Building Amber 8

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.

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"

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

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"

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

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

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

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

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.