General documentation is available from the
AMBER Home page
and in the doc subdirectory of the AMBER installation.
The Amber8 source code is available in loyd:/thr/loyd/case/mm/amber8_release. See the readme.txt file there for instructions on how to proceed. Please note that this code is licensed to scientists at TSRI only; it may not distributed to, or used by, anyone outside TSRI.
A complete AMBER serial installation, with statically linked Linux
executables, is in the
/redfish/applications/case/amber8_1cpu directory on Redfish.
You should be able to transport this to any Pentium IV Linux machine, point your
$AMBERHOME environment variable there, and use it (without having to do any
compilations). Be sure to add $AMBERHOME/exe to your path.
A complete AMBER serial installation, with dynamically linked SGI (R10k)
executables, is in the
/home/case/amber8 directory.
You should be able to transport this to any SGI R10000 machine, point your
$AMBERHOME environment variable there, and use it (without having to do any
compilations). Be sure to add $AMBERHOME/exe to your path.
Various software is available in
/redfish/applications/case.
A complete AMBER serial installation is in the
amber8_1cpu subdirectory.
Parallel sander and sander.LES are installed in the
amber8_lam_mpi subdirectory.
These parallel programs should be executed using the LAM-MPI in the
mpi/lam/intel-8.0 subdirectory.
Beware that other LAM-MPI installations lurk.
AMBER and LAM-MPI executables have been built with
Intel Version 8.0 Build 20031016Z
compilers and static linking.
An example run script for sander on 4cpus of redfish is provided below.
To use these AMBER installations
(on multiple cpus) with the provided scripts or using your own script be sure to define the
AMBERHOME environment variable
to the root of the AMBER directory tree, and the LAMHOME environment variable and path for example (.cshrc etc.):
| Shell | Command |
|---|---|
| csh, tcsh (~/.cshrc) | setenv AMBERHOME /redfish/applications/case/amber8_lam_mpi
setenv LAMHOME /redfish/applications/case/mpi/lam/intel-8.0
set path = (/redfish/applications/case/mpi/lam/intel-8.0/bin $path)
Make sure these 3 commands go last in your .cshrc file so that the LAM bin directory is the first directory in your PATH variable. |
| sh, ksh, bash (~/.cshrc or ~/.bashrc) | export AMBERHOME=/redfish/applications/case/amber8_lam_mpi
export LAMHOME=/redfish/applications/case/mpi/lam/intel-8.0
export PATH=/redfish/applications/case/mpi/lam/intel-8.0/bin:$PATH
Make sure these 3 commands go last in your .cshrc file so that the LAM bin directory is the first directory in your PATH variable. |
${AMBERHOME}/exe to your path:
| Shell | Command |
|---|---|
| csh, tcsh | setenv PATH "${AMBERHOME}/exe:${PATH}" |
| sh, ksh | export PATH="${AMBERHOME}/exe:${PATH}" |
LAMHOME and path must be defined in an appropriate dot file.
These Redfish executables should run on any 32 bit Intel Architecture Pentium 4 machine.
We recommend between 2 and 8 processors of redfish, using 2 cpus per node, for LAM-MPI sander production runs. As a guide here are some performance timings for the JAC benchmark (23558 atoms) on Redfish:
| Processors | Timings |
|---|---|
| 1 CPU | 916.35s [94.28 ps/day] [1x] |
| 2 CPU | 533.54s [161.94 ps/day] [1.72x] |
| 4 CPU | 342.27s [252.43 ps/day] [2.68x] |
| 8 CPU | 225.02s [383.97 ps/day] [4.07x] |
| 16 CPU | 186.20s [464.02 ps/day] [4.92x] |
|
#!/bin/csh # Run sander job on 4cpu (2x2 redfish) #PBS -l nodes=2:ppn=2 #PBS -l walltime=4:00:00 #PBS -l cput=16:00:00 #PBS -j oe #CHANGE THIS LINE TO POINT TO WHERE YOUR CALCULATION FILES ARE: cd /redfish/people/userid/directory_for_calculation setenv LAMRSH "rsh" echo "NODES ALLOCATED = $PBS_NODEFILE" cat $PBS_NODEFILE lamboot -s $PBS_NODEFILE lamnodes #IF YOU CHANGE THE NUMBER OF CPUS REQUESTED DON'T FORGET TO CHANGE THE -np x BELOW: mpirun -np 4 $AMBERHOME/exe/sander -i ../mdin -o jac.out.4proc -c ../inpcrd.equil -r restrt -p ../prmtop lamhalt echo "DONE" |
Various software is available in
/bluefish/people-b/applications/amber.
A complete AMBER serial installation is in the
amber8_1cpu subdirectory.
Parallel sander and sander.LES are installed in the
amber8_lam_mpi subdirectory.
These parallel programs should be executed using the LAM-MPI in the
/opt/intel8-lam directory.
Beware that other LAM-MPI installations lurk.
AMBER and LAM-MPI executables have been built with
Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version 8.1 Build 20050517 Package ID: l_fce_pc_8.1.028
compilers with static linking for the single cpu installation and dynamic linking for the parallel (MPI) installation.
An example run script for sander on 4cpus of bluefish is provided below.
To use these AMBER installations
(on multiple cpus) with the provided scripts or using your own script be sure to define the
AMBERHOME environment variable
to the root of the AMBER directory tree, and the LAMHOME environment variable and path for example (.cshrc etc.):
| Shell | Command |
|---|---|
| csh, tcsh (~/.cshrc) | setenv AMBERHOME /bluefish/people-b/applications/amber/amber8_lam_mpi
setenv LAMHOME /opt/intel8-lam
setenv path = (/opt/intel8-lam/bin $path)
setenv LD_LIBRARY_PATH /bluefish/people-b/applications/amber/lib
Make sure these 4 commands go last in your .cshrc file so that the LAM bin directory is the first directory in your PATH variable. |
| sh, ksh, bash (~/.cshrc or ~/.bashrc) | export AMBERHOME=/bluefish/people-b/applications/amber/amber8_lam_mpi
export LAMHOME=/opt/intel8-lam/
export PATH=/opt/intel8-lam/bin:$PATH
export LD_LIBRARY_PATH=/bluefish/people-b/applications/amber/lib
Make sure these 4 commands go last in your .cshrc file so that the LAM bin directory is the first directory in your PATH variable. |
${AMBERHOME}/exe to your path:
| Shell | Command |
|---|---|
| csh, tcsh | setenv PATH "${AMBERHOME}/exe:${PATH}" |
| sh, ksh | export PATH="${AMBERHOME}/exe:${PATH}" |
LAMHOME and path must be defined in an appropriate dot file.
These Bluefish executables should run on any ix86/64 Intel Architecture Pentium 4 (EM64T) machine.
We recommend between 2 and 8 processors of bluefish, using 2 cpus per node, for LAM-MPI sander production runs. As a guide here are some performance timings for the JAC benchmark (23558 atoms) on Bluefish:
| Processors | Timings |
|---|---|
| 1 CPU | XXX.xxs [XX.xx ps/day] [1x] |
| 2 CPU | XXX.xxs [XXX.xx ps/day] [X.XXx] |
| 4 CPU | XXX.xxs [XXX.xx ps/day] [X.XXx] |
| 8 CPU | XXX.xxs [XXX.xx ps/day] [X.XXx] |
| 16 CPU | XXX.xxs [XXX.xx ps/day] [X.XXx] |
|
#!/bin/csh # Run sander job on 4cpu (2x2 Bluefish) #PBS -l nodes=2:ppn=2 #PBS -l walltime=4:00:00 #PBS -l cput=16:00:00 #PBS -j oe #CHANGE THIS LINE TO POINT TO WHERE YOUR CALCULATION FILES ARE: cd /bluefish/people-a/userid/directory_for_calculation setenv LAMRSH "rsh" echo "NODES ALLOCATED = $PBS_NODEFILE" cat $PBS_NODEFILE lamboot -s $PBS_NODEFILE lamnodes #IF YOU CHANGE THE NUMBER OF CPUS REQUESTED DON'T FORGET TO CHANGE THE -np x BELOW: mpirun -np 4 $AMBERHOME/exe/sander -i ../mdin -o jac.out.4proc -c ../inpcrd.equil -r restrt -p ../prmtop lamhalt echo "DONE" |
Define the AMBERHOME environment variable
to the root of the AMBER directory tree:
| Shell | Command |
|---|---|
| csh, tcsh | setenv AMBERHOME /thr/loyd/sbrozell/amber/amber8.ia64 |
| sh, ksh | export AMBERHOME=/thr/loyd/sbrozell/amber/amber8.ia64 |
${AMBERHOME}/exe to your path:
| Shell | Command |
|---|---|
| csh, tcsh | setenv PATH "${AMBERHOME}/exe:${PATH}" |
| sh, ksh | export PATH="${AMBERHOME}/exe:${PATH}" |
The serial Yellowtail executables should run on any 64 bit Intel Architecture, i.e., Itanium and Itanium2.
The names of parallel executables have a .MPI extension.
The MPI executables were not statically linked;
the LD_LIBRARY_PATH environment variable should contain
/opt/intel_cc_80/lib:/opt/intel_fc_80/lib;
use the appropriate command for your shell as above.
unlimit
Alternatively, individual limits may be increased:
limit datasize unlimited
limit stacksize unlimited
limit memoryuse unlimited
Last update: April 30, 2004, [R Walker]