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GPU-ACCELERATED NAMD
The fastest, easiest way to improve simulations performance by up to 7x.
GPU ACCELERATED NAMD
System Requirements
NAMD should be portable to any parallel platform with a modern C++ compiler. Precompiled GPU-accelerated NAMD 2.11 binaries are available for download for Windows, Mac OS X, and Linux. NAMD makes use of both GPU and CPU, therefore we recommend to have a relatively modern CPU to achieve the best NAMD application performance. See the recommended System Configuration section for more details.

Download and Installation Instructions

NAMD developers provide complete, optimized binaries for all common platforms to which NAMD has been ported. The binaries can be obtained from the NAMD download page.

It should not be necessary to compile NAMD unless you want to add or modify features, improve performance by building a Charm++ version that takes advantage of special networking hardware, or if you have customized your version of NAMD. Complete directions for compiling NAMD are contained in the release notes, and are available on the NAMD web site and are included in all distributions.

Below is a brief summary of the compilation procedure:

1. Download NAMD Source code.
2. Extract the package and Charm++
tar xf NAMD_2.11_Source.tar.gz
cd NAMD_2.11_Source
tar xf charm-6.7.0.tar
3. Download and install TCL and FFTW.
Please see the release notes for the appropriate version of these libraries.
wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
tar xzf fftw-linux-x86_64.tar.gz
mv linux-x86_64 fftw
tar xzf tcl*-linux-x86_64.tar.gz
tar xzf tcl*-linux-x86_64-threaded.tar.gz
mv tcl*-linux-x86_64 tcl
mv tcl*-linux-x86_64-threaded tcl-threaded
4. Build Charm++.
The build script has an interactive mode, you can also specify options in the command line as explained below.
cd charm-6.7.0
./build charm++ {arch} {C compiler} {Fortran compiler} {other options}
For {arch}, it is required to use one of the following options: 'verbs-linux-x86_64' for multiple node configurations, 'multicore-linux64' for a single node system. Other options are not required but recommended for best performance: 'smp' to use SMP for multi-node builds (Click here for more details), '--with-production' to use production level optimizations.
Example 1. Charm++ build for multi-node configuration using Intel compilers and SMP with all production optimizations:
./build charm++ verbs-linux-x86_64 icc smp --with-production
Example 2. Charm++ build for single-node configuration using Intel compilers with all production optimizations.
./build charm++ multicore-linux64 icc --with-production
5. Build NAMD.
Make sure you're in the main NAMD directory, then configure and run make:
./config {namd-arch} --charm-arch {charm-arch} {opts}
cd {namd-arch}
make -j4
For {namd-arch} we recommend 'Linux-x86_64-icc', {charm-arch} should be the same arch that you built Charm++ with, {opts} should be set to '--with-cuda' to enable GPU acceleration, otherwise set to '--without-cuda' for CPU-only build. The build directory can be extended with .[comment] to build, e.g., Linux-x86_64.cuda. This is helpful to manage different builds of NAMD. Note that the extension does not have any meaning, so './config Linux-x86_64.cuda' won't be a CUDA build unless you also specify '--with-cuda'.
Optional flags for the CUDA build:
a. --cuda-prefix can be used to set correct path to your CUDA toolkit;
b. --cuda-gencode allows you to add different GPU compute architecture.
Example 1. NAMD build for x86_64 architecture using Intel compilers, with GPU acceleration and specified CUDA path, for single node:
./config Linux-x86_64-icc --charm-arch multicore-linux64-icc --with-cuda --cuda-prefix /usr/local/cuda
Example 2. NAMD build for x86_64 architecture using Intel compilers, with GPU acceleration and specified CUDA path, for multiple nodes:
./config Linux-x86_64-icc --charm-arch verbs-linux-x86_64-smp-icc --with-cuda --cuda-prefix /usr/local/cuda
Example 3. NAMD build for x86_64 architecture using Intel compilers, without GPU acceleration, for multiple nodes:
./config Linux-x86_64-icc --charm-arch verbs-linux-x86_64-smp-icc

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