Amber 9 on Fujitsu PRIMEPOWER 250/450/650/850/900/1500/2500


Download file bugfix.all from the http://amber.scripps.edu/bugfixes.html  into the $AMBERHOME directory and patch the Amber distribution:

cd $AMBERHOME

patch -p0 -N -r patch_rejects <bugfix.all

This should patch source files with the latest bugfixes.

Before compiling Amber 9 using the Fujitsu compiler several files of the Amber distribution should be modified. To simply procedure of applying the changes to the Amber code they have been gathered in one patch file, fujitsu-fix.all. The patch should be copied to the $AMBERHOME directory and applied after applying the Amber bug fixing patch.

patch -p0 -N -r patch_rejects <fujitsu-fix.all

Before compiling the serial or parallel version of Amber one needs to place file config.h, to the $AMBERHOME/src directory.

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

config.h.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_v.frt.nopar

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

./configure primepower_v frt nopar

make clean

make

make install

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

primepower_v.frt.mpi

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

./configure primepower_v frt mpi

make clean

make

make install