July 2020 update

ABAQUS/2015abaqus.slurm

+#!/bin/bash
+#SBATCH --ntasks=1
+#SBATCH --time=0:05:00
+#SBATCH --GRES=abaqus+5
+
+module purge
+source /usr/local/module/spartan_old.sh
+module load ABAQUS/6.14.2-linux-x86_64
+
+# Run the job 'Door'
+abaqus job=Door

ABINIT/2015abinit.slurm

+#!/bin/bash
+#SBATCH --partition=physical
+#SBATCH --time=1:00:00
+module purge
+source /usr/local/module/spartan_old.sh
+module load ABINIT/8.0.8b-intel-2016.u3
+abinit < tbase1_x.files >& log

ABRicate/2015ABRicate-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=2015ABRicate-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load ABRicate/0.8.7-spartan_intel-2017.u2
+
+# The command to actually run the job
+abricate ecoli_rel606.fasta

ABRicate/2019ABRicate-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=ABRicate-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load abricate/0.9.9-perl-5.30.0
+
+# The command to actually run the job
+abricate ecoli_rel606.fasta

ABySS/2015ABySS-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=ABySS-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load ABySS/2.0.2-goolf-2015a
+
+# Assemble a small synthetic data set
+tar xzvf test-data.tar.gz
+sleep 20
+abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'
+
+# Calculate assembly contiguity statistics
+abyss-fac test-unitigs.fa

ABySS/2019ABySS-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=ABySS-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load abyss/2.1.5
+
+# Assemble a small synthetic data set
+tar xzvf test-data.tar.gz
+sleep 20
+abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'
+
+# Calculate assembly contiguity statistics
+abyss-fac test-unitigs.fa

ADMIXTURE/2015ADMIXTURE-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=2015ADMIXTURE-test.slurm
+
+# Run with two threads
+#SBATCH --ntasks=1 
+#SBATCH --cpus-per-task=2
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module load ADMIXTURE/1.3.0
+
+# Untar sample files, run application
+# See admixture --help for options.
+tar xvf hapmap3-files.tar.gz
+admixture -j2 hapmap3.bed 1

ADMIXTURE/2019ADMIXTURE-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=2019ADMIXTURE-test.slurm
+
+# Run with two threads
+#SBATCH --ntasks=1 
+#SBATCH --cpus-per-task=2
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load admixture/1.3.0
+
+# Untar sample files, run application
+# See admixture --help for options.
+tar xvf hapmap3-files.tar.gz
+admixture -j2 hapmap3.bed 1

AFNI/2015AFNI-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=2015AFNI-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load AFNI/linux_openmp_64-spartan_intel-2017.u2-20190219
+
+# Untar dataset and run script
+tar xvf ARzs_data.tgz
+./@ARzs_analyze

AFNI/2019AFNI-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=AFNI-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load afni/18.3.00-python-3.7.4
+
+# Untar dataset and run script
+tar xvf ARzs_data.tgz
+./@ARzs_analyze

AFNI/README

+This is incomplete; still getting the tgz files organised. LL20200707

ANSYS/2015ansys.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYStest"
+
+# Note this order has to be kept. It's horrible, but it works.
+module purge
+source /usr/local/module/spartan_old.sh
+module load X11/20190311-spartan_gcc-6.2.0
+module load motif/2.3.5-goolf-2015a
+module load libXpm/3.5.11-goolf-2015a
+module load ANSYS_CFD/19.0
+
+ansys190 -b < OscillatingPlate.inp > OscillatingPlate.db

ARAGORN/2015ARAGORN-test.slurm

+#!/bin/bash
+
+# Job name and partition
+#SBATCH --job-name=ARAGORN-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load ARAGORN/1.2.36-GCC-4.9.2
+
+# Run the application
+
+aragorn -o results sample.fa

Amber/2015amber.slurm

+#!/bin/bash
+# Add your project account details here.
+# SBATCH --account=XXXX
+#SBATCH --partition=gpgpu
+#SBATCH --ntasks=4
+#SBATCH --time=1:00:00
+
+module purge
+source /usr/local/module/spartan_old.sh
+module load Amber/16-gompi-2017b-CUDA-mpi
+ 
+srun /usr/local/easybuild/software/Amber/16-gompi-2017b-CUDA-mpi/amber16/bin/pmemd.cuda_DPFP.MPI  -O -i mdin -o mdout -inf mdinfo -x mdcrd -r restrt

Array/README

+Array job indices can be specified in various number of ways.
+
+A job array with index values between 0 and 31:
+#SBATCH --array=0-31
+
+A job array with index values of 1, 2, 5, 19, 27:
+#SBATCH --array=1,2,5,19,27
+
+A job array with index values between 1 and 7 with a step size of 2 (i.e. 1, 3, 5, 7):
+#SBATCH --array=1-7:2
+
+As with all Slurm directives, the SBATCH command can be applied within the batch script or on the command line.
+
+To convert a directory of files to include an array ID see the following example:
+
+$ touch aaa.fastq.gz bbb.fastq.gz ccc.fastq.gz ddd.fastq.gz
+$ ls
+aaa.fastq.gz  bbb.fastq.gz  ccc.fastq.gz  ddd.fastq.gz
+$ n=1; for f in *fastq.gz; do mv "$f" "$((n++))$f"; done
+$ ls
+1aaa.fastq.gz  2bbb.fastq.gz  3ccc.fastq.gz  4ddd.fastq.gz
+
+See also the Octave array example in /usr/local/common/Octave.

Array/array.slurm

+#!/bin/bash
+#SBATCH --job-name="file-array"
+#SBATCH --ntasks=1
+#SBATCH --time=0-00:15:00
+#SBATCH --array=1-5
+# Note: SLURM defaults to running jobs in the directory
+# where they are submitted, no need for $PBS_O_WORKDIR
+mkdir ${SLURM_ARRAY_TASK_ID}

BAMM/2015BAMM-test.slurm

+#!/bin/bash
+
+# Job name and partition
+#SBATCH --job-name=2015BAMM-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Speciation-extinction analyses
+# You must have an ultrametric phylogenetic tree. 
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load BAMM/2.5.0-spartan_intel-2017.u2
+
+# Example from: `http://bamm-project.org/quickstart.html`
+
+# To run bamm you must specify a control file.
+# The following is for diversification.
+# You may wish to use traits instead
+# bamm -c template_trait.txt
+bamm -c template_diversification.txt  
+
+
+
+

BAMM/2019BAMM-test.slurm

+#!/bin/bash
+
+# Job name and partition
+#SBATCH --job-name=BAMM-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Speciation-extinction analyses
+# You must have an ultrametric phylogenetic tree. 
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load bamm/2.5.0
+
+# Example from: `http://bamm-project.org/quickstart.html`
+
+# To run bamm you must specify a control file.
+# The following is for diversification.
+# You may wish to use traits instead
+# bamm -c template_trait.txt
+bamm -c template_diversification.txt  
+
+
+
+

BBMap/2015BBMap-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=2015BBMap-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load BBMap/36.62-intel-2016.u3-Java-1.8.0_71  
+
+# See examples at:
+# http://seqanswers.com/forums/showthread.php?t=58221
+
+reformat.sh in=sample1.fq out=processed.fq
+

BBMap/2019BBMap-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=BBMap-test.slurm
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load bbmap/38.76
+
+# See examples at:
+# http://seqanswers.com/forums/showthread.php?t=58221
+
+reformat.sh in=sample1.fq out=processed.fq
+

BEDTools/2015BEDTools-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=BEDTools-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load BEDTools/2.28.0-spartan_intel-2017.u2 
+
+# BEDTools has an extensive test suite; but the tests assumes the wrong
+# location for the application!
+
+# So all these tests need to be be modified to include:
+# BT=$(which bedtools)
+cp -r /usr/local/easybuild/software/BEDTools/2.27.1-intel-2017.u2/test/* .
+
+find ./ -type f -exec sed -i -e 's/${BT-..\/..\/bin\/bedtools}/$(which bedtools)/g' {} \;
+
+sh test.sh
+
+# Specific example commands available here:
+# https://bedtools.readthedocs.io/en/latest/content/example-usage.html#bedtools-intersect

BEDTools/2019BEDTools-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=BEDTools-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load bedtools/2.27.1
+
+# BEDTools has an extensive test suite; but the tests assumes the wrong
+# location for the application!
+
+# So all these tests need to be be modified to include:
+# BT=$(which bedtools)
+cp -r /usr/local/easybuild/software/BEDTools/2.27.1-intel-2017.u2/test/* .
+
+find ./ -type f -exec sed -i -e 's/${BT-..\/..\/bin\/bedtools}/$(which bedtools)/g' {} \;
+
+sh test.sh
+
+# Specific example commands available here:
+# https://bedtools.readthedocs.io/en/latest/content/example-usage.html#bedtools-intersect

BLAST/2015blast.slurm

+#!/bin/bash
+
+# Set the number of processors that will be used.
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+
+# Set the walltime (5 hrs)
+#SBATCH --time=5:00:00
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load BLAST/2.2.26-Linux_x86_64
+
+# Run the job
+blastall -i ./rat-ests/rn_est -d ./dbs/rat.1.rna.fna -p blastn -e 0.05 -v 5 -b 5 -T F -m 9 -o rat_blast_tab.txt -a 8

BLAST/2019blast.slurm

+#!/bin/bash
+
+# Set the number of processors that will be used.
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+
+# Set the walltime (5 hrs)
+#SBATCH --time=5:00:00
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load blast/2.10.0-linux_x86_64
+
+# Run the job
+blastall -i ./rat-ests/rn_est -d ./dbs/rat.1.rna.fna -p blastn -e 0.05 -v 5 -b 5 -T F -m 9 -o rat_blast_tab.txt -a 8

BWA/2015BWA-test.slurm

+#!/bin/bash
+#SBATCH --time=2:00:00
+
+# Set up enviroment PATH
+module purge
+source /usr/local/module/spartan_old.sh
+module load BWA/0.7.17-intel-2017.u2
+module load SAMtools/1.9-intel-2017.u2
+module load web_proxy
+
+# Get source files
+mkdir -p data/ref_genome
+curl -L -o data/ref_genome/ecoli_rel606.fasta.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/017/985/GCA_000017985.1_ASM1798v1/GCA_000017985.1_ASM1798v1_genomic.fna.gz
+sleep 30
+gunzip data/ref_genome/ecoli_rel606.fasta.gz
+curl -L -o sub.tar.gz https://downloader.figshare.com/files/14418248
+sleep 60
+tar xvf sub.tar.gz
+mv sub/ data/trimmed_fastq_small
+mkdir -p results/sam results/bam results/bcf results/vcf
+
+# Run commands
+bwa index data/ref_genome/ecoli_rel606.fasta
+bwa mem data/ref_genome/ecoli_rel606.fasta data/trimmed_fastq_small/SRR2584866_1.trim.sub.fastq data/trimmed_fastq_small/SRR2584866_2.trim.sub.fastq > results/sam/SRR2584866.aligned.sam
+samtools view -S -b results/sam/SRR2584866.aligned.sam > results/bam/SRR2584866.aligned.bam
+samtools sort -o results/bam/SRR2584866.aligned.sorted.bam results/bam/SRR2584866.aligned.bam
+

BWA/2019BWA-test.slurm

+#!/bin/bash
+#SBATCH --time=2:00:00
+
+# Set up enviroment PATH
+module purge
+module load spartan_2019
+module load foss/2019b
+module load bwa/0.7.17
+module load samtools/1.9
+module load web_proxy
+
+# Get source files
+mkdir -p data/ref_genome
+curl -L -o data/ref_genome/ecoli_rel606.fasta.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/017/985/GCA_000017985.1_ASM1798v1/GCA_000017985.1_ASM1798v1_genomic.fna.gz
+sleep 30
+gunzip data/ref_genome/ecoli_rel606.fasta.gz
+curl -L -o sub.tar.gz https://downloader.figshare.com/files/14418248
+sleep 60
+tar xvf sub.tar.gz
+mv sub/ data/trimmed_fastq_small
+mkdir -p results/sam results/bam results/bcf results/vcf
+
+# Run commands
+bwa index data/ref_genome/ecoli_rel606.fasta
+bwa mem data/ref_genome/ecoli_rel606.fasta data/trimmed_fastq_small/SRR2584866_1.trim.sub.fastq data/trimmed_fastq_small/SRR2584866_2.trim.sub.fastq > results/sam/SRR2584866.aligned.sam
+samtools view -S -b results/sam/SRR2584866.aligned.sam > results/bam/SRR2584866.aligned.bam
+samtools sort -o results/bam/SRR2584866.aligned.sorted.bam results/bam/SRR2584866.aligned.bam
+

Beast/2015Beast-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=BEAST-test.slurm
+
+# Run on 4 cores
+#SBATCH --ntasks=4
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load Beast/2.3.1-intel-2016.u3
+
+beast testRNA.xml

Beast/2019Beast-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=BEAST-test.slurm
+
+# Run on 4 cores
+#SBATCH --ntasks=4
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load beast/2.5.1
+
+beast testRNA.xml

COMSOL/2015comsol.slurm

+#!/bin/bash
+#SBATCH --time=24:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+# You might need an external license file
+# export LM_LICENSE_FILE=port@licenseserver
+
+module purge
+source /usr/local/module/spartan_new.sh 
+module load COMSOL/5.2
+
+# Example batch command from csiro.org.au
+comsol batch -inputfile mymodel.mph  -outputfile mymodelresult.mph -batchlog mybatch.log -j b1 -np 8 -mpmode owner

CPMD/2015CPMD-test.slurm

+#!/bin/bash
+
+# Name and Partition
+#SBATCH --job-name=CPMD-test.slurm
+
+# Run on two cores
+#SBATCH --ntasks=2
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load CPMD/4.3-intel-2018.u4
+
+# Example taken from Axek Kohlmeyer's classic tutorial
+# http://www.theochem.ruhr-uni-bochum.de/~legacy.akohlmey/cpmd-tutor/index.html
+
+srun -n 2 cpmd.x 1-h2-wave.inp > 1-h2-wave.out

CPMD/2019CPMD-test.slurm

+#!/bin/bash
+
+# Name and Partition
+#SBATCH --job-name=CPMD-test.slurm
+
+# Run on four cores
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load cpmd/4.3
+
+# Example taken from Axek Kohlmeyer's classic tutorial
+# http://www.theochem.ruhr-uni-bochum.de/~legacy.akohlmey/cpmd-tutor/index.html
+
+srun -n 4 cpmd.x 1-h2-wave.inp > 1-h2-wave.out

Cufflinks/2015Cufflinks-test.slurm

+#!/bin/bash
+#SBATCH --job-name=Cufflinks-test.slurm
+
+# Multicore
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=2
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 1:00:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load Cufflinks/2.2.1-GCC-4.9.2
+
+# Set the Cufflinks environment
+
+CUFFLINKS_OUTPUT="${PWD}"
+
+cufflinks --quiet --num-threads $SLURM_NTASKS --output-dir $CUFFLINKS_OUTPUT sample.bam
+

Cufflinks/2019Cufflinks-test.slurm

+#!/bin/bash
+#SBATCH --job-name=Cufflinks-test.slurm
+
+# Multicore
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=2
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 1:00:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load cufflinks/20190706
+
+# Set the Cufflinks environment
+
+CUFFLINKS_OUTPUT="${PWD}"
+
+cufflinks --quiet --num-threads $SLURM_NTASKS --output-dir $CUFFLINKS_OUTPUT sample.bam
+

FDS/2015FDS.slurm

+#!/bin/bash
+
+#SBATCH --job-name FDS_example_job
+
+#How many nodes/cores? FDS is MPI enabled and can operate across multiple nodes
+
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+
+#What is the maximum time this job is expected to take? (Walltime) 
+#Format: Days-Hours:Minutes:Seconds
+
+#SBATCH --time=1-24:00:00
+
+module purge
+/usr/local/module/spartan_old.sh
+module load FDS/6.7.0-spartan_intel-2017.u2
+fds pplume5.fds 

FDS/pplume5.fds

+!!! General configuration
+
+&HEAD CHID='pplume5', TITLE='Plume case' /
+      name of the case and a brief explanation
+
+&TIME T_END=10.0 /
+      the simulation will end at 10 seconds
+
+&MISC SURF_DEFAULT='wall', TMPA=25. /
+      all bounding surfaces have
+      a 'wall' boundary condition
+      unless otherwise specified,
+      the ambient temperature is set to 25°C.
+
+&REAC ID='polyurethane', SOOT_YIELD=0.10,
+      N=1.0, C=6.3, H=7.1, O=2.1 /
+      predominant fuel gas for the mixture fraction model
+      of gas phase combustion
+
+!!! Computational domain
+
+&MESH IJK=32,32,16, XB=0.0,1.6,0.0,1.6,0.0,0.8 /
+&MESH IJK=32,32,16, XB=0.0,1.6,0.0,1.6,0.8,1.6 /
+&MESH IJK=32,32,16, XB=0.0,1.6,0.0,1.6,1.6,2.4 /
+&MESH IJK=32,32,16, XB=0.0,1.6,0.0,1.6,2.4,3.2 /
+      four connected calculation meshes
+      and their cell numbers
+
+!!! Properties
+
+&MATL ID='gypsum_plaster', CONDUCTIVITY=0.48,
+      SPECIFIC_HEAT=0.84, DENSITY=1440. /
+      thermophysical properties of 'gypsum plaster' material
+
+&PART ID='tracers', MASSLESS=.TRUE., SAMPLING_FACTOR=1 /
+      a type of Lagrangian particles
+
+&SURF ID='burner', HRRPUA=600.,
+      PART_ID='tracers', COLOR='RASPBERRY' /
+      a type of boundary conditions named 'burner'
+
+&SURF ID='wall', RGB=200,200,200, MATL_ID='gypsum_plaster',
+      THICKNESS=0.012 /
+      a type of boundary conditions named 'wall'
+
+!!! Solid geometry
+
+&VENT XB=0.5,1.1,0.5,1.1,0.1,0.1, SURF_ID='burner' /
+      the 'burner' boundary condition
+      is imposed to a plane face
+
+&OBST XB=0.5,1.1,0.5,1.1,0.0,0.1, SURF_ID='wall' /
+      a solid is created, 'wall' boundary condition
+      is imposed to all its faces
+
+&VENT XB=0.0,0.0,0.0,1.6,0.0,3.2, SURF_ID='OPEN'/
+&VENT XB=1.6,1.6,0.0,1.6,0.0,3.2, SURF_ID='OPEN'/
+&VENT XB=0.0,1.6,0.0,0.0,0.0,3.2, SURF_ID='OPEN'/
+&VENT XB=0.0,1.6,1.6,1.6,0.0,3.2, SURF_ID='OPEN'/
+&VENT XB=0.0,1.6,0.0,1.6,3.2,3.2, SURF_ID='OPEN'/
+      the 'OPEN' boundary condition is imposed to
+      the exterior boundaries of the computational domain
+
+!!! Output
+
+&DEVC XYZ=1.2,1.2,2.9, QUANTITY='THERMOCOUPLE', ID='tc1' /
+      send to output: the data collected by a thermocouple
+&ISOF QUANTITY='TEMPERATURE', VALUE(1)=100.0 /
+      3D contours of temperature at 100°C
+&SLCF PBX=0.8, QUANTITY='TEMPERATURE', VECTOR=.TRUE. /
+      vector slices colored by temperature
+&BNDF QUANTITY='WALL TEMPERATURE' /
+      surface 'WALL_TEMPERATURE' at all solid obstructions
+&TAIL / end of file

FFTW/2015FFTW-test.slurm

+#!/bin/bash
+
+# Name and partition
+#SBATCH --job-name=FFTW-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load FFTW/3.3.6-gompi-2017b
+
+# Compile and execute
+
+g++ -lfftw3 fftw_example.c -o fftw_example
+./fftw_example > results.txt
+
+# Example from : https://github.com/undees/fftw-example

FFTW/2019FFTW-test.slurm

+#!/bin/bash
+
+# Name and partition
+#SBATCH --job-name=FFTW-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load fftw/3.3.8
+
+# Compile and execute
+
+g++ -lfftw3 fftw_example.c -o fftw_example
+./fftw_example > results.txt
+
+# Example from : https://github.com/undees/fftw-example

FSL/2015FSLsample1.slurm

+#!/bin/bash
+#SBATCH -t 0:30:00
+
+module purge
+/usr/local/module/spartan_old.sh
+module load FSL/5.0.9-centos6_64 
+
+# FSL needs to be sourced
+source $FSLDIR/etc/fslconf/fsl.sh
+
+time srun bet /usr/local/common/FSL/intro/structural.nii.gz test1FSL -f 0.1
+

FSL/2015FSLsample2.slurm

+#!/bin/bash
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+#SBATCH -t 0:00:05
+
+module purge
+/usr/local/module/spartan_new.sh
+module load FSL/5.0.9-centos6_64 
+
+# FSL needs to be sourced
+source $FSLDIR/etc/fslconf/fsl.sh
+
+time bet /usr/local/common/FSL/intro/structural.nii.gz test1FSL -f 0.1

FSL/2019FSLsample1.slurm

+#!/bin/bash
+#SBATCH -t 0:30:00
+
+module purge
+module load spartan_2019
+module load foss/2019b
+module load fsl/6.0.1-python-3.7.4
+
+# FSL needs to be sourced
+source $FSLDIR/etc/fslconf/fsl.sh
+
+time srun bet /usr/local/common/FSL/intro/structural.nii.gz test1FSL -f 0.1
+

FSL/2019FSLsample2.slurm

+#!/bin/bash
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+#SBATCH -t 0:30:00
+
+module purge
+module load spartan_2019
+module load foss/2019b
+module load fsl/6.0.1-python-3.7.4
+
+# FSL needs to be sourced
+source $FSLDIR/etc/fslconf/fsl.sh
+
+time srun bet /usr/local/common/FSL/intro/structural.nii.gz test1FSL -f 0.1

FreeSurfer/2015FreeSurfer1.slurm

+#!/bin/bash
+#SBATCH -t 00:15:00
+
+module purge
+/usr/local/module/spartan_old.sh
+module load FreeSurfer/5.3.0-GCC-4.9.2-centos6_x86_64
+
+# Tutorial derived from `https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis`
+
+# Export directories
+export TUTORIAL_DATA=/usr/local/common/FreeSurfer
+export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
+
+# Create contrast; test the change in thickness with age, after removing the effects of gender.
+echo "0 0 0.5 0.5" > lh-Avg-thickness-age-Cor.mtx
+
+# Assemble the precached Data (mris_preproc)
+
+mris_preproc --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage  --hemi lh --out lh.gender_age.thickness.10.mgh
+
+# Assemble the data (non-cached)
+# mris_preproc --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd --target fsaverage --hemi lh --meas thickness --out $SUBJECTS_DIR/glm/lh.gender_age.thickness.00.mg
+
+# mri_surf2surf --hemi lh --s fsaverage --sval lh.gender_age.thickness.00.mgh --fwhm 10 --cortex --tval lh.gender_age.thickness.10B.mgh
+
+mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd dods --C $SUBJECTS_DIR/glm/lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
+
+
+

FreeSurfer/2019FreeSurfer1.slurm

+#!/bin/bash
+#SBATCH -t 01:00:00
+
+module purge
+module load spartan_2019
+module load freesurfer/7.1.0-centos7_x86_64
+
+# Tutorial derived from `https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis`
+
+# Export directories
+export TUTORIAL_DATA=/usr/local/common/FreeSurfer
+export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
+
+# Create contrast; test the change in thickness with age, after removing the effects of gender.
+echo "0 0 0.5 0.5" > lh-Avg-thickness-age-Cor.mtx
+
+# Assemble the precached Data (mris_preproc)
+
+mris_preproc --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage  --hemi lh --out lh.gender_age.thickness.10.mgh
+
+# Assemble the data (non-cached)
+# mris_preproc --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd --target fsaverage --hemi lh --meas thickness --out $SUBJECTS_DIR/glm/lh.gender_age.thickness.00.mg
+
+# mri_surf2surf --hemi lh --s fsaverage --sval lh.gender_age.thickness.00.mgh --fwhm 10 --cortex --tval lh.gender_age.thickness.10B.mgh
+
+mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd $SUBJECTS_DIR/glm/gender_age.fsgd dods --C $SUBJECTS_DIR/glm/lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir

GAMESS/2015GAMESS-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=GAMESS-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# GAMESS likes memory!
+#SBATCH --mem=64G
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load GAMESS-US/20160708-GCC-4.9.2
+
+rungms exam01.inp
+

GDB/2015README

+# This is a directory for memory and program debugging and profiling.
+
+# Launch an interactive job for these examples!
+
+sinteractive nodes=1 --ntasks-per-node=2 --time=1:00:00
+
+# Environment
+
+module purge
+/usr/local/module/spartan_old.sh
+
+# Valgrind
+# The test program valgrindtest.c is form Punit Guron. In this example the memory allocated to the pointer 'ptr' is never freed in the program. 
+# Load the module and compile with debugging symbols.
+
+module load Valgrind/3.13.0-goolf-2015a
+gcc -Wall -g valgrindtest.c -o valgrindtest
+valgrind --leak-check=full ./valgrindtest 2> valgrind.out
+
+# GDB
+# Compile with debugging symbols. A good compiler will give a warning here, and run the program.
+
+gcc -Wall -g gdbtest.c -o gdbtest
+
+$ ./gdbtest
+Enter the number: 3
+The factorial of 3 is 0
+
+# Load the GDB module e.g.,
+
+module load GDB/7.8.2-goolf-2015a
+
+# Launch GDB, set up a break point in the code, and execute
+
+gdb gdbtest
+..
+(gdb) break 10
+(gdb) run
+(gdb) print j
+
+# Basic commands in GDB
+# run = run a program until end, signit, or breakpoint. Use Ctrl-C to stop
+# break = set a breakpoint, either by linenumber, function etc. (shortcut b)
+# list = list the code above and below where the program stopped (shortcut l)
+# continue = restart execution of program where is stopped (shortcut c). 
+# print = print a variable (shortcut p)
+# next, step = after using a signal or breakpoint use next and step to 
+# continue a progame line-by-line.  
+# NB: next will go 'over' the function call to the next line of code, 
+# step will go 'into' the function call (shortcut s)
+#
+# Variables can be temporarily modified with the `set` command
+# e.g., set j=1
+
+
+# The code will hit the breakpoint where you can interrogate the variables.
+# Testing the variable 'j' will show it has not been initialised.
+
+# Create a new file, initialise j to 1, and test again.
+
+cp gdbtest.c gdbtest2.c
+gcc -Wall -g gdbtest2.c -o gdbtest2
+$ ./gdbtest
+
+# There is still another bug! Can you find it? Use GDB to help.
+
+# Once you have fixed the second bug, use diff and patch to fix the original.
+# The -u option provides unified content for both files.
+
+diff -u gdbtest.c gdbtest2.c > gdbpatch.patch
+
+# The patch command will overwrite the source with the modifications 
+# specified in the destination. Test the original again!
+
+patch gdbtest.c gdbpatch.patch
+
+# For Gprof, instrumentation code is inserted with the `-pg` option when 
+# compiled.
+#  
+# GPROF output consists of two parts; the flat profile and the call graph. 
+# The flat profile gives the total execution time spent in each function.
+# The textual call graph, shows for each function; 
+# (a) who called it (parent) and (b) who it called (child subroutines). 
+#
+# Sample progam from Himanshu Arora, published on The Geek Stuff
+# Compile, run the executable.
+# Run the gprof tool. Various output options are available.
+
+gcc -Wall -pg test_gprof.c test_gprof_new.c -o test_gprof
+./test_gprof
+gprof test_gprof gmon.out > analysis.txt
+
+# For parallel applications each parallel process can be given its own
+# output file, using the environment variable GMON_OUT_PREFIX
+# Then run the parallel application as normal.
+# Each grof will create a binary for each profile ID.
+# View the gmon.out's as one
+
+export GMON_OUT_PREFIX=gmon.out
+mpicc -Wall -pg mpi-debug.c -o mpi-debug
+srun -n mpi-debug
+gprof -s mpi-debug gmon.out.*
+
+# Last update 20200721 LL

GDB/2019README

+# This is a directory for memory and program debugging and profiling.
+
+# Launch an interactive job for these examples!
+
+sinteractive --nodes=1 --ntasks-per-node=2 --time=1:00:00
+
+# Environment
+
+module purge
+module load spartan_2019
+module load foss/2019b
+
+# Valgrind
+# The test program valgrindtest.c is form Punit Guron. In this example the memory allocated to the pointer 'ptr' is never freed in the program. 
+# Load the module and compile with debugging symbols.
+
+module load valgrind/3.14.0
+gcc -Wall -g valgrindtest.c -o valgrindtest
+valgrind --leak-check=full ./valgrindtest 2> valgrind.out
+
+# GDB
+# Compile with debugging symbols. A good compiler will give a warning here, and run the program.
+
+gcc -Wall -g gdbtest.c -o gdbtest
+
+$ ./gdbtest
+Enter the number: 3
+The factorial of 3 is 0
+
+# Load the GDB module e.g.,
+
+module load gdb/9.1-python-3.7.4
+
+# Launch GDB, set up a break point in the code, and execute
+
+gdb gdbtest
+..
+(gdb) break 10
+(gdb) run
+(gdb) print j
+
+# Basic commands in GDB
+# run = run a program until end, signit, or breakpoint. Use Ctrl-C to stop
+# break = set a breakpoint, either by linenumber, function etc. (shortcut b)
+# list = list the code above and below where the program stopped (shortcut l)
+# continue = restart execution of program where is stopped (shortcut c). 
+# print = print a variable (shortcut p)
+# next, step = after using a signal or breakpoint use next and step to 
+# continue a progame line-by-line.  
+# NB: next will go 'over' the function call to the next line of code, 
+# step will go 'into' the function call (shortcut s)
+#
+# Variables can be temporarily modified with the `set` command
+# e.g., set j=1
+
+
+# The code will hit the breakpoint where you can interrogate the variables.
+# Testing the variable 'j' will show it has not been initialised.
+
+# Create a new file, initialise j to 1, and test again.
+
+cp gdbtest.c gdbtest2.c
+gcc -Wall -g gdbtest2.c -o gdbtest2
+$ ./gdbtest
+
+# There is still another bug! Can you find it? Use GDB to help.
+
+# Once you have fixed the second bug, use diff and patch to fix the original.
+# The -u option provides unified content for both files.
+
+diff -u gdbtest.c gdbtest2.c > gdbpatch.patch
+
+# The patch command will overwrite the source with the modifications 
+# specified in the destination. Test the original again!
+
+patch gdbtest.c gdbpatch.patch
+
+# For Gprof, instrumentation code is inserted with the `-pg` option when 
+# compiled.
+#  
+# GPROF output consists of two parts; the flat profile and the call graph. 
+# The flat profile gives the total execution time spent in each function.
+# The textual call graph, shows for each function; 
+# (a) who called it (parent) and (b) who it called (child subroutines). 
+#
+# Sample progam from Himanshu Arora, published on The Geek Stuff
+# Compile, run the executable.
+# Run the gprof tool. Various output options are available.
+
+gcc -Wall -pg test_gprof.c test_gprof_new.c -o test_gprof
+./test_gprof
+gprof test_gprof gmon.out > analysis.txt
+
+# For parallel applications each parallel process can be given its own
+# output file, using the environment variable GMON_OUT_PREFIX
+# Then run the parallel application as normal.
+# Each grof will create a binary for each profile ID.
+# View the gmon.out's as one
+
+export GMON_OUT_PREFIX=gmon.out
+mpicc -Wall -pg mpi-debug.c -o mpi-debug
+srun -n 2 mpi-debug
+gprof -s mpi-debug gmon.out.*
+
+# Last update 20200721 LL

Gaussian/2015g09.slurm

+#!/bin/bash
+#SBATCH --job-name="Gaussian Test"
+
+# Change these as appropriate
+INPUT_FILE="test0001.com"
+OUTPUT_FILE="test0001.log"
+
+module purge
+module load spartan_2019
+module load pgi/18.10-gcc-8.3.0-2.32
+module load gaussian/g16c01
+
+g16 < $INPUT_FILE > $OUTPUT_FILE

Gaussian/2015gaussiantests.sh

+#!/bin/bash
+# This script generates slurm scripts for the standard Gaussian tests.
+# To submit the jobs use the following loop:
+# for test in {0001..1044}; do sbatch job${test}.slurm; done
+# Enjoy submitting 1044 Gaussian test jobs!
+# Lev Lafayette, 2017
+for test in {0001..1044}
+do
+cat <<- EOF > job${test}.slurm
+#!/bin/bash
+#SBATCH --job-name="Gaussian Test ${test}"
+#SBATCH --ntasks=1
+#SBATCH --time=12:00:00
+module purge
+/usr/local/module/spartan_old.sh
+module load Gaussian/g09
+g09 < test${test}.com > test${test}.log
+EOF
+done

Gaussian/2019g16c01.slurm

+#!/bin/bash
+#SBATCH --job-name="Gaussian Test"
+
+# Change these as appropriate
+INPUT_FILE="test0001.com"
+OUTPUT_FILE="test0001.log"
+
+module purge
+module load spartan_2019
+module load pgi/18.10-gcc-8.3.0-2.32
+module load gaussian/g16c01
+
+g16 < $INPUT_FILE > $OUTPUT_FILE
+

Gaussian/2019gaussiantests.sh

+#!/bin/bash
+# This script generates slurm scripts for the standard Gaussian tests.
+# To submit the jobs use the following loop:
+# for test in {0001..1044}; do sbatch job${test}.slurm; done
+# Enjoy submitting 1044 Gaussian test jobs!
+# Lev Lafayette, 2017
+# Updated with new build system, 2020, LL
+for test in {0001..1044}
+do
+cat <<- EOF > job${test}.slurm
+#!/bin/bash
+#SBATCH --job-name="Gaussian Test ${test}"
+#SBATCH --ntasks=1
+#SBATCH --time=12:00:00
+module purge
+module load spartan_2019
+module load pgi/18.10-gcc-8.3.0-2.32
+module load gaussian/g16c01
+g16 < test${test}.com > test${test}.log
+EOF
+done

GnuCOBOL/2015README

+# We have GnuCOBOL on Spartan!
+#
+# GnuCOBOL is a free version of the COBOL compiler. Best of all, it's a transpiler, which translates into C.
+#
+# Which means parallel COBOL!
+#
+# Various example programs from Lev Lafayette's talk to Linux Users of Victoria, 
+# GnuCOBOL: A Gnu Life for an Old Workhorse, July 2016
+# http://levlafayette.com/files/2016cobol.pdf
+#
+# Here's some various tests:
+
+sinteractive --time=0:1:00
+module purge
+/usr/local/module/spartan_old.sh
+
+module load gnucobol/3.0-rc1-GCC-6.2.0
+cobc -Wall -x -free hello.cob -o hello-world
+./hello-world
+
+cobc -Wall -m -free hello.cob
+cobc -Wall -C -free hello.cob
+
+cobc -x shortest.cob
+./shortest
+
+cobc -x hello-trad.cob
+./hello-trad
+
+cobc -Wall -x -free luv.cob
+./luv
+
+cobc -Wall -free -x literals.cob
+./literals
+
+cobc -Wall -free -x posmov1.cob
+./posmov1
+
+cobc -Wall -free -x posmov2.cob
+./posmov2
+
+cobc -Wall -free -x redefines.cob
+./redefines
+
+cobc -Wall -free -x renames.cob
+./renames
+
+cobc -Wall -free -x posmov3.cob
+./posmov3
+
+cobc -Wall -free -x posmov4.cob
+cobc -Wall -free -x class.cob
+./posmov4
+./class
+./evaluate

Gurobi/2015gurobi.slurm

+#!/bin/bash
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+module purge
+/usr/local/module/spartan_old.sh
+module load Gurobi/7.0.1
+# export GRB_LICENSE_FILE=/usr/local/easybuild/software/Gurobi/gurobi.lic 
+time gurobi_cl misc07.mps

Gurobi/2019gurobi.slurm

+#!/bin/bash
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+module purge
+module load spartan_2019
+module load gurobi/9.0.0
+time gurobi_cl misc07.mps

HMMER/2015HMMER-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=HMMER-test.slurm
+
+# One task, multi-threaded by default
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+/usr/local/module/spartan_old.sh
+module load HMMER/3.2.1-foss-2017b
+
+# Build a profile from a basic Stockholm alignment file
+hmmbuild globins4.hmm globins4.sto
+
+# Searche a profile against a sequence database.
+hmmsearch globins4.hmm globins45.fa > searchresults.txt
+

HMMER/2019HMMER-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=HMMER-test.slurm
+
+# One task, multi-threaded by default
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load hmmer/3.2.1
+
+# Build a profile from a basic Stockholm alignment file
+hmmbuild globins4.hmm globins4.sto
+
+# Searche a profile against a sequence database.
+hmmsearch globins4.hmm globins45.fa > searchresults.txt
+

HTSlib/2015HTSlib-test.slurm

+#!/bin/bash
+
+# Partition and name
+#SBATCH --job-name=HTSlib-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load HTSlib/1.9-intel-2018.u4
+
+# Start the tabix binary from htslib
+tabix -p gff sample.sorted.gff.gz;
+tabix sample.sorted.gff.gz chr1:10,000,000-20,000,000;

HTSlib/2019HTSlib-test.slurm

+#!/bin/bash
+
+# Partition and name
+#SBATCH --job-name=HTSlib-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load htslib/1.9
+
+# Start the tabix binary from htslib
+tabix -p gff sample.sorted.gff.gz;
+tabix sample.sorted.gff.gz chr1:10,000,000-20,000,000;

Interact/iterate.c

+/* iterate.c */
+/* ------------------------------------------------------------------- */
+/* A deliberately computationally-intensive task for an interative job */
+/* sinteractive */
+/* Compile with gcc iterate.c -o iterate, using your prefered compiler */
+/* Run with time ./iterate for single core */
+/* Original from https://stackoverflow.com/questions/21161175/example-of-very-cpu-intensive-c-function-under-5-lines-of-code */
+/* -----------------------------------------*/
+/* Multi-threaded version */
+/* Now includes pragma for OMP multithreaded */
+/* sinteractive --ntasks=1 --cpus-per-task=2 */
+/* export OMP_NUM_THREADS=2 */
+/* Compile with gcc -fopenmp iterate.c -o iterate with your preferred compiler */
+/* time ./iterate */
+/* Compare the difference! */
+/* ----------------------- */
+
+#include <stdio.h>
+
+int 
+main (void)
+{
+  printf("start\n");
+
+  volatile unsigned long long i;
+  #pragma omp parallel for
+  for (i = 0; i < 100000000000ULL; ++i);
+
+  printf("stop\n");
+
+  return 0;
+}

IntroLinux/hello-multi-core.slurm

+#!/bin/bash
+#SBATCH --ntasks=8
+module purge
+module load OpenMPI/1.10.0-GCC-4.9.2
+time srun mpi-helloworld

IntroLinux/hello-multi-node.slurm

+#!/bin/bash
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-node=4
+module purge
+module load OpenMPI/1.10.0-GCC-4.9.2
+time srun mpi-helloworld

IntroLinux/hello-single-core.slurm

+#!/bin/bash
+module purge
+module load OpenMPI/1.10.0-GCC-4.9.2
+time srun mpi-helloworld

JAGS/2015JAGS-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=JAGS-test.slurm
+
+# Run on four CPUs
+#SBATCH --ntasks=4
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 1:00:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load JAGS/4.3.0-intel-2017.u2 
+
+# Extract the classic BUGS examples
+tar xzvf classic-bugs.tar.gz
+sleep 240 
+cd classic-bugs/vol1
+make -j4 check
+cd ../vol2
+make -j4 check
+

JAGS/2019JAGS-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=JAGS-test.slurm
+
+# Run on four CPUs
+#SBATCH --ntasks=4
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 1:00:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load jags/4.3.0
+
+# Extract the classic BUGS examples
+tar xzvf classic-bugs.tar.gz
+sleep 240 
+cd classic-bugs/vol1
+make -j4 check
+cd ../vol2
+make -j4 check
+

Julia/2015julia.slurm

+#!/bin/bash
+
+module purge
+/usr/local/module/spartan_old.sh
+module load Julia/0.6.0-binary
+julia simple.jl

Julia/2019julia.slurm

+#!/bin/bash
+
+module purge
+module load spartan_2019
+module load julia/1.3.1-linux-x86_64
+julia simple.jl

MATLAB/2015matlab-p.slurm

+#!/bin/bash
+#SBATCH -p physical
+#SBATCH --ntasks=8
+module load MATLAB 
+time matlab -nodesktop -nodisplay -nosplash < tictoc.m
+time matlab -nodesktop -nodisplay -nosplash < tictoc-p.m
+

MATLAB/2015matlab.slurm

+#!/bin/bash
+#SBATCH --ntasks=1
+module purge
+source /usr/local/module/spartan_old.sh
+module load MATLAB/2016a
+matlab -nodesktop -nodisplay -nosplash< polar-plot.m

MATLAB/2019matlab-p.slurm

+#!/bin/bash
+#SBATCH --ntasks=8
+#SBATCH --time=1:0:0
+
+module purge
+module load spartan_2019
+module load matlab/2020a
+
+time matlab -nodesktop -nodisplay -nosplash < tictoc.m
+time matlab -nodesktop -nodisplay -nosplash < tictoc-p.m
+

MATLAB/2019matlab.slurm

+#!/bin/bash
+# One task, one core, default partition, ten minutes walltime
+module purge
+module load spartan_2019
+module load matlab/2020a
+matlab -nodesktop -nodisplay -nosplash< polar-plot.m

MATLAB/parpool.md

+# Managing MATLAB Parpool on Spartan
+
+## What is a parpool
+Short for 'Parallel Pool', it allows MATLAB to parallelise certain operations, reducing computation times. More info can be found at [https://www.mathworks.com/help/parallel-computing/parpool.html](https://www.mathworks.com/help/parallel-computing/parpool.html)
+
+## Create a parpool in your MATLAB code
+Firstly, let's create a MATLAB .m file
+
+```
+$ vim test-parpool.m
+```
+
+Then add
+
+```
+parpool('local', str2num(getenv('SLURM_CPUS_PER_TASK')))
+```
+
+For information about what parpools can do, see [https://hpc.nih.gov/apps/Matlabdct.html](https://hpc.nih.gov/apps/Matlabdct.html)
+
+## Create a batch file
+
+```
+vim test-parpool.slurm
+```
+
+Add to this file
+
+```
+#!/bin/bash
+#SBATCH --cpus-per-task=8
+#SBATCH --time=01:00:00
+
+module load MATLAB/2019a
+
+matlab -nodesktop -nosplash < test-parpool.m
+```
+
+You can use `sbatch` to submit it to the queue
+
+```
+sbatch test-parpool.slurm
+```
+

Mathematica/2015mathematica-test.slurm

+#!/bin/bash
+
+# Name and partition
+#SBATCH --job-name=Mathematica-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load Mathematica/12.0.0
+
+# Read and evaluate the .m file
+# Example derived from: https://pages.uoregon.edu/noeckel/Mathematica.html
+math -noprompt -run "<<test.m" > output.txt

Mathematica/2019mathematica-test.slurm

+#!/bin/bash
+
+# Name and partition
+#SBATCH --job-name=Mathematica-test.slurm
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load mathematica/12.0.0
+
+# Read and evaluate the .m file
+# Examples from https://rcc.uchicago.edu/docs/software/environments/mathematica/index.html
+
+math -run < math-simple.m
+math -run < sample-parallel.m

Mathematica/README

+Example test.m derived from: https://pages.uoregon.edu/noeckel/Mathematica.html
+
+It will work as interactive job with Mathematica, step-wise. 
+

Mathematica/math-simple.m

+A = Sum[i, {i,1,100}]
+B = Mean[{25, 36, 22, 16, 8, 42}]
+Answer = A + B
+Quit[];

Mathematica/sample-parallel.m

+(*Limits Mathematica to requested resources*)
+Unprotect[$ProcessorCount];$ProcessorCount = 8;
+ 
+(*Prints the machine name that each kernel is running on*)
+Print[ParallelEvaluate[$MachineName]];
+
+(*Prints all Mersenne PRime numbers less than 2000*)
+Print[Parallelize[Select[Range[2000],PrimeQ[2^#-1]&]]];

MrBayes/2015MrBayes-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=MrBayes-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
+module load MrBayes/3.2.6-intel-2016.u3
+
+mb Dengue4.env.xml

MrBayes/2019MrBayes-test.slurm

+#!/bin/bash
+
+# To give your job a name, replace "MyJob" with an appropriate name
+#SBATCH --job-name=MrBayes-test.slurm
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:15:00
+
+# Specify your email address to be notified of progress.
+# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-type=ALL
+
+# Load the environment variables
+module purge
+module load spartan_2019
+module load foss/2019b
+module load mrbayes/3.2.7
+
+mb Dengue4.env.xml

ORCA/2015ORCA.slurm

+#!/bin/bash
+#SBATCH --time=0-00:15:00
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+
+module purge
+/usr/local/module/spartan_old.sh
+module load ORCA/4_1_0-linux_x86-64-OpenMPI-3.1.3
+
+$EBROOTORCA/orca orca.in 1> orca.out

ORCA/2019ORCA.slurm

+#!/bin/bash
+#SBATCH --time=0-00:15:00
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+
+module purge
+module load spartan_2019
+module load foss/2019b
+module load orca/4.2.1
+
+$EBROOTORCA/orca orca.in 1> orca.out

Octave/2015octave-array.slurm

+#!/bin/bash
+#SBATCH --job-name="octave-array"
+#SBATCH --ntasks=1
+#SBATCH --time=0-00:15:00
+
+# This is the array
+#SBATCH --array=1-10
+
+module purge
+source /usr/local/module/spartan_old.sh
+module load Octave/3.8.2-goolf-2015a
+
+octave file-${SLURM_ARRAY_TASK_ID}.oct

Octave/2019octave-array.slurm

+#!/bin/bash
+#SBATCH --job-name="octave-array"
+#SBATCH --ntasks=1
+#SBATCH --time=0-00:15:00
+
+# This is the array
+#SBATCH --array=1-10
+
+module purge
+module load spartan_2019
+module load octave/4.2.1
+
+octave file-${SLURM_ARRAY_TASK_ID}.oct
+

OpenFOAM/2015README.md

+# Part I: Preprocess 1 core OpenFOAM Task
+
+This is the most simple process, based on the Lid-driven cavity flow from the OpenFOAM examples 
+(`https://www.openfoam.com/documentation/tutorial-guide/tutorialse2.php#x6-70002.1.1`)
+
+The first example simply copies the cavity example and, from with the blockMesh command from the parameters in `blockMeshDict` in 
+`cavity/cavity/system`.
+
+# Viewing the Mesh
+
+This requires an interactive job.
+
+1. Login with X-windows forwarding, launch the job
+
+ssh username -X
+sbatch openfoam-single-1.slurm
+
+When the job completes check the output e.g.,
+
+less slurm-7655177.out
+
+2. Launch an interactive job with X-windows forwarding
+
+sinteractive --x11=first --time=1:00:00
+
+3. Load the module and source the application parameters.
+
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenFOAM/5.0-intel-2017.u2
+source $FOAM_BASH
+cd cavity/cavity
+
+4. Launch Paraview
+
+paraFoam
+
+Select `Apply` under properties which will launch the Mesh
+After that you can change the Display to use the Representation `Wireframe`.
+
+# Part II Process 1 Core OpenFOAM Task
+
+1. Login with X-windows forwarding, launch the job
+
+ssh username -X
+sbatch openfoam-single-2.slurm
+
+When the job completes check the output	e.g.,
+
+less slurm-7655290.out
+
+2. Launch an interactive job with X-windows forwarding
+
+sinteractive --x11=first --time=1:00:00
+
+3. Load the module and source the application parameters.
+
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenFOAM/5.0-intel-2017.u2
+source $FOAM_BASH
+cd cavity/cavity
+
+4. Launch Paraview
+
+paraFoam
+`Select` Apply under properties which will launch the Mesh
+
+Select the Properties panel for the cavity.OpenFOAM case module. 
+
+After selecting `Apply`, chosing under `Coloring`, `p`, and `Rescale to Data Range` (button next to `Edit`).
+
+Run VCR Controls (play button, top menu)
+
+Change Preset for Blue-Red colour rainbow if desired. 
+
+# OpenFOAM and RapidCFD
+
+Please note that this tutorial is NOT YET COMPLETE
+
+OpenFOAM can use RapidCFD for GPU acceleration. With RapidCFD, you have to specify the devices you want to use.
+
+For example you set `--gres=gpu:1, and --nodes=4`, need to do
+
+`srun -N 4 pulsatilePipe -parallel -devices "(0 0 0 0)" > log0`
+
+The 0's after the devices option are the indices for the GPUs. Each node has 4 GPUs, and the indices range from 0-3 for the 4 GPUs. 0 is the 
+1st GPU on the node, 1 the second etc etc. So you are asking for the 1st GPU on each node.

OpenFOAM/2015openfoam-parallel-1.slurm

+#!/bin/bash
+#SBATCH --job-name="OpenFOAM test"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=6
+#SBATCH --time=0-00:10:00
+
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenFOAM/5.0-intel-2017.u2
+
+source $FOAM_BASH
+
+# OpenFOAM commands go here. For example;
+
+cd LES/oppositeBurningPanels 
+blockMesh
+foamJob decomposePar
+sleep 60
+foamJob -parallel icoFoam

OpenFOAM/2015openfoam-parallel.slurm

+#!/bin/bash
+# SBATCH --account=punim0396
+# SBATCH --partition=punim0396
+#SBATCH --job-name="OpenFOAM test"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=12
+#SBATCH --time=0-00:10:00
+
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenMPI/3.0.0-intel-2017.u2
+
+source $FOAM_BASH
+
+# OpenFOAM commands go here. For example;
+
+srun -n 1 decomposePar -latestTime -force
+srun -n 12  pimpleFoam -parallel
+srun -n 1 recontructPar -latestTime 

OpenFOAM/2015openfoam-single-1.slurm

+#!/bin/bash
+#SBATCH --job-name="OpenFOAM test"
+#SBATCH --partition=physical
+#SBATCH --ntasks=1
+#SBATCH --time=0-00:10:00
+
+module load OpenFOAM/5.0-intel-2017.u2
+
+source $FOAM_BASH
+
+# OpenFOAM commands go here. For example;
+
+cd cavity/cavity
+blockMesh
+

OpenFOAM/2015openfoam-single-2.slurm

+#!/bin/bash
+#SBATCH --job-name="OpenFOAM test"
+#SBATCH --partition=physical
+#SBATCH --ntasks=1
+#SBATCH --time=0-00:10:00
+
+module load OpenFOAM/5.0-intel-2017.u2
+
+source $FOAM_BASH
+
+# OpenFOAM commands go here. For example;
+
+cd cavity/cavity
+blockMesh
+icoFoam

OpenFOAM/2019README.md

+# Part I: Preprocess 1 core OpenFOAM Task
+
+This is the most simple process, based on the Lid-driven cavity flow from the OpenFOAM examples 
+(`https://www.openfoam.com/documentation/tutorial-guide/tutorialse2.php#x6-70002.1.1`)
+
+The first example simply copies the cavity example and, from with the blockMesh command from the parameters in `blockMeshDict` in 
+`cavity/cavity/system`.
+
+# Viewing the Mesh
+
+This requires an interactive job.
+
+1. Login with X-windows forwarding, launch the job
+
+ssh username -X
+sbatch openfoam-single-1.slurm
+
+When the job completes check the output e.g.,
+
+less slurm-7655177.out
+
+2. Launch an interactive job with X-windows forwarding
+
+sinteractive --x11=first --time=1:00:00
+
+3. Load the module and source the application parameters.
+
+module purge
+module load spartan_2019
+module load foss/2019b
+module load openfoam/7
+source $FOAM_BASH
+cd cavity/cavity
+
+4. Launch Paraview
+
+paraFoam
+
+Select `Apply` under properties which will launch the Mesh
+After that you can change the Display to use the Representation `Wireframe`.
+
+# Part II Process 1 Core OpenFOAM Task
+
+1. Login with X-windows forwarding, launch the job
+
+ssh username -X
+sbatch openfoam-single-2.slurm
+
+When the job completes check the output	e.g.,
+
+less slurm-7655290.out
+
+2. Launch an interactive job with X-windows forwarding
+
+sinteractive --x11=first --time=1:00:00
+
+3. Load the module and source the application parameters.
+
+module purge
+module load spartan_2019
+module load foss/2019b
+module load openfoam/7
+source $FOAM_BASH
+cd cavity/cavity
+
+4. Launch Paraview
+
+paraFoam
+`Select` Apply under properties which will launch the Mesh
+
+Select the Properties panel for the cavity.OpenFOAM case module. 
+
+After selecting `Apply`, chosing under `Coloring`, `p`, and `Rescale to Data Range` (button next to `Edit`).
+
+Run VCR Controls (play button, top menu)
+
+Change Preset for Blue-Red colour rainbow if desired. 
+
+# OpenFOAM and RapidCFD
+
+Please note that this tutorial is NOT YET COMPLETE
+
+OpenFOAM can use RapidCFD for GPU acceleration. With RapidCFD, you have to specify the devices you want to use.
+
+For example you set `--gres=gpu:1, and --nodes=4`, need to do
+
+`srun -N 4 pulsatilePipe -parallel -devices "(0 0 0 0)" > log0`
+
+The 0's after the devices option are the indices for the GPUs. Each node has 4 GPUs, and the indices range from 0-3 for the 4 GPUs. 0 is the 
+1st GPU on the node, 1 the second etc etc. So you are asking for the 1st GPU on each node.

OpenFOAM/2019openfoam-parallel-1.slurm

+#!/bin/bash
+#SBATCH --job-name="OpenFOAM test"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=6
+#SBATCH --time=0-00:10:00
+
+module purge
+module load spartan_2019
+module load foss/2019b
+module load openfoam/7
+
+source $FOAM_BASH
+
+# OpenFOAM commands go here. For example;
+
+cd LES/oppositeBurningPanels 
+blockMesh
+foamJob decomposePar
+sleep 60
+foamJob -parallel icoFoam

OpenFOAM/2019openfoam-parallel.slurm

+#!/bin/bash
+# SBATCH --account=punim0396
+# SBATCH --partition=punim0396
+#SBATCH --job-name="OpenFOAM test"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=12
+#SBATCH --time=0-00:10:00
+
+module purge
+module load spartan_2019
+module load foss/2019b
+module load openfoam/7
+
+source $FOAM_BASH
+
+# OpenFOAM commands go here. For example;
+
+srun -n 1 decomposePar -latestTime -force
+srun -n 12  pimpleFoam -parallel
+srun -n 1 recontructPar -latestTime 

OpenFOAM/2019openfoam-single-1.slurm

+#!/bin/bash
+#SBATCH --job-name="OpenFOAM test"
+#SBATCH --partition=physical
+#SBATCH --ntasks=1
+#SBATCH --time=0-00:10:00
+
+module load OpenFOAM/5.0-intel-2017.u2
+
+source $FOAM_BASH
+
+# OpenFOAM commands go here. For example;
+
+cd cavity/cavity
+blockMesh
+

OpenFOAM/2019openfoam-single-2.slurm

+#!/bin/bash
+#SBATCH --job-name="OpenFOAM test"
+#SBATCH --partition=physical
+#SBATCH --ntasks=1
+#SBATCH --time=0-00:10:00
+
+module load OpenFOAM/5.0-intel-2017.u2
+
+source $FOAM_BASH
+
+# OpenFOAM commands go here. For example;
+
+cd cavity/cavity
+blockMesh
+icoFoam

OpenMP/README.save

+# Don't do this on the head node.
+# Many of these examples are from Lev Lafayette, Sequential and Parallel Programming with C and Fortran, VPAC, 2015-2016, ISBN 978-0-9943373-1-3,  https://github.com/VPAC/seqpar 
+
+$ sinteractive --time=6:00:00 --ntasks=1 --cpus-per-task=8
+
+# 2015 modules system ..
+$ module purge
+$ source /usr/local/module/spartan_old.sh
+$ module load GCC/4.9.2
+
+# .. or 2019 modules system
+$ module purge
+$ module load spartan_2019
+$ module load gcc/8.3.0
+
+# Export with the number of threads desired. Note that it is most efficient to have a number of cpus equal to the number of threads.
+
+$ export OMP_NUM_THREADS=8
+
+# Compile with OpenMP directives. These examples use free-form for Fortran e.g., 
+$ gcc -fopenmp helloomp.c -o helloompc
+$ gfortran -fopenmp helloomp.f90 -o helloompf
+
+# Execute the programs
+
+$ ./helloompc
+$ ./helloompf
+
+# Note that creating executables with different compilers requires a different compiler command OpenMP flag. For example:
+
+$ module load intel/2017.u2
+$ icc -qopenmp helloomp.c -o hellompc
+$ ifort -qopenmp helloomp.f90 -o hellompf
+$ ./helloompc
+$ ./helloompf
+
+$ module load PGI/18.5
+$ pgcc -mp helloomp.c -o hellompc
+$ pgf90 -mp helloomp.f90 -o hellompf
+$ ./helloompc
+$ ./helloompf
+
+# Parallel regions can call functions within them with parallel regions. By default, these have 1 thread unless an environment variable is set.
+# This example from Oracle's Sun Studio 12: OpenMP API User's Guide
+
+$ gcc -fopenmp nested.c -o nestedc
+$ export OMP_NESTED=true
+$ ./nestedc
+$ export OMP_NESTED=false
+$ ./nestedc
+
+# The same variable name can have different values with the parallel section and outside it.
+
+$ gcc -fopenmp sharedhello.c -o sharedhelloompc
+$ gfortran -fopenmp sharedhello.f90 -o sharedhelloompf
+$ ./sharedhelloompc
+$ ./sharedhelloompf
+
+# One of the most typical applications is the parallelisation of loops. This includes a worksharing construct, which distributes the execution of the parallel region among the thread team members. There is an implicit barrier at the end of a loop construct, unless a `nowait` clause has been stated. Loop iteration variables are private by default. 
+# Note that this example makes use of "parallel for" and "parallel do". In most cases they are mostly equivalent; parallel spawns a group of threads, while the for/do divides loop iterations between the spawned threads.
+
+$ gcc -fopenmp hello1millomp.c -o hello1millc
+$ gfortran -fopenmp hello1millomp.f90 -o hello1millf
+$ ./hello1millc
+$ ./hello1millf
+
+# Sometimes separating them is a good idea for "thread aware" constructions. e.g.,
+
+#pragma omp parallel
+{ 
+    #pragma omp for
+    for(1...10) // first parallel block
+    {
+    }
+
+    #pragma omp single 
+    {} // single thread processing
+
+    #pragma omp for // second parallel block
+    for(1...10)
+    {
+    }
+
+    #pragma omp single 
+    {} // make some single thread processing again
+}
+
+# There is also the simd directive; this allows loop iterations to be executed on SIMD lanes that are available to the thead.
+# OpenMP only used to exploit multiple threads for multiple cores; the newer simd extention allows use of SIMD instructions on modern CPUs, such as Intel's AVX/SSE and ARM's NEON etc.
+# On Spartan, the AVX-512 instructions are on all of the physical nodes, phi nodes, and bm[053-066].
+# Use sbatch --constraint=avx512 to run specifically on the bm nodes with this.
+
+$ gfortran -fopenmp hello1millsimd.f90 -o hello1millsimdf
+$ gcc -fopenmp hello1millsimd.c -o hello1millsimdc
+
+$ ./hello1millsimdf
+$ ./hello1millsimdc
+
+# The sections construct distributes threads among structured blocks. Note the threadids
+
+gfortran -fopenmp hello3versomp.f90 -o hello3versompf
+gcc -fopenmp hello3versomp.c -o hello3versompc
+
+$ ./hello3versompf
+$ ./hello3versompc
+
+#  The `task` constructs are very useful to mosty efficiently implement parallelism. The general principle is that a thread generates tasks which are then executed according to the runtime system, either immediately or delayed.
+
+$ gfortran -fopenmp colourless-3.f90 -o colourless-3f
+$ gcc -fopenmp colourless-3.c -o colourless-3c
+
+$ ./colourless-3f
+$ ./colourless-3c
+
+# Internal control variables and their interactions with runtime library routines are illustrated by the examples icv1.f90 and icv1.c. 
+# Four ICV's - nest-var, mex-active-levels-var, dyn-var, and nthreads-var - are modified by calls their respective library routines (omp_set_nested(), omp_set_max_active_levels(), omp_set_dynamic(), and omp_set_num_threads()).
+
+$ gcc -fopenmp icv1.c -o icv1c
+$ gfortran -fopenmp icv1.f90 -o icv1f
+$ ./icv1c
+$ ./icv1f
+
+
+# When submitting OpenMP jobs to the cluster don't forget to include the environment variables in the job script!
+# See: hello3vers.slurm

OpenMPI/2015README

+# A number of these examples come from Lev Lafayette, Sequential and Parallel Programming with C and Fortran, VPAC, 2015-2016, ISBN 978-0-9943373-1-3
+
+# You will need to add a partition in each of these Slurm scripts; "physical" is recommended. e.g.,
+# #SBATCH --partition=physical
+
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenMPI/1.10.2-GCC-4.9.2
+
+mpicc mpi-helloworld.c -o mpi-helloworld
+sbatch mpi-helloworld.slurm
+
+mpif90 mpi-helloworld.f90 -o mpi-helloworld
+sbatch mpi-helloworld.slurm
+
+mpicc mpi-ping.c -o mpi-ping
+sbatch mpi-ping.slurm
+
+mpicc mpi-sendrecv.c -o mpi-sendrecv
+sbatch mpi-sendrecv.slurm
+
+mpif90 mpi-sendrecv.f90 -o mpi-sendrecv
+sbatch mpi-sendrecv.slurm
+
+mpicc mpi-pingpong.c -o mpi-pingpong
+sbatch mpi-pingpong.slurm
+
+mpicc mpi-gamethory.c -o mpi-gametheory
+sbatch mpi-gametheory.slurm
+
+# You'll need compile with the math library for this one!
+
+mpicc mpi-particle.c -lm -o mpi-particle
+sbatch mpi-gametheory.slurm
+
+mpicc mpi-group.c -o mpi-group
+sbatch mpi-group.slurm

OpenMPI/2015mpi-gametheory.slurm

+#!/bin/bash
+#SBATCH --job-name="GameTheory"
+#SBATCH --ntasks=2
+#SBATCH --time=0-00:10:00
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenMPI/1.10.2-GCC-4.9.2
+
+srun ./mpi-gametheory

OpenMPI/2015mpi-group.slurm

+#!/bin/bash
+#SBATCH --job-name="MPI Group"
+#SBATCH --ntasks=8
+#SBATCH --time=0-00:10:00
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenMPI/1.10.2-GCC-4.9.2
+
+srun ./mpi-group

OpenMPI/2015mpi-helloworld.slurm

+#!/bin/bash
+#SBATCH --ntasks=16
+
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenMPI/1.10.2-GCC-4.9.2
+
+srun mpi-helloworld

OpenMPI/2015mpi-particle.slurm

+#!/bin/bash
+#SBATCH --job-name="Particle Advector"
+#SBATCH --ntasks=8
+#SBATCH --time=0-00:10:00
+module purge
+/usr/local/module/spartan_old.sh
+module load OpenMPI/1.10.2-GCC-4.9.2
+
+srun ./mpi-particle