Fix email addresses and remove module load spartan_2019

.gitignore

@@ -43,3 +43,4 @@ Trimmomatic/.backup
 *.odb
 *.csv
 *.data
+*.inp

ABRicate/2015ABRicate-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

ABRicate/2019ABRicate-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

ABySS/2015ABySS-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

ABySS/2019ABySS-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

ADMIXTURE/2015ADMIXTURE-test.slurm

@@ -11,7 +11,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

ADMIXTURE/2019ADMIXTURE-test.slurm

@@ -11,7 +11,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

AFNI/2015AFNI-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

AFNI/2019AFNI-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

ANSYS/2dstress/2015ansys2dstress.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYS2dstress"
+
+# 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 < 2dstress.inp > 2dstress.out

ANSYS/2dtruss/2015ansys2dtruss.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYS2drtuss"
+#SBATCH --time=0:15:00
+
+# 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 < 2dtruss.inp > 2dtruss.out

ANSYS/3dbike/2015ansys3dbike.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYS3dbike"
+#SBATCH	--time=0:15:00
+
+# 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 < 3dbike.inp > 3dbike.out

ANSYS/Array/2015ansysArray.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYSArray"
+#SBATCH --time=0:15:00
+#SBATCH --array=1-2
+
+echo "Starting task $SLURM_ARRAY_TASK_ID"
+DIR=$(sed -n "${SLURM_ARRAY_TASK_ID}p" ansysdirs)
+cd $DIR
+
+
+# Note this order has to be kept. It's horrible, but it works.
+module purge
+source /usr/local/module/spartan_old.sh
+module load X11/20190311-spartan_gcc-6.2.0
+module load motif/2.3.5-goolf-2015a
+module load libXpm/3.5.11-goolf-2015a
+module load ANSYS_CFD/19.0
+
+# Place the code to execute here
+
+input=*.inp
+output=$(echo $input | cut  -d'.' -f 1)
+ansys190 -b < $input > ${output}.out
+

ANSYS/Array/ansysdirs

+../2dtruss
+../3dbike

ANSYS/Axisymmetry/2015ansysAxisymmetry.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYSAxisymmetry"
+#SBATCH --time=0:15:00
+
+# 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 < Axisymmetry.inp > Axisymmetry.out
+

ANSYS/BeamSolid/2015ansysbeam.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYSbeam"
+
+# 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 < beamsolid.inp > beamsolid.db

ANSYS/BucklingE/2015ansysBuckling1.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ansysBuckling"
+#SBATCH --time=0:15:00
+
+# 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 < Buckling1.inp > Buckling1.out

ANSYS/BucklingN/2015ansysBuckling2.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ansysBuckling"
+#SBATCH --time=0:15:00
+
+# 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 < Buckling2.inp > Buckling2.out

ANSYS/DistLoad/2015ansysDistLoad.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ansysDistLoad"
+#SBATCH --time=0:15:00
+
+# 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 < DistLoad.inp > DistLoad.out

ANSYS/DynamicHarmonic/2015ansysDynamicHarmonic.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ansysDynamicHarmonic"
+#SBATCH --time=0:15:00
+
+# 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 < DynamicHarmonic.inp > DynamicHarmonic.out

ANSYS/DynamicModal/2015ansysDynamicModal.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ansysDynamicModal"
+#SBATCH --time=0:15:00
+
+# 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 < DynamicModal.inp > DynamicModal.out

ANSYS/DynamicTransient/2015ansysDynamicTransient.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ansysDynamicTransient"
+#SBATCH --time=0:15:00
+
+# 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 < DynamicTransient.inp > DynamicTransient.out

ANSYS/NonLinearA/2015ansysNonLinearA.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ansysNonLinearA"
+#SBATCH --time=0:15:00
+
+# 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 < NonLinearA.inp > NonLinearA.out

ANSYS/NonLinearB/2015ansysNonLinearB.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ansysNonLinearB"
+#SBATCH --time=0:15:00
+
+# 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 < NonLinearB.inp > NonLinearB.out

ANSYS/2015ansys.slurm → ANSYS/OscillatingPlate/2015ansysplate.slurm

 #!/bin/bash
-#SBATCH --job-name="2015ANSYStest"
+#SBATCH --job-name="2015ANSYSplate"
 
 # Note this order has to be kept. It's horrible, but it works.
 module purge

ANSYS/Others/pbs-cfx-benchmark

+#!/bin/bash
+
+#     	job name:
+#PBS -N ansys_benchmark
+
+#     	how many cpus?
+#PBS -l nodes=1:ppn=2
+
+#     	How long to run the job? (hours:minutes:seconds)
+#       You will almost certainly need to change this.
+#PBS -l walltime=00:15:00
+
+#       Wait for license file
+#       Please leave this as it is, makes it a lot safer.
+# PBS -W x=gres:aa_r+1
+#PBS -W x=GRES:aa_r+1%aa_r_hpc+2
+
+#     	Environmental varibles to make it work:
+
+module load ansys/145
+
+cd $PBS_O_WORKDIR
+ 
+# Launching the job!
+
+NODES=$(cat $PBS_NODEFILE | sort | uniq -c | awk '{print $2 "*" $1}' | tr '\n' ',' | sed 's/,$//')
+
+echo "This job is allocated on $NODES"
+
+cfx5solve  -def Benchmark.def -parallel -par-dist $NODES

ANSYS/Others/pbs-script-cfx

+#!/bin/bash
+
+# ------------------------------------
+#       ANSYS - CFX FSI script.
+#       All you need change is wall time and name of input files.
+#       And possibly the job name.
+# -----------------------------------
+
+# 	pbs launching script example for ANSYS job:
+
+#     	job name: --- Change this if you like
+#PBS -N ansys_job_01
+
+#     	how many cpus? --- Probably best choice.
+#PBS -l nodes=8
+
+#     	How long to run the job? (hours:minutes:seconds)
+#       You will almost certainly need to change this.
+#PBS -l walltime=00:30:00
+
+#     	Name of output file:
+# PBS -o ansys_test_job_02.txt
+
+#       Wait for license file
+#       Please leave this as it is, makes it a lot safer.
+# PBS -l software=aa_r+1
+#PBS -W x=GRES:aa_r+1%aa_r_hpc+2
+
+#	For CFX use only
+# PBS -l software=cfx_par_proc+8
+
+#     	Environmental varibles to make it work:
+
+  module load ansys/145
+
+  cd $PBS_O_WORKDIR
+ 
+#     	Launching the job!
+
+NODES=$(cat $PBS_NODEFILE | sort | uniq -c | awk '{print $2 "*" $1}' | tr '\n' ',' | sed 's/,$//')
+
+echo "This job is allocated on $NODES"
+
+cfx5solve  -def  OscillatingPlate.def -ansys-input  OscillatingPlate.inp -parallel -par-dist $NODES

ANSYS/README.md

-Please note that this tutorial is not complete yet!
+# ANSYS Job Submission Examples
+
+## Introduction
+
+All the examples here use the old build system and ANSYS_CFD v19.0 (2019).
+
+The example OscillatingPlate is a classic from ANSYS involving a plate in a Fluid-Structure Interaction (FSI). The original example for High 
+Performance Computing was from the Victorian Partnership for Advanced Computing (2015) using TORQUE PBS and then ported to the Univeristy of 
+Melbourne using the Slurm Workload Manager.
+
+All other examples come from the rather impressive ANSYS tutorial collection from the University of Alberta 
+(https://sites.ualberta.ca/~wmoussa/AnsysTutorial/index.html). As should be evident from these, only part of ANSYS (the computation side for 
+solving) is represented in batch processing. Interactive visualisation and post-processing interpretation requires a different approach.
+
+## Directory Listing
+
+The directories are as follows:
+
+2dtruss: Basic functions will be shown to provide you with a general knowledge of command line codes.	
+
+3dbike: Intermediate ANSYS functions will be shown in detail to provide you with a more general understanding of how to use ANSYS.
+
+2dstress: Boolean operations, plane stress and uniform pressure loading will be introduced in the creation and analysis of this 2-Dimensional 
+object.
+
+Solid: This tutorial will introduce techniques such as filleting, extrusion, copying and working plane orienation to create 3-Dimensional 
+objects.
+
+SelfWeight: Incorporating the weight of an object into the finite element analysis is shown in this simple cantilever beam example.
+
+DistLoad: The application of distributed loads and the use of element tables to extract datal.	
+
+NonLinearA: A large moment is applied to the end of a cantilever beam to explore Geometric Nonlinear behaviour (large deformations).	
+
+BucklingE: Use both Eigenvalue and Nonlinear methods are used to solve a simple buckling problem.	
+
+BucklingN: Use both Eigenvalue and Nonlinear methods are used to solve a simple buckling problem.	
+
+NonLinearB: How to include material nonlinearities in an ANSYS model.	
+
+DynamicModal: Explore the modal analyis capabilities of ANSYS.	
+
+DynamicHarmonic: Explore the harmonic analyis capabilities of ANSYS.	
+
+DynamicTransient: Explore the transient analyis capabilities of ANSYS.	
+
+ThermalPure: Analysis of a pure conduction boundary condition example.	
+
+ThermalMix: Analysis of a Mixed Convection/Conduction/Insulated boundary condition example.	
+
+ThermalTrans: Analysis of heat conduction over time.	
+Axisymmetry: Utilizing axisymmetry to model a 3-D structure in 2-D to reduce computational time.	
+
+Again, it is re-iterated, these are not complete tutorials for ANSYS, just batch examples for the solver computation portion of the various 
+tasks. See the University of Alberta website for complete tutorials.
+
+## Array
+
+A sample directory-driven job array is provided that takes a list of ANSYS directories and runs the jobs simultaneously. This will save you a 
+lot of time!
+
+## Note for admins. 
+
+There will be changes to dependent software due to change in toolchain. Attempts to use a more consistent toolchain for X11 with GCC/4.9.2 
+result in libXp.so.6 shared object file not found. The modules we have in these examples, whilst truly ugly, does work.
+
+Last update: LL20210216

ANSYS/SelfWeight/2015ansysSelfWeight.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYSSelfWeight"
+#SBATCH --time=0:15:00
+
+# 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 < SelfWeight.inp > SelfWeight.out

ANSYS/Solid/2015ansys2dsolid.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ANSYSolid"
+
+# 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 < solid.inp > solid.out

ANSYS/ThermalMix/2015ansysThermalMix.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ThermalMix"
+#SBATCH --time=0:15:00
+
+# 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 < ThermalMix.inp > ThermalMix.out

ANSYS/ThermalPure/2015ansysThermalPure.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ThermalPure"
+#SBATCH --time=0:15:00
+
+# 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 < ThermalPure.inp > ThermalPure.out

ANSYS/ThermalTrans/2015ansysThermalTrans.slurm

+#!/bin/bash
+#SBATCH --job-name="2015ThermalTrans"
+#SBATCH --time=0:15:00
+
+# 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 < ThermalTrans.inp > ThermalTrans.out

ARAGORN/2015ARAGORN-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Array/README

@@ -13,11 +13,24 @@ As with all Slurm directives, the SBATCH command can be applied within the batch
 
 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.
+An alternative would be to read in the files using sed. Insert the following into the job submission script immediately after the Slurm 
+directives. For example;
+
+```
+item=$(ls *.fastq.gz | sed -n ${SLURM_ARRAY_TASK_ID}p)
+```
+
+The example "folders" illustrates the use of datasets in separate folders. This example is derived from Compute/Calcul Canada.
+
+See also the Octave array example in /usr/local/common/Octave for the use of multiple files or scripts as an array.
+
+See also the Array directory in /usr/local/common/ANSYS/Array and /usr/local/common/R/Array for the use of folders as an array.

Array/folders/case_list

+pacific2016
+pacific2017
+atlantic2016
+atlantic2017

Array/folders/directories.slurm

+#!/bin/bash
+#SBATCH --array=1-4
+
+echo "Starting task $SLURM_ARRAY_TASK_ID"
+DIR=$(sed -n "${SLURM_ARRAY_TASK_ID}p" case_list)
+cd $DIR
+
+# Place the code to execute here
+pwd
+ls

BAMM/2015BAMM-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Speciation-extinction analyses

BAMM/2019BAMM-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Speciation-extinction analyses

BBMap/2015BBMap-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

BBMap/2019BBMap-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

BEDTools/2015BEDTools-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

BEDTools/2019BEDTools-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Barrnap/2019Barrnap-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Beast/2015Beast-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Beast/2019Beast-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Bowtie/2019Bowtie-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Busco/2019Busco-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

CPMD/2015CPMD-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

CPMD/2019CPMD-test.slurm

@@ -11,7 +11,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Cufflinks/2015Cufflinks-test.slurm

@@ -9,7 +9,7 @@
 #SBATCH -t 1:00:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Cufflinks/2019Cufflinks-test.slurm

@@ -9,7 +9,7 @@
 #SBATCH -t 1:00:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Delft3D/Delft3D-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 1:00:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Diamond/2019Diamond-test.slurm

@@ -11,7 +11,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

FFTW/2015FFTW-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

FFTW/2019FFTW-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

FastQC/2019FastQC-test1.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the module to check the quality of the sequence data we will use a tool called FastQC.

FastQC/2019FastQC-test2.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the module to check the quality of the sequence data we will use a tool called FastQC.

FastQC/2019FastQCArray.slurm

+#!/bin/bash
+#SBATCH --job-name=FastQCArray
+#SBATCH --array=1-2
+
+# Load the module to check the quality of the sequence data we will use a tool called FastQC.
+module purge
+module load fastqc/0.11.9-java-11.0.2
+
+item=$(ls *.fastq.gz | sed -n ${SLURM_ARRAY_TASK_ID}p)
+
+fastqc $file
+

Fastp/2019Fastp-test.slurm

@@ -11,7 +11,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

FreePascal/FreePascal-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

FreeSurfer/2019FreeSurfer1.slurm

@@ -2,7 +2,6 @@
 #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`

GAMESS/2015GAMESS-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # GAMESS likes memory!

Gaussian/2015g09.slurm

@@ -6,7 +6,6 @@ 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
 

HMMER/2015HMMER-test.slurm

@@ -11,7 +11,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

HMMER/2019HMMER-test.slurm

@@ -11,7 +11,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

HTSlib/2015HTSlib-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

HTSlib/2019HTSlib-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

HTSlib/HTSlib-test.slurm

@@ -11,7 +11,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

ImageMagick/2019ImageMagick-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

JAGS/2015JAGS-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 1:00:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

JAGS/2019JAGS-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 1:00:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

KRAKEN/2019KRAKEN-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

MATLAB/patients/2019matlabpatients.slurm

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

MATLAB/patients/README.md

+## Mathematical Applications and Programming
+
+The following is derived from the Software Carpentries short session on Octave Programming, but modified for the Spartan HPC environment and 
+Slurm job submission (https://bagustris.github.io/octave-tutorial/01-intro/).
+
+Why is it in the MATLAB directory? Because (a) Octave is highly compatiable with MATLAB and this illustrates this and (b) Octave on Spartan 
+does not do graphical output and this example makes extensive use of plots etc.
+
+All these tasks are presented in a manner that can be carried out in an interactive session and with an job submission script.
+
+The example dataset is a study of inflammation in patients who have been given a new treatment for arthritis. The data sets are stored in a 
+comma-separated value (CSV) format, with each row holding information for a single patient, and each columns represent successive days of the 
+study.
+
+Collect example, start interactive session
+
+```
+cd ~
+cp -r /usr/local/common/MATLAB .
+sinteractive --time=4:0:0 --partition="snowy"
+cd MATLAB/patients/
+```
+
+Load modules, start octave
+
+```
+module load matlab/2020a
+```
+
+Interactive session
+
+Read in the csv file as csv and assign to the variable `patient_data`
+
+`patient_data = csvread('inflammation-01.csv');`
+
+Determine the size of the CSV file, in rows and columns
+`size(patient_data)`
+
+Determine the datatype of the contents
+`class(patient_data)`
+
+Average inflammation for all patients on all days
+`mean(patient_data(:))`
+
+# NOTE!
+# The command mean(patient_data) would compute the mean of each column in our table, and return an array of mean values. 
+# The expression mean(patient_data(:)) flattens the table into a one-dimensional array.
+# The `:` selects all elements along that dimension. So, the index (5, :) selects the elements on row 5, and all 
+# columns—effectively, the entire row. 
+
+# Compute other statistics, like the maximum, minimum and standard deviation.
+disp(['Maximum inflammation: ', num2str(max(patient_data(:)))]);
+disp(['Minimum inflammation: ', num2str(min(patient_data(:)))]);
+disp(['Standard deviation: ', num2str(std(patient_data(:)))]);
+
+# When analyzing data, we often want to look at partial statistics, such as the maximum value per patient or the average value per day. One 
+# way to do this is to assign the data we want to a new temporary array, then ask it to do the calculation:
+
+patient_1 = patient_data(1, :)
+disp(['Maximum inflation for patient 1: ', num2str(max(patient_1))]);
+
+# We don’t actually need to store the row in a variable of its own. Instead, we can combine the selection and the function call:
+
+max(patient_data(1, :))
+
+# What if we need the maximum inflammation for all patients, or the average for each day?
+# To support this, Octave allows us to specify the dimension we want to work on. 
+# If we ask for the average across the dimension 1, we get:
+
+mean(patient_data, 1)
+
+# If we average across axis 2, we get the average inflammation per patient across all days.
+
+mean(patient_data, 2)
+
+
+# Turn off image visibility. We're on the cluser!
+# This can be removed for FastX interactive jobs
+
+figure('visible', 'off')
+
+# A heat map of the data. The imagesc function represents the matrix as a color image. 
+# Every value in the matrix is mapped to a color. Blue regions in this heat map are low values, while red shows high values.
+imagesc(patient_data)
+
+# Let's take a look at the average inflammation over time:
+
+ave_inflammation = mean(patient_data, 1);
+plot(ave_inflammation);
+
+# The maximum and minimum inflammation per day across all patients.
+plot(max(patient_data, [], 1));
+title('Maximum inflammation per day');
+plot(min(patient_data, [], 1));
+title('Minimum inflammation per day');
+
+# It's common to put multiple figures "side-by-side" in a single window for presentation and convenience. 
+# Here's how to use the subplot function to do this:
+
+subplot(1, 2, 1);
+plot(max(patient_data, [], 1));
+ylabel('max')
+
+subplot(1, 2, 2);
+plot(min(patient_data, [], 1));
+ylabel('min')
+

MATLAB/patients/analyze.m

+% script analyze.m
+
+patient_data = csvread('inflammation-01.csv');
+
+disp(['Maximum inflammation: ', num2str(max(patient_data(:)))]);
+disp(['Minimum inflammation: ', num2str(min(patient_data(:)))]);
+disp(['Standard deviation: ', num2str(std(patient_data(:)))]);
+
+ave_inflammation = mean(patient_data, 1);
+
+# You're submitting a job on a cluster!
+figure('visible', 'off')
+
+ave_inflammation = mean(patient_data, 1);
+plot(ave_inflammation);
+
+% save plot to disk as png image:
+print ('ave_inflammation','-dpng')
+
+plot(max(patient_data, [], 1));
+title('Maximum inflammation per day');
+
+% save plot to disk as png image:
+print ('Max_inflammation','-dpng')
+
+plot(min(patient_data, [], 1));
+title('Minimum inflammation per day');
+
+% save plot to disk as png image:
+print ('Min_inflammation','-dpng')
+
+subplot(1, 3, 1);
+plot(ave_inflammation);
+ylabel('average')
+
+subplot(1, 3, 2);
+plot(max(patient_data, [], 1));
+ylabel('max')
+
+subplot(1, 3, 3);
+plot(min(patient_data, [], 1));
+ylabel('min')
+
+% save plot to disk as png image:
+print ('patient_data-01','-dpng')
+
+close()
+

MEGAHIT/2019MEGAHIT-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Math/Math_Basics.md

@@ -58,7 +58,7 @@ $ expr 2 \>= 2		# Greater than or equal to.
 $ expr A = A		# String test for equality, returns true. Ayn Rand likes this.
 $ expr a = A		# String test for equality, returns false. Operating system is case-sensitive.
 $ expr a + b		# Addition of strings generates error.
-$ expr a < b		# Comparison of strings not based on alphabetical order.
+$ expr a \< b		# Comparison of strings is based on alphabetical order.
 
 Strings are not quotes although one may wish to do this to protect against special or metacharacters (e.g., spaces). Quoted numbers 
 are treated like strings. Special operators for strings include length, index, and count of matching characters with regular 

Mathematica/2015mathematica-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Mathematica/2019mathematica-test.slurm

@@ -9,7 +9,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

Metagenome/2019Metagenome.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:45:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

MrBayes/2015MrBayes-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
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 # SBATCH --mail-type=ALL
 
 # Load the environment variables

MrBayes/2019MrBayes-test.slurm

@@ -7,7 +7,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables

MultiQC/2019MultiQC-test.slurm

@@ -10,7 +10,7 @@
 #SBATCH -t 0:15:00
 
 # Specify your email address to be notified of progress.
-# SBATCH --mail-user=youreamiladdress@unimelb.edu
+# SBATCH --mail-user=youremailaddress@unimelb.edu.au
 # SBATCH --mail-type=ALL
 
 # Load the environment variables