Amber 10 on Fujitsu PRIMEPOWER 250/450/650/850/900/1500/2500


Both distributions, Amber10 and AmberTools,  come as bz2 archives, Amber10.tar.bz2 and AmberTools-1.0.tar.bz2.

Decompress and untar both distributions:

bzip2 -d Amber10.tar.bz2

bzip2 -d AmberTools-1.2.tar.bz2

tar xvf Amber10.tar

tar xvf AmberTools-1.2.tar

Both the AmberTools and Amber10 tar files unpack into the same directory tree, with amber10 at its root.

Set up the AMBERHOME environment variable to point to where the Amber tree resides on a machine. For example, using csh, tcsh, etc:

setenv AMBERHOME /path/to/amber10

Download file bugfix.all from the http://ambermd.org/bugfixes10.html  into the $AMBERHOME directory and patch the Amber distribution:

cd $AMBERHOME

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

To patch AmberTools download file bugfix.all from the http://ambermd.org/bugfixesat.html into the $AMBERHOME directory and patch the Amber distribution:

cd $AMBERHOME
patch -p0 -N <bugfix.all

Prior to installing Amber one needs to download amber10-primepower-fix.all and to place it to the $AMBERHOME directory.

Apply patch:

patch -p0 -N -r patch_rejects <amber10-primepower-fix.all

Installing GNU make

sleap program requies GNU make utility to be built. Download GNU make source code from, for example, http://www.icewalkers.com/Linux/Software/517110/GNU-Make.html

Install GNU make:

gzip –d make-3.81.tar.gz

tar xvf make-3.81.tar

cd make-3.81

./configure --prefix=/where/to/install

make

make install

Make sure to add location of the make utility to your path.

Building Amber-10

Set up AMBERHOME environment variable

setenv AMBERHOME /path/to/amber-10

Go to the $AMBERHOME/src directory and run configure_amber script

./configure_amber -nobintraj primepower

It will create config_amber.h file. You might want to edit it to match your environment.

Now compile serial version:

make clean

make serial

To test the basic AMBER distribution, do this:

cd $AMBERHOME/test

make test

make test.serial.QMMM

Where "possible FAILURE" messages are found, go to the indicated directory under $AMBERHOME/test, and look at the "*.dif" files. Differences should involve round-off in the final digit printed, or occasional messages that differ from machine to machine.

For convenience, all of the failure messages are collected in the file $AMBERHOME/test/TEST_FAILURES.diff; you can quickly see from these if there is anything more than round-off errors

If you have trouble with individual tests, you may wish to invoke "make" with the ignore errors option (make -i) or comment out certain lines in the Makefile, and/or go directly to the $AMBERHOME/test subdirectories to examine the inputs and outputs in detail

Now we can build parallel version of Amber.

Go to the $AMBERHOME/src directory, and create a configuration file for a parallel version:

cd $AMBERHOME/src

./configure_amber –nobintraj -mpi primepower

This will create a config_amber.h file for a machine using the mpifrt compiler and Fujitsu MPI. You can examine and edit this file to match your local environment.

Now compile everything:

make clean

make parallel

This creates two new executables: sander.MPI and sander.LES.MPI. The serial versions will still be available in $AMBERHOME/exe, just without the "MPI" extension.

To test parallel programs, you need first to set the DO_PARALLEL environment variable as follows (some test cases need 4 CPUs):

cd $AMBERHOME/test

setenv DO_PARALLEL ’mpiexec -n 2’

make test.parallel

make test.parallel.QMMM

make test.parallel.EVB

Building Serial Version of PMEMD

Create file config.h in the directory $AMBERHOME/src/pmemd by running a script

./configure primepower frt nopar

You might want to edit config.h file to match your environment.

Compile Pmemd:

$ make clean

$ make

$ make install

To test a serial version of pmemd one needs to switch to the directory $AMBERHOME/test and run tests for the pmemd:

make test.pmemd

Where "possible FAILURE" messages are found, one needs to go to the indicated directory under $AMBERHOME/test, and look at the "*.dif" files. Differences should involve round-off in the final digit printed, or occasional messages that differ from machine to machine.

Building Parallel Version of PMEMD

Create file config.h in the directory $AMBERHOME/src/pmemd by running a script

./configure primepower frt mpi

You might want to edit config.h file to match your environment.

Compile Pmemd:

$ make clean

$ make

$ make install

To test parallel version of pmemd one needs to switch to the directory $AMBERHOME/test and run tests for the pmemd:

setenv DO_PARALLEL “mpiexec –n 2 “

make test.pmemd

Inslalling AmberTools

Currently, for installation of AmberTools we shall use GNU make and GNU C and C++ compilers, gcc and g++, respectively.

Go to $AMBERHOME/src and run

./configure_at –nobintraj primepower

It will create config.h file which you could edit to match your environment.

make –f Makefile_at clean

make –f Makefile_at

The make will fail at the point of compiling gleap. A simple workaround is to edit the $AMBERHOME/src/config.h file and change lines

CC=c99

CXX=FCC

CPLUSPLUS=FCC

to

CC=gcc

CXX=g++

CPLUSPLUS=g++

i.e. we are switching from Fujitsu to the GNU compilers.

Then type in command prompt:

(cd gleap && make clean )

(cd gleap && make install )

To validate AmberTools installation go to $AMBERHOME/test and type

make –f Makefile_at

which will run tests and will report successes or failures.