batch-shipyard/recipes/NAMD-Infiniband-IntelMPI

NAMD-Infiniband-IntelMPI

This recipe shows how to run NAMD on Linux using the Intel MPI libraries over Infiniband/RDMA Azure VM instances in an Azure Batch compute pool. Execution of this distributed workload requires the use of multi-instance tasks.

Configuration

Please see refer to this set of sample configuration files for this recipe.

Pool Configuration

The pool configuration should enable the following properties:

• vm_size should be a CPU-only RDMA-enabled instance.
• vm_configuration is the VM configuration. Please select an appropriate platform_image with IB/RDMA as supported by Batch Shipyard.
• inter_node_communication_enabled must be set to true
• max_tasks_per_node must be set to 1 or omitted

Global Configuration

The global configuration should set the following properties:

• docker_images array must have a reference to a valid NAMD-Infiniband-IntelMPI image compiled against Intel MPI. This can be alfpark/namd:2.11-icc-mkl-intelmpi which is published on Docker Hub.

Jobs Configuration

The jobs configuration should set the following properties within the tasks array which should have a task definition containing:

• docker_image should be the name of the Docker image for this container invocation, e.g., alfpark/namd:2.11-icc-mkl-intelmpi
• command should contain the mpirun command. If using the sample run_namd.sh script then "/sw/run_namd.sh <benchmark> <steps> <ppn>" can be used to run the included benchmarks:
  • <benchmark> is the benchmark to run: apoa1 or stmv
  • <steps> is the number of steps to execute
  • <ppn> is the number of cores on each compute node. This is optional and, if omitted, will be determined dynamically.
• infiniband can be set to true, however, it is implicitly enabled by Batch Shipyard when executing on a RDMA-enabled compute pool.
• multi_instance property must be defined
  • num_instances should be set to pool_specification_vm_count_dedicated, pool_vm_count_low_priority, pool_current_dedicated, or pool_current_low_priority
  • coordination_command should be unset or null. For pools with native container support, this command should be supplied if a non-standard sshd is required.
  • resource_files array can be empty

Dockerfile and supplementary files

The Dockerfile for the Docker image can be found here. Please note that you must agree with the NAMD license before using this Docker image.