Building Amber 8

Building Amber 8

AMBER is an acronym for Assisted Model Building with Energy
Refinement. It is a general purpose molecular mechanics/dynamics
package which is designed for the refinement of macro molecular
conformations using analytical potential energy function. Amber
consists of a suite of programs for molecular modeling and
molecular simulations, each of which is designed to carry out a
specific task.

Steps to building

To build Amber 8, you will need to download the source, patch it,
configure it, and then build and test it. You can also build Amber 8
with ACML, and build it to run with MPI. These steps, and any known
limitations, are described in the sections below.

Downloading Amber 8
Patching the source
Building with ACML
Building with MPICH
Configuring Amber 8
Building Amber 8
Testing Amber 8
Known limitations

Downloading Amber 8

Amber 8 can be obtained from the Scripps Institute. After you have uncompressed the source
code, you should set $AMBERHOME to the source directory
path. $AMBERHOME typically will end with "amber8" and will have directories like
"test" and "src" underneath it.

export AMBERHOME="path_to_Amber8"

Patching the source

One line in a distributed Makefile needs to be modified to
allow for builds on 64-bit systems. Make this change to
line 114 of $AMBERHOME/src/leap/src/leap/Makefile:

< ../Xmu/libXmu.a -L$(XHOME)/lib -lXt -lXext -lSM -lICE -lX11 -lm -lpthread
> ../Xmu/libXmu.a -L$(XLIBS) -lXt -lXext -lSM -lICE -lX11 -lm -lpthread

Building with ACML

While Amber 8 is distributed with source for the required BLAS
routines, an optimized BLAS library greatly improves performance. We
recommend the ACML library which can be downloaded from the
AMD website -- download
the PathScale version.

If you do download ACML, then you should set the ACML_DIR
environmental variable to the the name of the directory that contains
the ACML libraries (libacml.so and libacml.a). If
you decide to use the distributed routines, then no action is
required.

export ACML_DIR="path_to_ACML"

Building with MPICH

To build Amber 8 with MPICH support, you will need
to set the variable MPICH_HOME to the root directory
of your MPICH install. For example:

export MPICH_HOME=/opt/mpich/ch-p4

Configuring Amber 8

Replace the distributed Amber 8 configure file with this
configure file. If you are building a serial
64-bit executable then you can now run the configure command:

cd $AMBERHOME/src                    
./configure pathscale

To build using MPICH, then you need to add the -mpich option
to the configuration command.

cd $AMBERHOME/src 
./configure -mpich pathscale

To build a 32-bit executable, you need to add the option -p4
to the configuration command given above.

cd $AMBERHOME/src                     
./configure -p4 pathscale

Building Amber 8

If you are building Amber 8 as a serial application
then run the following command:

make serial

If you have opted to build Amber 8 with MPICH then
run the following command:

make parallel

Testing Amber 8

To test the binaries you have just built change to the directory
$AMBERHOME/test and run make test.

cd $AMBERHOME/test                    
make test

If you have built with MPICH then you may wish to define
the variable DO_PARALLEL to an appropriate mpirun
command. If defined, all tests will be run as arguments
to this command. For example,

export DO_PARALLEL="mpirun -np 8"     
cd $AMBERHOME/test                    
make test

Known limitations

There are no known bugs related to Amber 8. While the self-tests may
report "possible failures" these are simply the result of small
floating-point roundoff and can safely be ignored.

We recommend you record what steps you took, along with their output,
in case of problems. You can include this in your email to support.
Here is an example of changing a make command to record the output in a
text file:

make foo 2>&1 | tee make-foo-log.txt

If you have any comments or suggestions about additions to these
pages, please contact support@pathscale.com.

Building Amber 8

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