The entire GALAMOST package is a Free Software under the GNU General Public License. The package is mainly distributed as source code and binary program for Linux operating system. The binary program and the source code can be Downloaded from our website. If there is any problem,  you can contact the corresponding authors (Dr. You-Liang Zhu, Email: youliangzhu@ciac.ac.cn).

Here is the guide for installation by source code. Before compiling and installing of the source code, you should set configuration firstly, i.e. installation path, by following command.
./configuration --prefix=/opt/galamost3   (Note: chmod +x configuration gives the file execute permission)
More configuration options are given here:

Introductions Commands Examples
set installation path --prefix --prefix=/opt/galamost
set computation capability of devices --cuda_arch --cuda_arch=20
set double or single precision, single or double --precision --precision=double
set profiling function, on or off --gprof --gprof=on
set gdb function, on or off --gdb --gdb=on
set cuda tookit path --cuda --cuda=/usr/local/cuda-7.5/
set boost path --boost --boost=/usr/
set python path
--python --python=/usr/

After configuring, a Makefile will be generated in current directory. Then you can compile and install the package by the following command,
make install -j4
where -j indicates the number of threads to compile the code.

2 Usage by script

The C++ and CUDA C code has been written as an extended module of Python. We can use the functions of GALAMOST by loading and calling its modules through a Python script (More Script Examples). With the prepared script, you should now be able to try running GALAMOST as:
./dpd.gala --gpu=0 >a.log&
where you may specify the GPU id with the "--gpu=" option and output the screen information into "a.log" file. If the script file has no executive permission, the command of "chmod +x dpd.gala" should be executed before running above command.