The GriDock package includes executables for Linux 32 bit, Linux 64 bit, Windows 32 bit and Windows 64 bit. Each executable exists in two versions: the standard parallel version for unified memory systems (e.g. single workstation/PC with one ore more CPUs/cores) and the MPI (MPICH2) version for grid arrays.
2.1 Linux installation
Before to proceed with the installation, you must have the following packages:
|GriDock_X.X.X.tar.gz||Generic multiplatform GriDock package.|
|Vega_X.X.X_Linux_86-32.tar.gz||VEGA command-line for Linux 32 bit.|
|Vega_X.X.X_Linux_86-64.tar.gz||VEGA command-line for Linux 64 bit. This package is the alternative of the previous one if your system has a 64 bit operating system.|
where X.X.X is the package version. You can download all needed packages from www.vegazz.net or www.ddl.unimi.it. The pre-compiled GriDock executables were built by CentOS 4.3 and they require the libc version 6.
2.1.1 Standard Linux installation
You must choose this installation procedure if you want to run GriDock locally on a single node (e.g. HPC system with shared memory architecture). All installed CPUs can be used by GriDock.
chmod 755 $VEGADIR/autodock4 chmod 755 $VEGADIR/autogrid4 chmod 755 $VEGADIR/gridock
To test the installation, type in the command shell:vega gridock
If the installation is right, no error messages will be shown.
2.1.2 MPI Linux installation with shared directories
This is the installation for grid array systems x86-based. MPICH2 is required to run this MPI version. If you have already installed MPICH2, skip this section and go to the next one.
126.96.36.199 MPICH2 installation
This is the procedure to install the MPICH2 package on a single node. You must repeat the installation for each node that you intend to use in the grid array. For more information about the installation, you can read the Installer's Guide available at the MPICH2 main site in the documentation section.
tar -zxvf mpich2-X.X.X.tar.gz
where X.X.X is the MPICH2 version.
cd $HOME touch .mpd.conf chmod 600 .mpd.conf
ortouch /etc/mpd.conf chmod 600 mpd.conf
the new MPICH2 releases require a different line:MPI_SECRETWORD=<MY_PASSWORD>
where <MY_PASSWORD> is the access password and it must the same for all nodes that you want use in the grid.
the output must be localhost or any other host name.
mpiexec -n 1 /bin/hostname
the output must be localhost.localdomain or any other host and domain names.
To stop the mpd daemon, you must use the mpdallexit command. To configure the remote hosts, you must consult the Installer's Guide.
188.8.131.52 VEGA and GriDock installation
chmod 755 VEGA_SHARED_PATH/vega chmod 755 VEGA_SHARED_PATH/autodock4 chmod 755 VEGA_SHARED_PATH/autogrid4 chmod 755 VEGA_SHARED_PATH/gridockmpi
mpiexec -n <NUMBER_OF_PROCESSES> gridockmpi
where <NUMBER_OF_PROCESSES> is the total number of processes that you want create that is usually the number of CPUs/cores installed in your system.
The mpirun command has a buggy implementation of the MPI arguments that can be interpreted by GriDock as optional parameters. For this reason, when you use mpirun, you must specify always the receptor file name, the database and the AutoDock template.
2.2 Windows installation
GriDock and a special build of AutoDock 4 are included in VEGA ZZ package that can be downloaded from www.vegazz.net or www.ddl.unimi.it.