RCAC NGC Containers Documentation!

_images/nvidia_logo.jpg

This is the user guide for NGC Container modules deployed in Purdue High Performance Computing clusters. More information about our center is avaiable here (https://www.rcac.purdue.edu).

If you have any question, contact me(Yucheng Zhang) at: zhan4429@purdue.edu

Frequently Asked Questions

Question

  • Answer

Question

  • Answer

Question

  • Answer

Question

  • Answer

Autodock

Introduction

The AutoDock Suite is a growing collection of methods for computational docking and virtual screening, for use in structure-based drug discovery and exploration of the basic mechanisms of biomolecular structure and function. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:autodock

Versions

  • 2020.06

Commands

  • autodock_gpu_128wi

Module

You can load the modules by:

module load ngc
module load autodock

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run autodock on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=autodock
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc autodock

Chroma

Introduction

The Chroma package provides a toolbox and executables to carry out calculation of lattice Quantum Chromodynamics (LQCD). It is built on top of the QDP++ (QCD Data Parallel Layer) which provides an abstract data parallel view of the lattice and provides lattice wide types and expressions, using expression templates, to allow straightforward encoding of LQCD equations. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:chroma

Versions

  • 2018-cuda9.0-ubuntu16.04-volta-openmpi

  • 2020.06

  • 2021.04

Commands

  • chroma

  • hmc

  • mpirun

Module

You can load the modules by:

module load ngc
module load chroma

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run chroma on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=chroma
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc chroma

Gamess

Introduction

The General Atomic and Molecular Electronic Structure Systems (GAMESS) program simulates molecular quantum chemistry, allowing users to calculate various molecular properties and dynamics. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:gamess

Versions

  • 17.09-r2-libcchem

Commands

  • rungms

Module

You can load the modules by:

module load ngc
module load gamess

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run gamess on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gamess
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc gamess

Gromacs

Introduction

GROMACS is a molecular dynamics application designed to simulate Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is designed to simulate biochemical molecules like proteins, lipids, and nucleic acids that have a lot of complicated bonded interactions. More info on GROMACS can be found at http://www.gromacs.org/ For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:gromacs

Versions

  • 2018.2

  • 2020.2

  • 2021.3

  • 2021

Commands

  • gmx

Module

You can load the modules by:

module load ngc
module load gromacs

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run gromacs on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gromacs
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc gromacs

Julia

Introduction

The Julia programming language is a flexible dynamic language, appropriate for scientific and numerical computing, with performance comparable to traditional statically-typed languages. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:julia

Versions

  • v1.5.0

  • v2.4.2

Commands

  • julia

Module

You can load the modules by:

module load ngc
module load julia

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run julia on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=julia
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc julia

Lammps

Introduction

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a software application designed for molecular dynamics simulations. It has potentials for solid-state materials (metals, semiconductor), soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:lammps

Versions

  • 10Feb2021

  • 15Jun2020

  • 24Oct2018

  • 29Oct2020

Commands

  • lmp

  • mpirun

Module

You can load the modules by:

module load ngc
module load lammps

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run lammps on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=lammps
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc lammps

Milc

Introduction

MILC represents part of a set of codes written by the MIMD Lattice Computation (MILC) collaboration used to study quantum chromodynamics (QCD), the theory of the strong interactions of subatomic physics. It performs simulations of four dimensional SU(3) lattice gauge theory on MIMD parallel machines. “Strong interactions” are responsible for binding quarks into protons and neutrons and holding them all together in the atomic nucleus. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:milc

Versions

  • quda0.8-patch4Oct2017

Commands

  • mpirun

  • su3_rhmd_hisq

Module

You can load the modules by:

module load ngc
module load milc

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run milc on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=milc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc milc

Namd

Introduction

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:namd

Versions

  • 2.13-multinode

  • 2.13-singlenode

  • 3.0-alpha3-singlenode

Commands

  • charmrun

  • flipbinpdb

  • flipdcd

  • namd3

  • psfgen

  • sortreplicas

  • vmd

Module

You can load the modules by:

module load ngc
module load namd

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run namd on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=namd
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc namd

Nvhpc

Introduction

The NVIDIA HPC SDK is a comprehensive suite of compilers, libraries and tools essential to maximizing developer productivity and the performance and portability of HPC applications. The NVIDIA HPC SDK C, C++, and Fortran compilers support GPU acceleration of HPC modeling and simulation applications with standard C++ and Fortran, OpenACC directives, and CUDA. GPU-accelerated math libraries maximize performance on common HPC algorithms, and optimized communications libraries enable standards-based multi-GPU and scalable systems programming. Performance profiling and debugging tools simplify porting and optimization of HPC applications, and containerization tools enable easy deployment on-premises or in the cloud. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/nvidia:nvhpc

Versions

  • 20.11

  • 20.7

  • 20.9

  • 21.5

  • 21.9

Commands

  • nvc

  • nvc++

  • nvfortran

  • nvcc

  • pgcc

  • pgc++

  • pgfortran

  • cuda-gdb

  • ncu

  • nv-nsight-cu-cli

  • nvprof

  • nsight-sys

  • nsys

Module

You can load the modules by:

module load ngc
module load nvhpc

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run nvhpc on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=nvhpc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc nvhpc

Paraview

Introduction

ParaView is an open-source, multi-platform data analysis and visualization application. This ParaView container is enabled with the NVIDIA IndeX plugin and the OptiX ray-tracing backend. It can be used in tandem with an official ParaView ]] .. ver .. [[ client or standalone as ParaView Web. Note: no ParaView client GUI in this container. However, ParaView Web Visualizer app is included for a ParaView-like experience inside a web browser. You can start ParaView Web with a ‘pvweb’ command and point your browser to proper http://HOST:PORT/ Default port is 8080 (’–port NNNN’ to change, ‘–help’ for help). For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/nvidia-hpcvis:paraview

Versions

  • 5.9.0

Commands

  • pvserver

  • pvbatch

  • pvpython

  • pvdataserver

  • pvrenderserver

  • mpirun

Module

You can load the modules by:

module load ngc
module load paraview

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run paraview on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=paraview
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc paraview

Pytorch

Introduction

PyTorch is a GPU accelerated tensor computational framework with a Python front end. Functionality can be easily extended with common Python libraries such as NumPy, SciPy, and Cython. Automatic differentiation is done with a tape-based system at both a functional and neural network layer level. This functionality brings a high level of flexibility and speed as a deep learning framework and provides accelerated NumPy-like functionality. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/nvidia:pytorch

Versions

  • 20.02-py3

  • 20.03-py3

  • 20.06-py3

  • 20.11-py3

  • 20.12-py3

  • 21.06-py3

  • 21.09-py3

Commands

  • python

  • python3

Module

You can load the modules by:

module load ngc
module load pytorch

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run pytorch on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pytorch
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc pytorch

Qmcpack

Introduction

QMCPACK is an open-source, high-performance electronic structure code that implements numerous Quantum Monte Carlo algorithms. Its main applications are electronic structure calculations of molecular, periodic 2D and periodic 3D solid-state systems. Variational Monte Carlo (VMC), diffusion Monte Carlo (DMC) and a number of other advanced QMC algorithms are implemented. By directly solving the Schrodinger equation, QMC methods offer greater accuracy than methods such as density functional theory, but at a trade-off of much greater computational expense. Distinct from many other correlated many-body methods, QMC methods are readily applicable to both bulk (periodic) and isolated molecular systems. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:qmcpack

Versions

  • v3.5.0

Commands

  • mpirun

  • qmcpack

Module

You can load the modules by:

module load ngc
module load qmcpack

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run qmcpack on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=qmcpack
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc qmcpack

Quantum_espresso

Introduction

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale based on density-functional theory, plane waves, and pseudopotentials. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:quantum_espresso

Versions

  • v6.6a1

  • v6.7

Commands

  • mpirun

  • pw.x

Module

You can load the modules by:

module load ngc
module load quantum_espresso

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run quantum_espresso on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=quantum_espresso
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc quantum_espresso

Rapidsai

Introduction

The RAPIDS suite of software libraries gives you the freedom to execute end-to-end data science and analytics pipelines entirely on GPUs. It relies on NVIDIA® CUDA® primitives for low-level compute optimization, but exposes that GPU parallelism and high-bandwidth memory speed through user-friendly Python interfaces. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/nvidia:rapidsai:rapidsai

Versions

  • 0.12

  • 0.13

  • 0.14

  • 0.15

  • 0.16

  • 0.17

  • 21.06

  • 21.10

Commands

  • ipython3

  • ipython3

  • jupyter

  • python

  • python3

  • python3.8

Module

You can load the modules by:

module load ngc
module load rapidsai

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run rapidsai on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=rapidsai
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc rapidsai

Relion

Introduction

RELION (for REgularized LIkelihood OptimizatioN) implements an empirical Bayesian approach for analysis of electron cryo-microscopy (Cryo-EM). Specifically it provides methods of refinement of singular or multiple 3D reconstructions as well as 2D class averages. RELION is an important tool in the study of living cells. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:relion

Versions

  • 2.1.b1

  • 3.0.8

  • 3.1.0

  • 3.1.2

  • 3.1.3

Commands

  • mpirun

  • relion

  • relion_refine_mpi

Module

You can load the modules by:

module load ngc
module load relion

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run relion on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=relion
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc relion

Tensorflow

Introduction

TensorFlow is an open-source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) that flow between them. This flexible architecture lets you deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device without rewriting code. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/nvidia:tensorflow

Versions

  • 20.02-tf1-py3

  • 20.02-tf2-py3

  • 20.03-tf1-py3

  • 20.03-tf2-py3

  • 20.06-tf1-py3

  • 20.06-tf2-py3

  • 20.11-tf1-py3

  • 20.11-tf2-py3

  • 20.12-tf1-py3

  • 20.12-tf2-py3

  • 21.06-tf1-py3

  • 21.06-tf2-py3

  • 21.09-tf1-py3

  • 21.09-tf2-py3

Commands

  • python

  • python3

Module

You can load the modules by:

module load ngc
module load tensorflow

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run tensorflow on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=tensorflow
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc tensorflow

Torchani

Introduction

TorchANI is a PyTorch implementation of ANI(Accurate NeurAl networK engINe for Molecular Energies), created and maintained by the Roitberg group. TorchANI contains classes like AEVComputer, ANIModel, and EnergyShifter that can be pipelined to compute molecular energies from the 3D coordinates of molecules. It also include tools to: deal with ANI datasets(e.g. ANI-1, ANI-1x, ANI-1ccx, ANI-2x) at torchani.data, import various file formats of NeuroChem at torchani.neurochem, and more at torchani.utils. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:torchani

Versions

  • 2021.04

Commands

  • mpirun

  • python

  • python3

  • jupyter

Module

You can load the modules by:

module load ngc
module load torchani

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run torchani on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=torchani
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc torchani