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AmberTools12.pdf

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Both amber12 and ambertools-12 have been installed.

Introduction

http://ambermd.org/
Build Instruction: http://jswails.wikidot.com/installing-amber12-and-ambertools-12

Usage

module load amber/12-gnu
OR
module load amber/12-openmpi
OR
module load amber/12-cuda-gnu (To use gpus, please make sure you send the job to queue named "gpu" )

There is a special version (see notes below in the installation section. This can be used with:

module load amber/12-openmpi-modified

Installation

amber12-gnu

cd /sw/amber/12
tar -xvf AmberTools12.tar
tar -xvf Amber12.tar
mv  /sw/amber/12/amber12 /sw/amber/12/amber12-gnu
export AMBERHOME=/sw/amber/12/amber12-gnu
cd $AMBERHOME

./configure gnu  
make install 
make test 

>>>>>>>>>
 ./configure  gnu
Checking for updates...
AmberTools12 is up to date
Amber12 is up to date
Searching for python2... Found python2.6: /usr/bin/python2.6
Obtaining the gnu suite version:
      gcc -v
The version is 4.4.6
Testing the gcc compiler:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o testp testp.c
OK
Testing the gfortran compiler:
     gfortran  -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -c -o testp.c.o testp.c
     gfortran  -O0 -c -o testp.f.o testp.f
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Configuring NetCDF (may be time-consuming)...
    NetCDF configure succeeded.
Checking for zlib: OK
Checking for libbz2: OK
Configuring fftw-3.3 (may be time-consuming)...
    fftw-3.3 configure succeeded.
Configuring XBLAS (may be time-consuming)...
    XBLAS configure succeeded.
Configuring MTK++ (may be time-consuming)...
    MTK++-0.2.0 configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
>>>>>>>>>

amber12-mpi

export AMBERHOME=/sw/amber/12/amber12-openmpi
cd $AMBERHOME
module load mpi/openMPI/1.4.3-gnu
./configure -mpi gnu  
make install 
make test 

>>>>>>>>>>>
Obtaining the gnu suite version:
      gcc -v
The version is 4.4.6
Testing the gcc compiler:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o testp testp.c
OK
Testing the gfortran compiler:
     gfortran  -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -c -o testp.c.o testp.c
     gfortran  -O0 -c -o testp.f.o testp.f
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Configuring NetCDF (may be time-consuming)...
    NetCDF configure succeeded.
Checking for zlib: OK
Checking for libbz2: OK
Skipping configuration of FFTW3
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
You have new mail in /var/spool/mail/root
>>>>>>>>>>>

amber12-modified

cd /sw/amber/12/
tar xvf /data1/software/amber/AmberTools12.tar
tar xvf /data1/software/amber/Amber12.tar
mv amber12 amber12-modified
cp -i /tmp/sa_driver.F90 /sw/amber/12/amber12-modified/AmberTools/src/pbsa/sa_driver.F90
export AMBERHOME=/sw/amber/12/amber12-modified
cd $AMBERHOME
module load fftw/3.2.2-gnu
module load python/2.7.1-shared
module load intel-cmkl-11/11.1.072
./configure --help
./configure  gnu
make install 
make test

amber12-mpi-modified

This version, amber12-mpi-modified, was made to make AMBER be able to automatically assign Poisson-Boltzman (PB) radii to FF99SBILDN forcefield. This modification does not affect other users, unless they want to calculate PBSA on the ILDN forcefields and even then, this modification simply extends the option while not changing anything else.

The main change that needs to be done is replacing
/sw/amber/12/amber12-openmpi-modified/AmberTools/src/pbsa/sa_driver.F90

Changes to the content of this file has been tagged with the lines with "MODIFICATION" comment.

export AMBERHOME=/sw/amber/12/amber12-openmpi-modified
cd $AMBERHOME
module load mpi/openMPI/1.4.3-gnu
./configure -mpi gnu  
make install 
make test

amber12-intelmpi-modified

cd /sw/amber/12/

tar xvf /data1/software/amber/AmberTools12.tar
tar xvf /data1/software/amber/Amber12.tar
#cp -r amber12-modified amber12-openmpi-modified
mv amber12 amber12-intelmpi-modified
cp -i /tmp/sa_driver.F90 /sw/amber/12/amber12-intelmpi-modified/AmberTools/src/pbsa/sa_driver.F90
export AMBERHOME=/sw/amber/12/amber12-intelmpi-modified
cd $AMBERHOME

module load fftw/3.2.2-gnu
module load python/2.7.1-shared
module load intel-cmkl-11/11.1.072
module load intel-mpi/4.0.1.007
module load intel-fc-11/11.1.072
module load intel-cc-11/11.1.072
module load intel-tools-11/11.1.072


make clean all
./configure --help
./configure intel
make install 
make test 
./configure -mpi intel
vi config.h
FC= mpiifort
make install 
make test

amber12-cuda

ssh n021
export AMBERHOME=/sw/amber/12/amber12-cuda-gnu
cd $AMBERHOME

module load cuda/4.0
export CUDA_HOME=/usr/local/cuda
 ./configure -cuda gnu 
make install 
make test 

 ./configure -cuda gnu
Checking for updates...
AmberTools12 is up to date
Amber12 is up to date

Searching for python2... Found python2.6: /usr/bin/python2.6

Obtaining the gnu suite version:
      gcc -v
The version is 4.4.5

Testing the gcc compiler:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o testp testp.c
OK

Testing the gfortran compiler:
     gfortran  -O0 -o testp testp.f
OK

Testing mixed C/Fortran compilation:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -c -o testp.c.o testp.c
     gfortran  -O0 -c -o testp.f.o testp.f
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w
OK

Testing pointer size:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.

Testing flex: OK

Configuring NetCDF (may be time-consuming)...

    NetCDF configure succeeded.

Checking for zlib: OK

Checking for libbz2: OK
Skipping configuration of FFTW3

The configuration file, config.h, was successfully created.

The next step is to type 'make install'

Cleaning the src directories. This may take a few moments.
Configure complete.

Sample PBS Script

#!/bin/sh
#PBS -m abe
#PBS -M nnnnn@griffith.edu.au
#PBS -N Ambertest
#PBS -q workq
#PBS -l walltime=01:00:00
#PBS -l select=1:ncpus=1
#####PBS -l ngpus=1
#####Above not needed if not using gpu
module load amber/12-gnu
module load cuda/4.0
echo "Starting job"
pmemd -O -i mdin -o mdout -p prmtop -c inpcrd -r restrt -x mdcrd 
echo "test Done"
echo "Done with job"

There are some sample input files located here:
/sw/amber/12/amber12-gnu/src/mm_pbsa/Examples/mm_pbsa.in

Reference

1. http://nf.nci.org.au/facilities/software/software_host.php?software=Amber&host=xe&site=ANU&from_site=INT&all_sites=&id=3&host_id=103&e=yes&version=4006&sid_value=1

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