2020/07/22 update

ABAQUS/README

+Current Error
+=============
+
+so: undefined symbol: __intel_avx_rep_memcpy
+
+
+Instructions
+============
+
 Abaqus example modified from Lev Lafayette, "Supercomputing with Linux", Victorian Partnership for Advanced Computing, 2015
 
 The Abaqus FEA suite is commonly used in automatic engineering problems using a common model data structure and integrated solver technology. As licensed software it requires a number of license tokens based on the number of cores required, which can be calculated by the simple formula int(5 x N^0.422), where N is the number of cores. Device Analytics offers an online calculator at http://deviceanalytics.com/abaqus-token-calculator .

ABAQUS/abaqus.slurm

-#!/bin/bash
-#SBATCH --ntasts=1
-#SBATCH --time=0:05:00
-#SBATCH --GRES=abaqus+5
-
-module load ABAQUS/6.14.2-linux-x86_64
-
-# Run the job 'Door'
-abaqus job=Door

ABINIT/abinit.slurm

-#!/bin/bash
-#SBATCH --partition=physical
-#SBATCH --time=1:00:00
-#SBATCH --ntasks=8
-module load ABINIT/8.0.8b-intel-2016.u3
-abinit < tbase1_x.files >& log
-

ABRicate/ABRicate-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=ABRicate-test.slurm
-#SBATCH -p cloud
-
-# 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 load ABRicate/0.8.7-spartan_intel-2017.u2
-
-# The command to actually run the job
-abricate ecoli_rel606.fasta

ABySS/ABySS-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=ABySS-test.slurm
-#SBATCH -p cloud
-
-# 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 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

ADMIXTURE/ADMIXTURE-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=ADMIXTURE-test.slurm
-#SBATCH -p cloud
-
-# 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

AFNI/AFNI-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=AFNI-test.slurm
-#SBATCH -p cloud
-
-# 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 load AFNI/linux_openmp_64-spartan_intel-2017.u2-20190219
-
-# Untar dataset and run script
-tar xvf ARzs_data.tgz
-./@ARzs_analyze

ANSYS/ansys.slurm

-#!/bin/bash
-# SBATCH --account=punim0396 
-# SBATCH --partition=punim0396
-#SBATCH --job-name="ANSYS test"
-#SBATCH --partition=physical-cx4
-#SBATCH --ntasks=1
-#SBATCH --time=0-00:10:00
-#SBATCH --gres=aa_r+1%aa_r_hpc+12
-
-module load ansys/19.0-intel-2017.u2
-
-ansys19 -b < OscillatingPlate.inp > OscillatingPlate.db

ARAGORN/ARAGORN-test.slurm

-#!/bin/bash
-
-# Job name and partition
-#SBATCH --job-name=ARAGORN-test.slurm
-#SBATCH -p cloud
-
-# 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 load ARAGORN/1.2.36-GCC-4.9.2
-
-# Run the application
-
-aragorn -o results sample.fa

Amber/amber.slurm

-#!/bin/bash
-# Add your project account details here.
-# SBATCH --account=XXXX
-#SBATCH --partition=gpgpu
-#SBATCH --ntasks=4
-#SBATCH --time=1:00:00
-
-module load Amber/16-gompi-2017b-CUDA-mpi
- 
-mpiexec /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

BAMM/BAMM-test.slurm

-#!/bin/bash
-
-# Job name and partition
-#SBATCH --job-name=BAMM-test.slurm
-#SBATCH -p cloud
-
-# 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 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  
-
-
-
-

BBMap/BBMap-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=ABySS-test.slurm
-#SBATCH -p cloud
-
-# 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 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
-

BEDTools/BEDTools-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=BEDTools-test.slurm
-#SBATCH -p cloud
-
-# 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 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
-
-
-
-# Calculate assembly contiguity statistics
-abyss-fac test-unitigs.fa

BLAST/blast.slurm

-#!/bin/bash
-
-# Set the partition
-
-#SBATCH -p cloud 
-
-# Set the number of processors that will be used.
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=8
-
-# Set the walltime (10 hrs)
-
-#SBATCH --time=10:00:00
-
-# Load the environment variables
-
-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

BWA/BWA-test.slurm

-#!/bin/bash
-#SBATCH --partition=cloud
-#SBATCH --time=2:00:00
-#SBATCH --ntasks=1
-
-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
-
-module load BWA/0.7.17-intel-2017.u2
-
-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/Beast-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=BEAST-test.slurm
-#SBATCH -p cloud
-
-# 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 load Beast/2.3.1-intel-2016.u3
-
-beast Dengue4.env.xml

COMSOL/comsol.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 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/CPMD-test.slurm

-#!/bin/bash
-
-# Name and Partition
-#SBATCH --job-name=CPMD-test.slurm
-#SBATCH -p cloud
-
-# 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 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
-
-mpiexec -np 2 cpmd.x 1-h2-wave.inp > 1-h2-wave.out

Cufflinks/Cufflinks-test.slurm

-#!/bin/bash
-#SBATCH --job-name=Cufflinks-test.slurm
-#SBATCH -p cloud
-
-# Multicore
-#SBATCH --ntasks=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 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
-

Delft3D/Delft3D-test.slurm

 #!/bin/bash
 
 # Name and Partition
-#SBATCH --job-name=ABySS-test.slurm
-#SBATCH -p cloud
-
-# Run on single CPU
-#SBATCH --ntasks=1
+#SBATCH --job-name=Deflt3D-test.slurm
 
 # set your minimum acceptable walltime=days-hours:minutes:seconds
-#SBATCH -t 0:15:00
+#SBATCH -t 1:00:00
 
 # Specify your email address to be notified of progress.
 # SBATCH --mail-user=youreamiladdress@unimelb.edu
@@ -16,6 +12,7 @@
 
 # Load the environment variables
 module purge
+source /usr/local/module/spartan_old.sh
 module load Delft3D/7545-intel-2016.u3
 
 ./run_all_examples.sh

FDS/FDS.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 load FDS
-
-fds inputfile.fds outputfile.fds 

FFTW/FFTW-test.slurm

-#!/bin/bash
-
-# Name and partition
-#SBATCH --job-name=FFTW-test.slurm
-#SBATCH -p cloud
-
-# Run on single CPU. This can run with MPI if you have a bit problem.
-#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 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

FSL/FSLsample1.slurm

-#!/bin/bash
-
-#SBATCH -p cloud
-
-#SBATCH --ntasks=1
-
-#SBATCH -t 0:15:00
-
-module load FSL/5.0.9-centos6_64 
-
-# FSL needs to be sourced
-source $FSLDIR/etc/fslconf/fsl.sh
-
-srun bet /usr/local/common/FSL/intro/structural.nii.gz test1FSL -f 0.1
-

FSL/FSLsample2.slurm

-#!/bin/bash
-#SBATCH -p cloud
-#SBATCH --ntasks=1
-#SBATCH --cpus-per-task=8
-#SBATCH -t 0:00:05
-
-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

FreePascal/FreePascal-test.slurm

@@ -2,7 +2,6 @@
 
 # To give your job a name, replace "MyJob" with an appropriate name
 #SBATCH --job-name=FreePascal-test.slurm
-#SBATCH -p cloud
 
 # Run on single CPU
 #SBATCH --ntasks=1
@@ -15,6 +14,8 @@
 # SBATCH --mail-type=ALL
 
 # Load the environment variables
+module purge
+source /usr/local/module/spartan_old.sh
 
 module load fpc/3.0.4
 

FreePascal/README

-We have a FreePascal compiler on Spartan!
+# We have a FreePascal compiler on Spartan!
 
-`module load fpc/3.0.4`
+module purge
+/usr/local/module/spartan_old.sh
+module load fpc/3.0.4
 
-However, you will also need a fpc.cfg and a fp.cfg, for command-line and gui IDE. This includes PATHs to the various units etc.
-
-These are all included in this directory, along with a simple "Hello World" program.
-
-Compile with 
-
-`fpc hello.pas`
+# However, you will also need a fpc.cfg and a fp.cfg, for command-line and gui IDE. This includes PATHs to the various units etc.
+# These are all included in this directory, along with a simple "Hello World" program.
+#
+# Compile with 
 
+fpc hello.pas

FreeSurfer/FreeSurfer1.slurm

 #!/bin/bash
-#SBATCH -p cloud
 #SBATCH --ntasks=1
 #SBATCH -t 00:15:00
 

FreeSurfer/README

@@ -2,7 +2,7 @@ We don't have the complete set of libraries installed (yet) on the compute nodes
 
 The following is an example session for visualisation.
 
-[lev@cricetomys HPCshells]$ ssh spartan -Y
+[lev@cricetomys HPCshells]$ ssh spartan -X
 ..
 [lev@spartan ~]$ module load FreeSurfer/6.0.0-GCC-4.9.2-centos6_x86_64
 [lev@spartan ~]$ module load X11/20160819-GCC-4.9.2

GAMESS/GAMESS-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=GAMESS-test.slurm
-#SBATCH -p cloud
-
-# Run on 1 cores
-#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
-
-# GAMESS likes memory!
-#SBATCH --mem=64G
-
-# Load the environment variables
-module load GAMESS-US/20160708-GCC-4.9.2
-
-rungms exam01.inp
-

GDB/README

-# This is a directory for memory and program debugging and profiling.
-
-# Launch an interactive job for these examples!
-
-sinteractive --partition=physical --ntasks=2 --time=1:00:00
-
-# 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
-
-gbd 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 undocumented 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 -n2 mpi-debug
-gprof mpi-debug gmon.out.*
-
-# Last update 20190416 LL

Gaussian/g09.slurm

-#!/bin/bash
-#SBATCH --job-name="Gaussian Test"
-#SBATCH --ntasks=1
-#SBATCH --time=0-0:10:00
-
-# Change these as appropriate
-INPUT_FILE="test0001.com"
-OUTPUT_FILE="test0001.log"
-
-module load Gaussian/g09
-
-g09 < $INPUT_FILE > $OUTPUT_FILE

Gaussian/gaussiantests.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 ${test}"
-#SBATCH --partition=cloud
-#SBATCH --ntasks=1
-#SBATCH --time=12:00:00
-module load Gaussian/g09TEST
-g09 < test${test}.com > test${test}.log
-EOF
-done

GnuCOBOL/README

-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:
-
-`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/gurobi.slurm

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

HMMER/HMMER-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=HMMER-test.slurm
-#SBATCH -p cloud
-
-# 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 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
-

HPCshells/.bash_profile

-# .bash_profile
-
-# Get the aliases and functions
-if [ -f ~/.bashrc ]; then
-	. ~/.bashrc
-fi
-
-# User specific environment and startup programs
-
-PATH=$PATH:$HOME/.local/bin:$HOME/bin
-
-export PATH
-
-alias ls='ls -F' 
-alias cp='cp -i' 
-alias ll='ls -laxp' 
-alias lo='exit' 
-
-# Undocumented feature which sets the size to "unlimited". 
-# http://stackoverflow.com/questions/9457233/unlimited-bash-history 
-export HISTFILESIZE= 
-export HISTSIZE= 
-export HISTTIMEFORMAT="[%F %T] " 
-# Change the file location because certain bash sessions truncate .bash_history file upon close. 
-# http://superuser.com/questions/575479/bash-history-truncated-to-500-lines-on-each-login 
-export HISTFILE=~/.bash_eternal_history 
-# Force prompt to write history after every command. 
-# http://superuser.com/questions/20900/bash-history-loss 
-PROMPT_COMMAND="history -a; $PROMPT_COMMAND" 
-
-

HPCshells/README

-AWK examples, from Supercomputing with Linux, Lev Lafayette, VPAC, 2015
-
-awk '$7=="A" { ++count } END { print count }' simple1.txt
-awk '{sum+=$7} END {print sum}' simple2.txt
-awk '{ for(i=1; i<=NF;i++) j+=$i; print j; j=0 }' simple3.txt

HPCshells/backup1.sh

-#!/bin/bash          
-tar cvfz homeuser.tgz /home/lev/

HPCshells/backup2.sh

-#!/bin/bash          
-BU=homeuser$(date +%Y%m%d).tgz 
-tar cvfz $BU $(pwd)

HPCshells/break.sh

-#!/bin/bash
-LIMIT=19  # Upper limit 
-echo 
-echo "Printing Numbers 1 through 20 (but breaks loop at 3)." 
-
-count=0
-
-while [ "$count" -le "$LIMIT" ]
-do
- count=$(($count+1))
-
- if [ "$count" -gt 2 ]
- then
-   break  # Skip entire rest of loop.
- fi
-
- echo -n "$count "
-done
-
-echo; echo; echo
-
-exit 0

HPCshells/case.sh

-#!/bin/bash
-# Handy Extract Program
-	if [[ -f $1 ]]; then
-		case $1 in
-			*.tar.bz2) tar xvjf $1 ;;
-			*.tar.gz) tar xvzf $1 ;;
-			*.bz2) bunzip2 $1 ;;
-			*.rar) unrar x $1 ;;
-			*.gz) gunzip $1 ;;
-			*.tar) tar xvf $1 ;;
-			*.tbz2) tar xvjf $1 ;;
-			*.tgz) tar xvzf $1 ;;
-			*.zip) unzip $1 ;;
-			*.Z) uncompress $1 ;;
-			*.7z) 7z x $1 ;;
-			*) echo "'$1' cannot be extracted via >extract<" ;;
-		esac
-	else
-	echo "'$1' is not a valid file!"
-	fi

HPCshells/check_my_bad_jobs.sh

-#!/bin/bash
-
-if [ "$1" == "-n" ];then
-	NAGIOS=1
-fi
-
-SQUEUE=/usr/local/slurm/latest/bin/squeue
-#SACCT=/usr/local/slurm/latest/bin/sacct
-
-if [ \! -x ${SQUEUE} ]; then
-	if [ "${NAGIOS}" ]; then
-		echo -n "WARNING: "
-	fi
-	echo "ERROR: no squeue - wrong machine?"
-	exit 1
-fi
-
-# If run by a normal user.
-if [ $(id -u) != 0 ]
-then
-	SQUEUE="$SQUEUE -u `whoami`"
-fi
-
-# If we have no jobs queued, abort
-
-if [ -z "$(${SQUEUE} -h)" ]; then
-	if [ "${NAGIOS}" ]; then
-		echo -n "OK: "
-	fi
-	#echo "No jobs queued"
-	exit 0
-fi
-
-ACTIVEJOBS=$(${SQUEUE} -t R -ho "%.15i %D" | fgrep -vw 1 | awk '{print $1}' | tr '\n' ',' | sed -e 's/,$/\n/')
-if [ -z ${ACTIVEJOBS} ]; then
-        if [ "${NAGIOS}" ]; then
-                echo -n "OK: "
-        fi
-        #echo "No bad jobs found"
-        exit 0
-fi
-
-JOBLIST=$(${SQUEUE} -o %i -hs -j ${ACTIVEJOBS} | awk -F. '{print $1}' | uniq -c | fgrep -w 2 | awk '{print $2}' | tr '\n' ',' | sed -e 's/,$//')
-
-export SQUEUE_FORMAT='%.10i %.9P %.15u  %.8D %.8C %N'
-if [ -z "$JOBLIST" ]; then
-
-	if [ "${NAGIOS}" ]; then
-		echo -n "OK: "
-	fi
-	#echo "No bad jobs found"
-	exit 0;
-fi
-
-if [ "${NAGIOS}" ]; then
-	echo "CRITICAL: bad jobs found ${JOBLIST}"
-	exit 2
-fi
-
-echo ""
-echo "The following candidate jobs were found:"
-echo "----------------------------------------"
-${SQUEUE} -o "${SQUEUE_FORMAT}" -j ${JOBLIST}
-echo ""

HPCshells/continue.sh

-#!/bin/bash 
-LIMIT=19  # Upper limit 
-echo 
-echo "Printing Numbers 1 through 20 (but not 3 and 11)." 
-count=0 
-while [ $count -le "$LIMIT" ] 
-do 
- count=$(($count+1)) 
-
- if [ "$count" -eq 3 ] || [ "$count" -eq 11 ]  # Excludes 3 and 11. 
- then 
-   continue      # Skip rest of this particular loop iteration. 
- fi 
-
- echo -n "$count "   # This will not execute for 3 and 11. 
-done
-echo; echo; echo
-exit 0

HPCshells/filetest.sh

-#! /bin/bash 
-# Tests whether a specified file exists of not, illustrates if/then/else.
-file=$1 
-if [ -e $file ] 
-then 
-	echo -e "File $file exists" 
-else 
-	echo -e "File $file doesn't exists" 
-fi 
-exit 0

HPCshells/findemails.sh

-#!/bin/bash
-# Search for email addresses in file, extract, turn into csv with designated file name
-
-# Constants
-INPUT=${1}
-OUTPUT=${2}
-
-# Filecheck Subroutine
-filecheck() {
-if [ ! $INPUT -o ! $OUTPUT ]; then
-    echo "Input file not found, or output file not specified. Exiting script."
-    exit 0
-fi
-}
-
-# Search and Sort Subroutine
-
-searchsort() {
-grep --only-matching -E '[.[:alnum:]]+@[.[:alnum:]]+' $INPUT > $OUTPUT
-sed -i 's/$/,/g' $OUTPUT
-sort -u $OUTPUT -o $OUTPUT
-sed -i '{:q;N;s/\n/ /g;t q}' $OUTPUT
-}
-
-# View and Print Subroutine
-viewprint() {
-echo "Data file extracted to" $OUTPUT
-read -t5 -n1 -r -p "Press any key to see the list, sorted and with unique record"
-if [ $? -eq 0 ]; then
-    echo A key was pressed
-    else
-    echo No key was pressed
-    exit
-fi
-less $OUTPUT | \
-# Output file piped through sort and uniq. 
-# Show that line extension still works with comments.
-sort | uniq
-} 
-
-main() {
-	filecheck
-	searchsort
-	viewprint
-}
-
-# Main function
-main
-exit

HPCshells/functiongeneral.sh

-#!/bin/bash   
-subroutineA() {    
-    codeblock   
-}   
-subroutineB() {   
-    codeblock   
-}   
-main() {   
-    subroutineA   
-    subroutineB   
-}   
-main   
-exit

HPCshells/hellofunction.sh

-#!/bin/bash
-# Enter two names when invoking script
-
-# Define your function here
-# Firstname and Surname are first two parameters.
-
-Hello () {
-   echo "Hello World $Firstname $Surname"
-   return $(bc -l <<< ${#1}+${#2})
-}
-
-# Invoke your function
-Hello ${1} ${2}
-
-# Capture value returned by last command
-echo The name has this many characters $?
-
-exit

HPCshells/here/herescript.sh

-#!/bin/bash
-for a in {1..99}
-do
-cat <<- EOF > job${a}
-#!/bin/bash
-#SBATCH -p cloud
-#SBATCH -N ${a}
-#SBATCH --nodes=1
-#SBATCH --tasks-per-node=1
-#echo $(pwd) >> results.txt
-EOF
-done

HPCshells/hidden.txt

-Talking chamber foxtrot@example.com as shewing an it minutes. Trees fully of blind do. Exquisite favourite at do extensive listening. Improve up 
-musical welcome he. Gay attended vicinity prepared now diverted. Esteems it ye sending reached lima@example.com as. Longer lively her design settle 
-tastes advice mrs off who.indigo@example.com kilo@example.com May indulgence difficulty ham can put especially. Bringing remember echo@example.com for 
-supplied her why was confined. Middleton principle did she procuring extensive believing add. Weather adapted prepare oh is calling. bravo@example.com 
-Far advanced settling say finished raillery. Offered chiefly farther of my no colonel shyness.  hotel@example.com juliet@example.com Inhabit hearing 
-perhaps on ye do no. It maids decay as there he. Smallest on suitable disposed do although blessing he juvenile in. Society or if excited forbade. 
-Here name off yet delta@example.com she long sold easy whom. Differed oh cheerful procured pleasure securing suitable in. Hold rich on an he oh fine. 
-Chapter ability shyness alpha@example.com Inquietude simplicity terminated she compliment remarkably few her nay. The weeks are ham mike@.... asked 
-jokes. Neglected perceived shy nay concluded. Not mile draw plan snug charlie@example.com ext all. Houses latter an valley be indeed wished mere 
-golf@example.com In my. Money doubt oh drawn every or an china
-

HPCshells/loops.txt

-
-# The following are simple examples of a "for" loop.
-# You may require specific software installed e.g., ffmpeg, image magick, liberoffice, calibre.
-# Note the use of command substitution by using $(command); sometimes you will find the use of backticks instead (e.g., for i in * ; do mv $i `echo $i | tr "A-Z" "a-z"` ; done); this is not recommended.
-
-for item in ./*.mp3 ; do ffmpeg -i "${item}" "${item/%mp3/ogg}" ; done
-for item in ./*.jpeg ; do convert "$item" "${item%.*}.png" ; done
-for item in ./*; do convert "$item" -define jpeg:extent=512kb "${item%.*}.jpg" ; done
-for item in ./*.doc ; do /usr/bin/soffice --headless --convert-to-pdf *.doc ; done
-for item in ./*.pdf ' do ebook-convert "$item" "${item}.mobi ; done
-
-# Loops can be applied in a step-wise manner.
-
-$ cd ~/Genomics/shell_data
-$ for filename in *.fastq
-> do
-> head -n 2 ${filename} >> seq_info.txt
-> done
-
-# Basename in a loop.
-# Basename is removing a uniform part of a name from a list of files. 
-# In this case remove the .fastq extension and echo the output.
-
-$ for filename in *.fastq
-> do
-> name=$(basename ${filename} .fastq)
-> echo ${name}
-> done
-
-# What would happen if backticks were used instead of $() for shell substitution? What if someone mistook the backticks for single quotes?
-
-for item in ./* ; do mv $item $(echo $item | tr "A-Z" "a-z") ; done
-
-# What's wrong with spaces in filenames?
-
-touch "This is a long file name"
-for item in $(ls ./*); do echo ${item}; done
-
-# The following examples remove spaces from filenames and apostrophes. The script is designed to prevent expansion from the wildcard, but remember that a `mv` command will overwrite existing files that have the same name.
-
-for item in ./*; do mv "$item" "$(echo "$item" | tr -d " ")"; done
-
-# Finally a few simple examples of loops with conditional tests.
-
-x=1; while [ $x -le 5 ]; do echo "While-do count up $x"; x=$(( $x + 1 )); done
-x=5; until [ $x -le 0 ]; do echo "Until-do count down $x"; x=$(( $x - 1 )); done
-x=1; until [ $x = 6 ]; do echo "Until-do count up $x"; x=$(( $x + 1 )); done
-
-# A while loop that reads in data from a file and runs a command on that data.
-# This is what we used to originally set quotas on home and project directories.
-# The 'read' command reads one line from standard input or a specified file.
-
-while read line; do sleep 5; ./setquota.sh $line; done < quotalist.txt
-
-# when searching for lines that contain a particular sequence in a file (e.g., from grep), reading those lines for processing can be accomplished with the something like the following:
-
-grep sequence datafile.dat | while read -r line ; do   
-    echo "Processing $line"   
-    # Processing code #   
-done   
-
-# Curly braces are used to encapsulate statements or variables with {} or ${}
-
-var		# Set a variable
-$var		# Invoke the variable
-${var}bar	# Invoke the variable, append "bar".
-
-# Example of determining jobs running on a set of nodes.
-
-for host in "spartan-rc"{001..10}; do squeue -w $host; done

HPCshells/lowercaserename.sh

-#!/bin/bash
-# Converts ("moves") all files in the directory run to lowercase.
-for i
-do 
-	mv $i $(echo $i | tr "A-Z" "a-z")
-done

HPCshells/quotes.sh

-#!/bin/bash
-# Illustrates the difference between various types (and lack of) quoting.
-
-SAMPLE="The quick brown fox jumps over the lazy dog"
-echo "Double quotes gives you $SAMPLE"
-echo 'Single quotes gives you $SAMPLE'
-
-exit

HPCshells/select.sh

-#!/bin/bash 
-OPTIONS="Sedimentary Igneous Metamorphic Quit" 
-select opt in $OPTIONS; do 
-	if [ "$opt" = "Quit" ]; then 
-		echo done 
-	exit 
-	elif [ "$opt" = "Sedimentary" ]; then 
-	echo "Sedimentary rocks are formed by sedminentation of particles at or near the Earth's surface and within bodies of water." 
-	elif [ "$opt" = "Igneous" ]; then 
-	echo "Igneous rock forms through the cooling and solidification of magma or lava." 
-	elif [ "$opt" = "Metamorphic" ]; then 
-	echo "Metamorphic rocks are formed by subjecting any rock type -sedimentary rock, igneous rock or another older metamorphic rock - to different temperature and pressure conditions than those in which the original rock was formed." 
-	else 
-	echo "Select again; 1, 2, 3 or 4" 
-	fi 
-done 

HPCshells/simple1.txt

-A C C T A G T
-C A A A G T A
-C A T T A C C
-A G T A C A A

HPCshells/simple2.txt

-1 2 3 4 5 6 7 8 9
-2 3 4 5 6 7 8 9 10
-3 4 5 6 7 8 9 11 12

HPCshells/simple3.txt

-1 2 3 4 5
-6 7 8 9 10
-11 12 13 14 15

HPCshells/sshtrigger.sh

-#! /bin/bash 
-# Access to a system is tested with ping every few minutes until a connection is made whereupon it opens an SSH session.
-read -p "Enter Hostname:" nethost 
-echo $nethost 
-until ping -c 1 $nethost 
-do 
-        sleep 180; 
-done 
-ssh $nethost 

HPCshells/trap.sh

-#!/bin/bash
-# Prevents use of Control-C to prematurely end important script.
-# User can override if they're really, really sure.
-
-    ctrlc_count=0
-
-function test_ctrlc()
-{
-    let ctrlc_count++
-    echo
-    if [[ $ctrlc_count == 1 ]]; then
-        echo "Cntrl-C prevented unless you're sure."
-    elif [[ $ctrlc_count == 2 ]]; then
-        echo "Really sure?"
-    elif [[ $ctrlc_count == 3 ]]; then
-        echo "Really, really sure?"
-    else
-        echo "OK, you're really, really sure.."
-        exit
-    fi
-}
-
-trap test_ctrlc SIGINT
-
-while true
-do
-    echo "This is a sleeping loop. The loop that keeps on sleeping on."
-    sleep 2
-done
-
-exit

HPCshells/warning.sh

-#!/bin/bash
-# This is an abstract example of things that could do wrong!
-#SBATCH --output=/home/example/data/output_%j.out
-
-for for file in /home/example/data/* 
-	do
-        sbatch application ${file}
-	done

HTSlib/HTSlib-test.slurm

@@ -15,6 +15,8 @@
 # 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

Interact/README

@@ -4,10 +4,14 @@
 
 sinteractive --nodes=1 --ntasks-per-node=2 --time=0:10:0
 
-# Example interactive job that specifies cloud partition with X-windows forwarding, after loggin in with secure X-windows forwarding. Note that X-windows forwarding is not highly recommended; try to do compute on Spartan and visualisation locally. However if one absolutely has to visualise from Spartan, the following can be used.
+# Example multi-threaded application. Read file for instructions. Run it single-threaded and multi-threaded.
+
+iterate.c
+
+# Example interactive job with X-windows forwarding, after loggin in with secure X-windows forwarding. Note that X-windows forwarding is not highly recommended; try to do compute on Spartan and visualisation locally. However if one absolutely has to visualise from Spartan, the following can be used.
 
 ssh <username>@spartan.hpc.unimelb.edu.au -X
-sinteractive -p cloud --x11=first
+sinteractive --x11=first
 xclock
 
 # If you are running interactive jobs on GPU partitions you have to include the appropriate QOS commands or account.
@@ -18,7 +22,6 @@ sinteractive --x11=first --partition=deeplearn --qos=gpgpudeeplearn --gres=gpu:v
 
 sinteractive --partition=gpgpu --account=hpcadmingpgpu --gres=gpu:2
 
-
 # If the user is not using a Linux local machine they will need to install an X-windows client, such as Xming for MS-Windows or X11 on Mac OSX from the XQuartz project. 
 
 # If you need to download files whilst on an interactive job you must use the University proxy.

IntroLinux/README

 The file `gattaca.txt` is used for diff examples in the Introductory course and for regular expressions in the Intermediate course.
 
-The file `default.slurm` uses all the default values for slurm on this system; cloud partition, one node, one task, one cpu-per-task, no mail, jobid as job name, ten minute walltime, etc.
+The file `default.slurm` uses all the default values for slurm on this system; physical partition, one node, one task, one cpu-per-task, no mail, jobid as job name, ten minute walltime, etc. It has no specific Slurm directives other than the default!
 
 The file `specific.slurm` runs on a specific node. The list may be specified as a comma-separated list of hosts, a range of hosts (host[1-5,7,...] for example), or a filename. 
 

IntroLinux/constraint.slurm

 #!/bin/bash
-#SBATCH --partition=physical
+# SBATCH --partition=physical
 #SBATCH --constraint=physg4
 #SBATCH --ntasks=72
 # Load modules, show commands etc

IntroLinux/filenames.md

@@ -11,7 +11,7 @@ touch * # What are you thinking?!
 rm * # Really?! You want to remove all files in your directory?
 rm '*' # Safer, but shouldn't have been created in the first place.
 
-# Best to keep to plain, old fashioned, alphanumerics. CamelCase is helpful.
+# Best to keep to plain, old fashioned, alphanumerics. Snake_case or CamelCase is helpful.
 
 touch "This_is_a_long_filename"
 touch "ThisIsALongFilename

IntroLinux/sinfo.md

@@ -2,11 +2,14 @@ The following as some sinfo examples that you might find useful on Spartan.
 
 `sinfo -s`
 
-Provides summary information the system's partitions, from the partition name, whether the partition is available, walltime limits, node information (allocated, idle, out, total), and the nodelist.
+Provides summary information the system's partitions, from the partition name, whether the partition is available, walltime limits, 
+node information (allocated, idle, out, total), and the nodelist.
 
 `sinfo -p $partition`
 
-Provides information about the particular partition specified. Breaks sinfo up for that partition into node states (drain, drng, mix, alloc, idle) and the nodes in that state. `Drain` means that the node is marked for maintenance, and whilst existing jobs will run it will not accept new jobs.
+Provides information about the particular partition specified. Breaks sinfo up for that partition into node states (drain, drng, 
+mix, alloc, idle) and the nodes in that state. `Drain` means that the node is marked for maintenance, and whilst existing jobs will 
+run it will not accept new jobs.
 
 `sinfo -a`
 
@@ -14,6 +17,7 @@ Similar to `sinfo -p` but for all partitions.
 
 `sinfo -n $nodes -p $partition`
 
-Print information only for specified nodes in specified partition; can use comma-separated values or range expression e.g., `sinfo -n spartan-rc[001-010] -p cloud`.
+Print information only for specified nodes in specified partition; can use comma-separated values or range expression e.g., `sinfo 
+-n spartan-bm[001-010]`.
 
 

IntroLinux/specific.slurm

 #!/bin/bash
-#SBATCH --partition=cloud
 #SBATCH --ntasks=1
-#SBATCH --nodelist=spartan-rc005
+#SBATCH --nodelist=spartan-bm005
 # Alternative to exclude specific nodes.
-# SBATCH --exclude=spartan-rc005
+# SBATCH --exclude=spartan-bm005
 echo $(hostname ) $SLURM_JOB_NAME running $SLURM_JOBID >> hostname.txt

JAGS/JAGS-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=JAGS-test.slurm
-#SBATCH -p cloud
-
-# 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 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
-

Julia/julia.slurm

-#!/bin/bash
-#SBATCH -p cloud
-#SBATCH ntasks=1
-
-module load Julia/0.6.0-binary
-julia simple.jl

Julia/simple.jl

@@ -21,8 +21,10 @@ function quadratic2(a::Float64, b::Float64, c::Float64)
 end
 
 vol = sphere_vol(3)
+
 # @printf allows number formatting but does not automatically append the \n to statements, see below
-@printf "volume = %0.3f\n" vol 
+# @printf "volume = %0.3f\n" vol 
+# @printf deprecated, removed from example, 202007LL
 
 quad1, quad2 = quadratic2(2.0, -2.0, -12.0)
 println("result 1: ", quad1)

LAMMPS/README

@@ -8,7 +8,7 @@ unset I_MPI_PMI_LIBRARY
 
 In order to use LAMMPS with the GPU module enabled you need to use the -sf and -pk flags, as per the following command: 
 
-mpiexec -np 2 lmp_mpi -sf gpu -pk gpu 1 -in <in.input>
+srun -n 2 lmp_mpi -sf gpu -pk gpu 1 -in <in.input>
 
 the number after the -pk flag indicates the number of gpu instances you are requesting, and it should line up with the number requested in your gres gpu request. For example, a slurm script with the following line: 
 

MATLAB/XMATLAB

@@ -2,8 +2,8 @@ It is not highly recommended, but if a user wants to do X-Windows forwarding wit
 
 If the user is not using a Linux local machine they will need to install an X-windows client, such as Xming for MS-Windows or X11 on Mac OSX from the XQuartz project.
 
-ssh <username>@spartan.hpc.unimelb.edu.au -Y
-sinteractive -p cloud --x11=first
+ssh <username>@spartan.hpc.unimelb.edu.au -X
+sinteractive --x11=first
 module load MATLAB/2017a
 matlab
 

MATLAB/derive_pi.slurm

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

MATLAB/matlab-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/matlab.slurm

-#!/bin/bash
-#SBATCH -p cloud
-#SBATCH --ntasks=1
-module load MATLAB/2016a
-matlab -nodesktop -nodisplay -nosplash< polar-plot.m

MATLAB/tictoc-p.m

 tic
-n = 200;
-A = 500;
+n = 400;
+A = 1000;
 a = zeros(n);
 parfor i = 1:n
     a(i) = max(abs(eig(rand(A))));

MATLAB/tictoc.m

 tic
-n = 200;
-A = 500;
+n = 400;
+A = 1000;
 a = zeros(n);
 for i = 1:n
     a(i) = max(abs(eig(rand(A))));

Mathematica/Mathematica-test.slurm

-#!/bin/bash
-
-# Name and partition
-#SBATCH --job-name=Mathematica-test.slurm
-#SBATCH -p cloud
-
-# 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 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

MrBayes/MrBayes-test.slurm

-#!/bin/bash
-
-# To give your job a name, replace "MyJob" with an appropriate name
-#SBATCH --job-name=MrBayes-test.slurm
-#SBATCH -p cloud
-
-# Run on 1 cores
-#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 load MrBayes/3.2.6-intel-2016.u3
-
-mb Dengue4.env.xml

NAMD/Ubiquitin2/BUILD_DIR/build_example

-#  VMD psfgen example:
-#  this script generates a psf and pdb file of a given
-#  structure in preparation of a namd simulation.
-#
-# 
-#  usage:  at the command line type:
-#  vmd -dispdev text -e build_example.pgn
-
-package require psfgen
-topology top_all27_prot_na.rtf
-
-
-
-# Alias residue names
-alias residue HIS HSE
-alias atom ILE CD1 CD
-
-# Build protein segment
-
-segment A {pdb 1ubq_chainA.pdb}
-
-# Patch protein segment:  for adding disulphide bonds etc: segment MF {pdb nad.pdb}
-
-# patch DISU A:97  A:104
-# patch TP2 A:199  
-# regenerate angles dihedrals
-
-coordpdb 1ubq_chainA.pdb A
-
-guesscoord
-
-# Write structure and coordinate files
-
- writepsf model_ubq_x.psf
- writepdb model_ubq_x.pdb
-
-# Still need to solvate and ionize! 
-# do that with vmd modules
-
-exit
-

NAMD/Ubiquitin2/namd-ubiq2.slurm

-#!/bin/bash
-
-# SLURM job script, Lev Lafayette (October 2016) 
-
-# Which partition?
-#SBATCH --partition=cloud
-
-# Job name:
-#SBATCH --job-name ubiquitin2 
-
-# How many cores ?
-#SBATCH --nodes=2
-#SBATCH --ntasks-per-node=8
-
-# How long to run the job? (hours:minutes:seconds)
-#SBATCH --time=00:15:00
-
-# Environmental varibles to make it work:
-
-# NAMD/2.10-intel-2016.u3-mpi
- 
-module load NAMD/2.10-gompi-2015a-mpi
- 
-# Launching the job!
-
-mpiexec namd2 namd_1ubq_example.conf  
-

NAMD/Ubiquitin2/namd_1ubq_example.conf

-##############################################################################
-## Namd configuration file.                                         
-##############################################################################
-# Simple NAMD script                      m.kuiper April 2012
-#
-# -this is an example configuration file is to demonstrate a simple   
-#  simulation of a molecular system within namd.
-#  
-##############################################################################
-## Input Parameters:                                            
-##############################################################################
-
-structure            1ubq_example.psf
-coordinates          1ubq_example.pdb
-outputName           1ubq_output
-
-firsttimestep        0
-set Temp  	     310
-temperature 	     $Temp
-
-##############################################################################
-## Simulation Parameters:
-##############################################################################
-
-## Parameters ----------------------------------------------------------------
-##  -make sure to use the right parameter set!
-
-paraTypeCharmm	on
-parameters  	par_all27_prot_na.prm
-
-## Additional constraints: --------------------------------------------------
-#   -can use this section to constrain various parts of the simulation, -for 
-#   example protein backbone, with either harmonic constraints or fixed atoms.
-#   - make sure to assign a non-zero values to the B column of the pdb file an uncomment the 
-#   appropriate section.
-
-# constraints         on 
-# consexp             2
-# consref             InputFiles/change_me.pdb
-# conskfile           InputFiles/change_me.pdb
-# conskcol            B
-# constraintScaling   0.5
-
-# fixedAtoms          on
-# fixedAtomsFile      InputFiles/change_me.pdb 
-# fixedAtomsCol       B
-
-## Example of interactive molecular dynamics: (Uncommment next 4 lines) 
-
-# IMDon on 
-# IMDport 5678
-# IMDfreq 10
-# IMDwait no
-
-## parameter settings:-------------------------------------------------------
-# Force-Field Parameters
-exclude        	scaled1-4
-1-4scaling    	1.0
-cutoff        	12
-switching     	on
-switchdist     	10
-pairlistdist   	14
-
-# Integrator Parameters
-timestep            2
-rigidBonds          all
-nonbondedFreq       1
-fullElectFrequency  2  
-stepspercycle       10
-
-# Constant Temperature Control
-langevin            on
-langevinDamping     5  
-langevinTemp        $Temp
-langevinHydrogen    off 
-
-
-##  Periodic Boundary Conditions: ----------------------------------------------
-# make sure to check that the cell dimensions match your input files! 
-
-cellBasisVector1    48.      0.      0.
-cellBasisVector2     0.     48.      0.
-cellBasisVector3     0.      0.     48.
-cellOrigin           0       0       0
-wrapAll             on
-wrapWater           on
-
-## PME (for full-system periodic electrostatics) -------------------------------
-
-PME                 yes
-PMEGridSpacing      1.0 
-
-## Constant Pressure Control (variable volume) ---------------------------------
-
-useGroupPressure      yes 
-useFlexibleCell       yes
-useConstantArea       yes
-
-langevinPiston        on
-langevinPistonTarget  1.01325
-langevinPistonPeriod  100.
-langevinPistonDecay   50.
-langevinPistonTemp    $Temp
-
-## Output settings: -----------------------------------------------------------
-## ** Note! **  this file is for a short example run.  dcdfreq is *very* small
-## which means data will be written out very frequently leading to HUGE files. 
-## Make sure to change for production runs. 
-
-restartfreq         5000 
-dcdfreq              100
-xstFreq              100
-outputEnergies       100
-outputPressure       100
-outputTiming         100
-
-###############################################################################
-## Execution script:                       
-###############################################################################
-
-minimize          500
-run             10000 
-
-

NAMD/Ubiquitin2/namd_1ubq_restart_example.conf

-##############################################################################
-## Namd configuration file.                                         
-##############################################################################
-# Simple NAMD restart script                      m.kuiper April 2012
-#
-# -this is an example configuration file is to demonstrate a simple   
-#  simulation restart of a molecular system within namd.
-#  
-##############################################################################
-## Input Parameters:                                            
-##############################################################################
-
-structure            1ubq_example.psf
-coordinates          1ubq_example.pdb
-outputName           1ubq_restart_output_run_1
-
-# firsttimestep        0
-set Temp  	     310
-
-# temperature 	     $Temp  <- temperature not needed in restart file!
-
-
-##############################################################################
-## Simulation Parameters:
-##############################################################################
-
-## Parameters ----------------------------------------------------------------
-##  -make sure to use the right parameter set!
-
-paraTypeCharmm	on
-parameters  	par_all27_prot_na.prm
-
-
-
-set inputname      1ubq_output.restart
-
-binCoordinates     $inputname.coor  ;# coordinates from last run (binary)
-binVelocities      $inputname.vel   ;# velocities from last run (binary)
-extendedSystem     $inputname.xsc   ;# cell dimensions from last run
-firsttimestep            0          ;# last step of previous run
-numsteps             50000          ;# run stops when this step is reached
-
-
-## Additional constraints: --------------------------------------------------
-#   -can use this section to constrain various parts of the simulation, -for 
-#   example protein backbone, with either harmonic constraints or fixed atoms.
-#   - make sure to assign a non-zero values to the B column of the pdb file an uncomment the 
-#   appropriate section.
-
-# constraints         on 
-# consexp             2
-# consref             InputFiles/change_me.pdb
-# conskfile           InputFiles/change_me.pdb
-# conskcol            B
-# constraintScaling   0.5
-
-# fixedAtoms          on
-# fixedAtomsFile      InputFiles/change_me.pdb 
-# fixedAtomsCol       B
-
-## Example of interactive molecular dynamics: (Uncommment next 4 lines) 
-
-# IMDon on 
-# IMDport 5678
-# IMDfreq 10
-# IMDwait no
-
-## parameter settings:-------------------------------------------------------
-# Force-Field Parameters
-exclude        	scaled1-4
-1-4scaling    	1.0
-cutoff        	12
-switching     	on
-switchdist     	10
-pairlistdist   	14
-
-# Integrator Parameters
-timestep            2
-rigidBonds          all
-nonbondedFreq       1
-fullElectFrequency  2  
-stepspercycle       10
-
-# Constant Temperature Control
-langevin            on
-langevinDamping     5  
-langevinTemp        $Temp
-langevinHydrogen    off 
-
-
-##  Periodic Boundary Conditions: ----------------------------------------------
-# make sure to check that the cell dimensions match your input files! 
-
-#cellBasisVector1    48.      0.      0.     <- not needed in restart file!
-#cellBasisVector2     0.     48.      0.
-#cellBasisVector3     0.      0.     48.
-#cellOrigin           0       0       0
-wrapAll             on
-wrapWater           on
-
-## PME (for full-system periodic electrostatics) -------------------------------
-
-PME                 yes
-PMEGridSpacing      1.0 
-
-## Constant Pressure Control (variable volume) ---------------------------------
-
-useGroupPressure      yes 
-useFlexibleCell       yes
-useConstantArea       yes
-
-langevinPiston        on
-langevinPistonTarget  1.01325
-langevinPistonPeriod  100.
-langevinPistonDecay   50.
-langevinPistonTemp    $Temp
-
-## Output settings: -----------------------------------------------------------
-## ** Note! **  this file is for a short example run.  dcdfreq is *very* small
-## which means data will be written out very frequently leading to HUGE files. 
-## Make sure to change for production runs. 
-
-restartfreq         50000 
-dcdfreq              1000
-xstFreq              1000
-outputEnergies       1000
-outputPressure       1000
-outputTiming         1000
-
-###############################################################################
-## Execution script:                       
-###############################################################################
-
-# minimize          500                <-  not needed for restart file
-# run             10000 
-
-

NAMD/Ubiquitin2/sbatch_namd_restartjob_bluegene

-#!/bin/bash
-## sbatch launching script                     March 2014  m.kuiper
-##  - A script to run a simple NAMD job on the vlsci BlueGene/Q cluster, Avoca.
-##  - using a restart script
-
-
-#SBATCH --nodes=4
-ntpn=8        # number of tasks per node: 
-ppn=8         # processors per node: 
-
-## 60 minute walltime:
-#SBATCH --time=1:0:0
-
-# add your account number here if you have multiple accounts. 
-##SBATCH --account=VLSCI    
-
-module load namd-xl-pami-smp/2.9
-
-# Note: newer versions of namd may exist.  Alter module accordingly. 
-
-
-# -Submit the job: ----------------------- 
-
-srun  --ntasks-per-node $ntpn  namd2 +ppn $ppn namd_1ubq_restart_example.conf > Namd_1ubq_restart_example_output.txt 
-
-

NAMD/Ubiquitin2/sbatch_namd_start_bluegene

-#!/bin/bash
-## sbatch launching script                     March 2014  m.kuiper
-##  - A script to run a simple NAMD job on the vlsci BlueGene/Q cluster, Avoca.
-
-#SBATCH --nodes=4
-ntpn=8        # number of tasks per node: 
-ppn=8         # processors per node: 
-
-## 30 minute walltime:
-#SBATCH --time=0:30:0
-
-# add your account number here if you have multiple accounts. 
-##SBATCH --account=VLSCI    
-
-module load namd-xl-pami-smp/2.9
-
-# Note: newer versions of namd may exist.  Alter module accordingly. 
-
-
-# -Submit the job: ----------------------- 
-
-srun  --ntasks-per-node $ntpn  namd2 +ppn $ppn namd_1ubq_example.conf > Namd_1ubq_example_output.txt 
-
-

NAMD/ubiq/Ubiquitin_example.conf

-#############################################################
-## JOB DESCRIPTION                                         ##
-#############################################################
-#
-#  Example configuration file for a NAMD simulation 
-#  of ubiquitin. (In vacuum, for quick demonstration purposes!)    
-#                                   by Mike  Feb 2008 
-#
-#  Some features have been commented out, -uncomment sections 
-#  to enable! 
-##############################################################
-
-##   INPUT FILES
-#############################################################
-
- structure             1ubq_example.psf
- coordinates           1ubq_example.pdb
- outputName            1ubq_example_output_01
-
- firsttimestep         0
-
-## set simulation temperature (in Kelvin):
-
- set temp 	       310
- temperature           $temp
-
-##  SIMULATION PARAMETERS         
-###########################################################
-
-## Parameter file:
-
- paraTypeCharmm	       on
- parameters            par_all27_prot_na.inp 
-
-## Force-Field Parameters
-
- exclude               scaled1-4
- 1-4scaling            1.0
- cutoff                18
- switching             on
- switchdist            16
- pairlistdist          20
-
-## Integrator Parameters
-
- timestep              1
- rigidBonds            all
- nonbondedFreq         1
- fullElectFrequency    2  
- stepspercycle         10
-
-## Constant Temperature Control
-
- langevin              on
- langevinDamping       5  
- langevinTemp          $temp
- langevinHydrogen      off 
- 
-## Periodic Boundary Conditions
-
- cellBasisVector1    42.      0.      0.
- cellBasisVector2     0.     42.      0.
- cellBasisVector3     0.      0.     42.
- cellOrigin           0       0       0
- wrapAll             on
- wrapWater           on
-
-## PME (for full-system periodic electrostatics)
-## (uncomment next 4 lines to use PME ) 
-# PME                 yes
-# PMEGridSizeX        42
-# PMEGridSizeY        42
-# PMEGridSizeZ        42
-
-## Constant Pressure Control (variable volume)
-
- useGroupPressure      yes 
- useFlexibleCell       no
- useConstantArea       no
-
- langevinPiston        on
- langevinPistonTarget  1.01325
- langevinPistonPeriod  100.
- langevinPistonDecay   50.
- langevinPistonTemp    $temp
-
-## Output files:
-
- restartfreq         20000 
- dcdfreq             50
- xstFreq             20000
- outputEnergies      50
- outputPressure      50
- outputTiming        1000
-
-## EXECUTION SCRIPT 
-#############################################################
-
-## Minimize , reinitialize velocities, run dynamics:
- 
- minimize          100
- reinitvels        $temp
- run               5000 
-
-

NAMD/ubiq/namd-ubiq.slurm

-#!/bin/bash
-
-# SLURM job script, Lev Lafayette (August 2016) 
-# Derived from PBS/TORQUE script by Mike Kuiper (March 2007)     
-
-# Job name:
-#SBATCH --job-name namd_example_job_01
-
-# How many cores ?
-#SBATCH --nodes=1
-#SBATCH --ntasks-per-node=4
-
-# How long to run the job? (hours:minutes:seconds)
-#SBATCH --time=00:15:00
-
-# Environmental varibles to make it work:
-
-module load NAMD/2.10-gompi-2015a-mpi
- 
-# Launching the job!
-
-srun namd2 Ubiquitin_example.conf 

ORCA/ORCA.slurm

-#!/bin/bash
-
-#SBATCH -p cloud
-#SBATCH --time=0-00:05:00
-#SBATCH --nodes=1
-#SBATCH --ntasks=4
-
-module load ORCA/4_1_0-linux_x86-64-OpenMPI-3.1.3
-
-$EBROOTORCA/orca orca.in 1> orcaNEW3.out