Compiling and Installing AmberTools

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following commands to set environment variables:

   export PATH=/path/to/GNU/bin:$PATH
   export LD_LIBRARY_PATH=/path/to/GNU/lib64:$LD_LIBRARY_PATH
   export PATH=/path/to/OPENMPI/bin:$PATH
   export LD_LIBRARY_PATH=/path/to/OPENMPI/lib:$LD_LIBRARY_PATH

3. Run the following commands to decompress the AmberTools installation package:

   cd /path/to/AMBER
   tar -xvf AmberTools19.tar.bz2

4. Run the following commands to update the config.guess and config.sub scripts in the fftw3-3.3 directory:

   cd /path/to/AMBER/amber18/AmberTools/src/fftw-3.3
   http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
   vi config.guess
   http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
   vi config.sub

5. Run the following commands to update the config.guess and config.sub scripts in the xblas directory:

   cd /path/to/AMBER/amber18/AmberTools/src/xblas/config
   http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
   vi config.guess
   http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
   vi config.sub

6. Run the following commands to perform serial compilation and installation:

   cd /path/to/AMBER/amber18
   ./configure --skip-python -nosse gnu
   test -f /path/to/AMBER/amber18/amber.sh && source /path/to/AMBER/amber18/amber.sh
   make install

7. Run the following command to perform a serial test:

   make test

8. Run the following commands to perform parallel compilation and installation:

   cd /path/to/AMBER/amber18
   ./configure --skip-python -nosse -mpi gnu
   make install
   export DO_PARALLEL="mpirun --allow-run-as-root -np 96 -mca btl ^openib"
   ./configure --skip-python -nosse -openmp gnu
   make openmp