Rosetta-Sapelo2: Difference between revisions
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'''Example of shell scripts to run Rosetta MPI on the batch partition:''' | '''Example of shell scripts to run Rosetta MPI on the batch partition:''' | ||
To run minirosetta.mpi.linuxiccrelease as a parallel job, using e.g. 1 node and | To run minirosetta.mpi.linuxiccrelease as a parallel job, using e.g. 1 node and 24 cores per node (sub.sh) | ||
<pre class="gscript"> | <pre class="gscript"> | ||
# | #!/bin/bash | ||
# | #SBATCH --job-name=j_rosetta | ||
# | #SBATCH --partition=batch | ||
# | #SBATCH --nodes=1 | ||
# | #SBATCH --ntasks=1 | ||
# | #SBATCH --cpus-per-task=24 | ||
# | #SBATCH --mem=100gb | ||
# | #SBATCH --time=120:00:00 | ||
# | #SBATCH --output=log.%j.out | ||
#SBATCH --error=log.%j.err | |||
#SBATCH --mail-user=username@uga.edu | |||
#SBATCH --mail-type=ALL | |||
cd $ | cd $SLURM_SUBMIT_DIR | ||
module load Rosetta/2020.28.61328-intel-2019b | module load Rosetta/2020.28.61328-intel-2019b | ||
mpirun minirosetta.mpi.linuxgccrelease [options] | mpirun minirosetta.mpi.linuxgccrelease [options] | ||
Revision as of 14:16, 6 April 2021
Category
Chemistry
Program On
Sapelo2
Version
2020.28.61328
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.
Example of shell scripts to run Rosetta MPI on the batch partition:
To run minirosetta.mpi.linuxiccrelease as a parallel job, using e.g. 1 node and 24 cores per node (sub.sh)
#!/bin/bash #SBATCH --job-name=j_rosetta #SBATCH --partition=batch #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=24 #SBATCH --mem=100gb #SBATCH --time=120:00:00 #SBATCH --output=log.%j.out #SBATCH --error=log.%j.err #SBATCH --mail-user=username@uga.edu #SBATCH --mail-type=ALL cd $SLURM_SUBMIT_DIR module load Rosetta/2020.28.61328-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