NAMD¶

NAMD is a parallel molecular dynamics code based on Charm++, designed for high-performance simulation of large biomolecular systems.

Licensing Terms and Conditions

NAMD is distributed free of charge for research purposes only and not for commercial use: users must agree to NAMD license in order to use it at CSCS. Users agree to acknowledge use of NAMD in any reports or publications of results obtained with the Software (see NAMD Homepage for details).

Single-node build¶

The single-node build works on a single node and benefits from the new GPU-resident mode (see NAMD 3.0b6 GPU-Resident benchmarking results for more details). The single-node build provides the following views:

namd-single-node (standard view, with NAMD)
develop-single-node (development view, without NAMD)

Building from source¶

TCL Version

According to the NAMD 3.0 release notes, TCL 8.6 is required. However, the source code for the 3.0 release still contains hard-coded flags for TCL 8.5. The UENV provides tcl@8.6, therefore you need to manually modify NAMD 3.0's arch/Linux-ARM64.tcl file as follows: change -ltcl8.5 to -ltcl8.6 in the definition of the TCLLIB variable.

The NAMD uenv provides all the dependencies required to build NAMD from source. You can follow these steps to build NAMD from source:

export DEV_VIEW_NAME="develop-single-node"

# Start uenv and load develop view
uenv start <NAMD_UENV>
uenv view ${DEV_VIEW_NAME}

# Set variable VIEW_PATH to the view
export DEV_VIEW_PATH=/user-environment/env/${DEV_VIEW_NAME}

cd <PATH_TO_NAMD_SOURCE>

# ~~~~~
# Modify the "<PATH_TO_NAMD_SOURCE>/arch/Linux-ARM64.tcl" file now!
# Change "-ltcl8.5" with "-ltcl8.6" in the definition of the "TCLLIB" variable
# ~~~~~

# Build bundled Charm++
tar -xvf charm-8.0.0.tar && cd charm-8.0.0
./build charm++ multicore-linux-arm8 gcc --with-production --enable-tracing -j 32

# Configure NAMD build for GPU
cd .. 
./config Linux-ARM64-g++.cuda \
    --charm-arch multicore-linux-arm8-gcc --charm-base $PWD/charm-8.0.0 \
    --with-tcl --tcl-prefix ${DEV_VIEW_PATH} \
    --with-fftw --with-fftw3 --fftw-prefix ${DEV_VIEW_PATH} \
    --cuda-gencode arch=compute_90,code=sm_90 --with-single-node-cuda --with-cuda --cuda-prefix ${DEV_VIEW_PATH}
cd Linux-ARM64-g++.cuda && make -j 32

# !!! BEGIN OPTIONAL !!!
# Configure NAMD build for CPU
cd ..
./config Linux-ARM64-g++ \
    --charm-arch multicore-linux-arm8-gcc --charm-base $PWD/charm-8.0.0 \
    --with-tcl --tcl-prefix ${DEV_VIEW_PATH} \
    --with-fftw --with-fftw3 --fftw-prefix ${DEV_VIEW_PATH}
cd Linux-ARM64-g++ && make -j 32
# !!! END OPTIONAL !!!

cd ..
export LD_LIBRARY_PATH=${DEV_VIEW_PATH}/lib/

# Run NAMD (GPU version)
Linux-ARM64-g++.cuda/namd3 <NAMD_OPTIONS>

# !!! BEGIN OPTIONAL !!!
# Run NAMD (CPU version)
Linux-ARM64-g++/namd3 <NAMD_OPTIONS>
# !!! END OPTIONAL !!!

The optional section provides instructions on how to build a CPU-only build, should you need it (for constant pH MD simulations, for example).

Multi-node build¶

The multi-node build works on multiple nodes and it is based on Charm++ MPI backend. The multi-node build provides the following views:

namd
develop (development view, without NAMD)

GPU-resident mode

The multi-node build based on Charm++ MPI backend can't take advantage of the new GPU-resident mode. Unless you require the multi-node build or you can prove it is faster for your use case, we recommend using the single-node build with the GPU-resident mode.

Building from source¶

TCL Version

According to the NAMD 3.0 release notes, TCL 8.6 is required. However, the source code for the 3.0 release still contains hard-coded flags for TCL 8.5. The UENV provides tcl@8.6, therefore you need to manually modify NAMD 3.0's arch/Linux-ARM64.tcl file as follows: change -ltcl8.5 to -ltcl8.6 in the definition of the TCLLIB variable.

The NAMD uenv provides all the dependencies required to build NAMD from source. You can follow these steps to build NAMD from source:

export DEV_VIEW_NAME="develop"

# Start uenv and load develop view
uenv start <NAMD_UENV>
uenv view ${DEV_VIEW_NAME}

# Set variable VIEW_PATH to the view
export DEV_VIEW_PATH=/user-environment/env/${DEV_VIEW_NAME}

cd <PATH_TO_NAMD_SOURCE>

# ~~~~~
# Modify the "arch/Linux-ARM64.tcl" file now!
# Change "-ltcl8.5" with "-ltcl8.6" in the definition of the "TCLLIB" variable
# ~~~~~

# Build bundled Charm++
tar -xvf charm-8.0.0.tar && cd charm-8.0.0
env MPICXX=mpicxx ./build charm++ mpi-linux-arm8 smp --with-production -j 32

# Configure NAMD build for GPU
cd .. 
./config Linux-ARM64-g++.cuda \
    --charm-arch mpi-linux-arm8-smp --charm-base $PWD/charm-8.0.0 \
    --with-tcl --tcl-prefix ${DEV_VIEW_PATH} \
    --with-fftw --with-fftw3 --fftw-prefix ${DEV_VIEW_PATH} \
    --cuda-gencode arch=compute_90,code=sm_90 --with-single-node-cuda --with-cuda --cuda-prefix ${DEV_VIEW_PATH}
cd Linux-ARM64-g++.cuda && make -j 32

# !!! BEGIN OPTIONAL !!!
# Configure NAMD build for CPU
cd ..
./config Linux-ARM64-g++ \
    --charm-arch mpi-linux-arm8-smp --charm-base $PWD/charm-8.0.0 \
    --with-tcl --tcl-prefix ${DEV_VIEW_PATH} \
    --with-fftw --with-fftw3 --fftw-prefix ${DEV_VIEW_PATH}
cd Linux-ARM64-g++ && make -j 32
# !!! END OPTIONAL !!!

cd ..
export LD_LIBRARY_PATH=${DEV_VIEW_PATH}/lib/

# Run NAMD (GPU version)
Linux-ARM64-g++.cuda/namd3 <NAMD_OPTIONS>

# !!! BEGIN OPTIONAL !!!
# Run NAMD (CPU version)
Linux-ARM64-g++/namd3 <NAMD_OPTIONS>
# !!! END OPTIONAL !!!

The optional section provides instructions on how to build a CPU-only build, should you need it (for constant pH MD simulations, for example).

Useful Links¶

NAMD Spack package
NAMD Tutorials
Charm++ Spack package
Running Charm++ Programs
What you should know about NAMD and Charm++ but were hoping to ignore by J. C. Phillips