Rosetta-Sapelo2

Category

Chemistry

Program On

Sapelo2

Version

2020.28.61328, 2021.16.61629

Author / Distributor

Please see https://www.rosettacommons.org/

Description

Rosetta is a software suite for macromolecular modeling. Please see https://www.rosettacommons.org/

Running Program

Also refer to Running Jobs on Sapelo2.

For more information on Environment Modules on Sapelo2 please see the Lmod page.

Version 2020.28.61328

Compiled with GNU compilers v. 8.3.0 and Intel MPI libraries v. 2018.5.288. It is installed in /apps/eb/Rosetta/2020.28.61328-intel-2019b, and the binaries (mpi) are available in /apps/eb/Rosetta/2020.28.61328-intel-2019b/bin .

To use this version of rosetta, first load the module with

module load Rosetta/2020.28.61328-intel-2019b

This module also loads the gcc/8.3.0 and the Intel MPI module that it needs.

Version 2021.16.61629

To use this version of rosetta, first load the module with

module load Rosetta/2021.16.61629-intel-2019b

This module also loads the gcc/8.3.0 and the Intel MPI module that it needs.

Example of shell scripts to run Rosetta MPI version 2020.28.61328 on the batch partition:

To run minirosetta.mpi.linuxiccrelease as a parallel job, using e.g. 2 nodes and 48 cores (24 cores per node) (sub.sh)

#!/bin/bash
#SBATCH --job-name=j_rosetta          # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --constraint=EDR              # node feature
#SBATCH --nodes=2                     # Number of nodes
#SBATCH --ntasks=48                   # Number of MPI ranks
#SBATCH --ntasks-per-node=24          # How many tasks on each node
#SBATCH --cpus-per-task=1             # Number of cores per MPI rank 
#SBATCH --mem-per-cpu=500mb           # Memory per processor
#SBATCH --time=48:00:00               # Time limit hrs:min:sec
#SBATCH --output=log.%j.out           # Standard output log
#SBATCH --error=log.%j.err            # Standard error log
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail


cd $SLURM_SUBMIT_DIR

module load Rosetta/2020.28.61328-intel-2019b

mpirun minirosetta.mpi.linuxiccrelease [options] 

where [options] needs to be replaced by the options and input files that you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.

Example of shell scripts to run Rosetta MPI version 2021.16.61629 on the batch partition:

To run minirosetta.mpi.linuxgccrelease as a parallel job, using e.g. 2 nodes and 48 cores (24 cores per node) (sub.sh)

#!/bin/bash
#SBATCH --job-name=j_rosetta          # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --constraint=EDR              # node feature
#SBATCH --nodes=2                     # Number of nodes
#SBATCH --ntasks=48                   # Number of MPI ranks
#SBATCH --ntasks-per-node=24          # How many tasks on each node
#SBATCH --cpus-per-task=1             # Number of cores per MPI rank 
#SBATCH --mem-per-cpu=500mb           # Memory per processor
#SBATCH --time=48:00:00               # Time limit hrs:min:sec
#SBATCH --output=log.%j.out           # Standard output log
#SBATCH --error=log.%j.err            # Standard error log
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail


cd $SLURM_SUBMIT_DIR

module load Rosetta/2021.16.61629-intel-2019b

mpirun minirosetta.mpi.linuxgccrelease [options] 

where [options] needs to be replaced by the options and input files that you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.

Sample job submission command:

sbatch sub.sh

Documentation

Please see https://www.rosettacommons.org/

Installation

• Version 2020.28.61328 - Compiled with GNU compilers v. 8.3.0 and Intel MPI 2018.5.288 libraries.

System

64-bit Linux