Amber 8 on Fujitsu "Generic" PRIMEPOWER Computers


Installation


configure script in the $AMBERHOME/src directory creates a configuration file, config.h, with the necessary options for complition and building. Configuration file can be examined and edited to match local environment. Below are samples of a config.h file for some Fujitsu platforms.

To install PMEMD one needs to generate a config.h file in the $AMBERHOME/src/pmemd directory by running configure script, i.e.

./configure <platform> <compiler> <parallel implementation>

and then enter the command 'make install'. To generate config.h file configure script uses files from the $AMBERHOME/src/pmemd/config_data directory. Below are samples of configuration files for some Fujitsu platforms.

Before Compiling ptraj

ptraj is a mixed C/Fortran program for analysing Molecular Dynamics results

To be compatible with a C/Fortran interface conventions a main module (in C language) of the ptraj program should be modified:

     int

     MAIN__(unsigned int argCount, char **argPointer)

     /*main(unsigned int argCount, char **argPointer)*/

where the last line is the original (now commented) code.


Configuration files contain good (not the best) building options for any Fujitsu PRIMEPOWER computer.

Amber

Configuration file for serial version (shift-click or right-mouse-click for download):

config.h.primepower.serial

Copy it in the $AMBERHOME/src directory, rename into config.h and enter

make serial

Configuration file for MPI version (shift-click or right-mouse-click for download):

config.h.primepower.mpi

Copy it in the $AMBERHOME/src directory, rename into config.h and enter

make parallel

Pmemd

Configuration file for serial version (shift-click or right-mouse-click for download):

primepower.frt.nopar

Copy it in the $AMBERHOME/src/pmemd/config_data directory and enter

./configure primepower frt nopar

make install

Configuration file for MPI version (shift-click or right-mouse-click for download):

primepower.frt.mpi

Copy it in the $AMBERHOME/src/pmemd/config_data directory and enter

./configure primepower frt mpi

make install