Role and Dockerfile for disvis and powerfit application

Roles and Dockerfiles to install the disvis or powerfit application:

• https://github.com/haddocking/disvis.git
• https://github.com/haddocking/powerfit.git

The application can be chosen from a role variable.

Introduction

The repository contains ansible-roles that are published in ansible galaxy: https://galaxy.ansible.com/indigo-dc/disvis-powerfit/

The directories docker-disvis and docker-powerfit are linked to dockerhub with automatic build of those 2 images. These images can run disvis or powerfit either in CPUs, or in GPUs, the NVIDIA driver version is show below in the the ansible-role default variable nvidia_driver_version

Requirements

The role LIP-Computing.ansible-role-nvidia should be run before in order to install the nvidia driver and is hosted in the repository:

• https://github.com/LIP-Computing/ansible-role-nvidia

Check the README to install and run the role

Role Variables

The variables that can be passed to this role and a brief description about them are as follows.

1. Haddocking application: disvis or powerfit
   • haddock_app: Default = disvis
2. URL with opencl headers
   • opencl_url: Default = http://www.lip.pt/~david/cl_include.tgz

Install the Playbook

To install the role:

$ ansible-galaxy install indigo-dc.disvis-powerfit

Run the playbook

An example of playbook for the disvis:

---
- hosts: localhost
  roles:
    - { role: indigo-dc.disvis-powerfit haddock_app: disvis }

Or execute:

$ ansible-playbook /etc/ansible/roles/indigo-dc.disvis-powerfit/tests/disvis.yml

An example of playbook for the powerfit:

---
- hosts: localhost
  roles:
    - { role: indigo-dc.disvis-powerfit, haddock_app: powerfit }

Or execute:

$ ansible-playbook /etc/ansible/roles/indigo-dc.disvis-powerfit/tests/powerfit.yml

Run the disvis application

The example runs disvis on the CPU with 2 threads:

$ cd /home
$ mkdir out
$ export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:/usr/local/lib64
$ export EX_DIR=/usr/local/disvis/test-cases/PRE5-PUP2-complex
$ disvis ${EX_DIR}/O14250.pdb ${EX_DIR}/Q9UT97.pdb ${EX_DIR}/restraints.dat -p 2 -a 20.0 -vs 2 -d /home/out

To run in the GPU:

$ cd /home
$ mkdir out
$ export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:/usr/local/lib64
$ export EX_DIR=/usr/local/disvis/test-cases/PRE5-PUP2-complex
$ disvis ${EX_DIR}/O14250.pdb ${EX_DIR}/Q9UT97.pdb ${EX_DIR}/restraints.dat -g -a 20.0 -vs 2 -d /home/out

Run the powerfit application

The example runs powerfit on the CPU with 2 threads:

$ cd /home
$ ./run-powerfitCPU.sh

To run in the GPU:

$ cd /home
$ ./run-powerfitGPU.sh

License

Apache v2

Author Information

Mario David: [email protected]

LIP Lisbon: http://www.lip.pt

Indigo DataCloud: https://www.indigo-datacloud.eu/

Acknowledgments

• https://github.com/haddocking/disvis.git
• https://github.com/haddocking/powerfit.git