Compiling VinaLC
VinaLC[1][2] is a parallelized version of Autodock Vina[3]. VinaLC was created by Lawrence Livermore National Lab.
Compiling on Picotte
Modulefiles
intel/composerxe/2020u4
picotte-openmpi/intel/2020/4.1.0
boost/intel/2020/1.75.0
Build
Same steps as for Proteus below.
Compiling on Proteus
The VinaLC code is built with standard tools called
autoconf and automake.
However, the setup seems to be a little out of date. E.g. the file
configure.in should properly be named configure.ac.
A modified version for building on Proteus with Intel Composer XE and
Open MPI 1.8.1 is available https://github.com/prehensilecode/vinalc
The main changes were to the file configure.ac. Cloning the whole
repository and following the official build instructions[4] should work.
This requires Boost and MPI.
Modulefiles
The following modulefiles are required:
git/2.16.1
texlive/2016
doxygen/1.8.12
autoconf/2.69
automake/1.16
intel/composerxe/2015.1.133
proteus-openmpi/intel/2015/1.8.1-mlnx-ofed
boost/openmpi/intel/2015/1.65.1
zlib/cloudflare/intel/2015/1.2.8
Generate configure Script
./autogen.sh
Configure
Configure, setting prefix, and locations of Boost and MPI:
./configure --prefix=/mnt/HA/groups/myrsrchGrp/opt --with-boost=$BOOSTDIR --with-mpi=$MPI_HOME > & Configure.out &
Build and Install
make -j 4 >& Make.out
make install
References
[2] Xiaohua Zhang, Sergio E. Wong, and Felice C. Lightstone. (2013)
Message Passing Interface and Multithreading Hybrid for Parallel
Molecular Docking of Large Databases on Petascale High Performance
Computing Machines. J. Comput. Chem.