Add more samples

.gitignore

 BLAST/dbs
 BLAST/rat-ests
+Cufflinks/sample.bam
 digits/digits.img
 FreeSurfer/buckner_data
 FreeSurfer/buckner_data-tutorial_subjs.tar.gz
@@ -16,4 +17,7 @@ NAMD/stmv
 Python/minitwitter.csv
 SAMtools/sample.sam.gz
 Singularity/vsoch-hello-world-master.simg
+Trimmomatic/*.gz
+Trimmomatic/*.fa
+Trimmomatic/.backup
 

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

ARAGORN/sample.fa

+>derice
+ACTGACTAGCTAGCTAACTG
+>sanka
+GCATCGTAGCTAGCTACGAT
+>junior
+CATCGATCGTACGTACGTAG
+>yul
+ATCGATCGATCGTACGATCG
\ No newline at end of file

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  
+
+
+
+

BAMM/template_diversification.txt

+# BAMM configuration file for speciation/extinction analysis 
+# ==========================================================
+#
+# Format
+# ------
+#
+#     - Each option is specified as: option_name = option_value
+#     - Comments start with # and go to the end of the line
+#     - True is specified with "1" and False with "0"
+
+
+################################################################################
+# GENERAL SETUP AND DATA INPUT
+################################################################################
+
+modeltype = speciationextinction        
+# Specify "speciationextinction" or "trait" analysis
+                                  
+treefile = whaletree.txt 
+# File name of the phylogenetic tree to be analyzed
+
+runInfoFilename = run_info.txt
+# File name to output general information about this run
+
+sampleFromPriorOnly = 0                 
+# Whether to perform analysis sampling from prior only (no likelihoods computed)
+
+runMCMC = 1                             
+# Whether to perform the MCMC simulation. If runMCMC = 0, the program will only
+# check whether the data file can be read and the initial likelihood computed
+
+simulatePriorShifts = 1
+# Whether to simulate the prior distribution of the number of shift events,
+# given the hyperprior on the Poisson rate parameter. This is necessary to
+# compute Bayes factors
+
+loadEventData = 0                       
+# Whether to load a previous event data file
+
+eventDataInfile = event_data_in.txt
+# File name of the event data file to load, used only if loadEventData = 1
+
+initializeModel = 1                     
+# Whether to initialize (but not run) the MCMC. If initializeModel = 0, the
+# program will only ensure that the data files (e.g., treefile) can be read
+
+useGlobalSamplingProbability = 1        
+# Whether to use a "global" sampling probability. If False (0), expects a file
+# name for species-specific sampling probabilities (see sampleProbsFilename)
+                                        
+globalSamplingFraction = 1.0            
+# The sampling probability. If useGlobalSamplingFraction = 0, this is ignored
+# and BAMM looks for a file name with species-specific sampling fractions
+
+sampleProbsFilename = sample_probs.txt
+# File name containing species-specific sampling fractions
+
+# seed = 12345
+# Seed for the random number generator. 
+# If not specified (or is -1), a seed is obtained from the system clock
+
+overwrite = 0
+# If True (1), the program will overwrite any output files in the current
+# directory (if present)
+
+
+################################################################################
+# PRIORS
+################################################################################
+
+expectedNumberOfShifts = 1.0
+# prior on the number of shifts in diversification
+# Suggested values: 
+#     expectedNumberOfShifts = 1.0 for small trees (< 500 tips)
+#	  expectedNumberOfShifts = 10 or even 50 for large trees (> 5000 tips) 
+ 
+lambdaInitPrior = 1.0
+# Prior (rate parameter of exponential) on the initial lambda value for rate
+# regimes
+
+lambdaShiftPrior = 0.05
+# Prior (std dev of normal) on lambda shift parameter for rate regimes
+# You cannot adjust the mean of this distribution (fixed at zero, which is
+# equal to a constant rate diversification process)
+
+muInitPrior = 1.0
+# Prior (rate parameter of exponential) on extinction rates  
+
+lambdaIsTimeVariablePrior = 1
+# Prior (probability) of the time mode being time-variable (vs. time-constant)
+
+
+################################################################################
+# MCMC SIMULATION SETTINGS & OUTPUT OPTIONS
+################################################################################
+
+numberOfGenerations = 5000 
+# Number of generations to perform MCMC simulation
+
+mcmcOutfile = mcmc_out.txt
+# File name for the MCMC output, which only includes summary information about
+# MCMC simulation (e.g., log-likelihoods, log-prior, number of processes)
+
+mcmcWriteFreq = 1000
+# Frequency in which to write the MCMC output to a file
+
+eventDataOutfile = event_data.txt
+# The raw event data (these are the main results). ALL of the results are
+# contained in this file, and all branch-specific speciation rates, shift
+# positions, marginal distributions etc can be reconstructed from this output.
+# See R package BAMMtools for working with this output
+
+eventDataWriteFreq = 1000
+# Frequency in which to write the event data to a file
+
+printFreq = 100
+# Frequency in which to print MCMC status to the screen
+
+acceptanceResetFreq = 1000
+# Frequency in which to reset the acceptance rate calculation
+# The acceptance rate is output to both the MCMC data file and the screen
+
+# outName = BAMM
+# Optional name that will be prefixed on all output files (separated with "_")
+# If commented out, no prefix will be used
+
+
+################################################################################
+# OPERATORS: MCMC SCALING OPERATORS
+################################################################################
+
+updateLambdaInitScale = 2.0
+# Scale parameter for updating the initial speciation rate for each process
+
+updateLambdaShiftScale = 0.1
+# Scale parameter for the exponential change parameter for speciation
+
+updateMuInitScale = 2.0
+# Scale parameter for updating initial extinction rate for each process
+
+updateEventLocationScale = 0.05
+# Scale parameter for updating LOCAL moves of events on the tree
+# This defines the width of the sliding window proposal
+ 
+updateEventRateScale = 4.0
+# Scale parameter (proportional shrinking/expanding) for updating
+# the rate parameter of the Poisson process 
+
+
+################################################################################
+# OPERATORS: MCMC MOVE FREQUENCIES
+################################################################################
+
+updateRateEventNumber = 0.1
+# Relative frequency of MCMC moves that change the number of events
+
+updateRateEventPosition = 1
+# Relative frequency of MCMC moves that change the location of an event on the
+# tree
+
+updateRateEventRate = 1
+# Relative frequency of MCMC moves that change the rate at which events occur 
+
+updateRateLambda0 = 1
+# Relative frequency of MCMC moves that change the initial speciation rate
+# associated with an event
+
+updateRateLambdaShift = 1
+# Relative frequency of MCMC moves that change the exponential shift parameter
+# of the speciation rate associated with an event
+
+updateRateMu0 = 1
+# Relative frequency of MCMC moves that change the extinction rate for a given
+# event
+
+updateRateLambdaTimeMode = 0
+# Relative frequency of MCMC moves that flip the time mode
+# (time-constant <=> time-variable)
+
+localGlobalMoveRatio = 10.0
+# Ratio of local to global moves of events 
+
+
+################################################################################
+# INITIAL PARAMETER VALUES
+################################################################################
+
+lambdaInit0 = 0.032
+# Initial speciation rate (at the root of the tree)
+
+lambdaShift0 = 0
+# Initial shift parameter for the root process
+
+muInit0 = 0.005
+# Initial value of extinction (at the root)
+
+initialNumberEvents = 0
+# Initial number of non-root processes
+ 
+
+################################################################################
+# METROPOLIS COUPLED MCMC
+################################################################################
+
+numberOfChains = 4
+# Number of Markov chains to run
+
+deltaT = 0.01
+# Temperature increment parameter. This value should be > 0
+# The temperature for the i-th chain is computed as 1 / [1 + deltaT * (i - 1)]
+
+swapPeriod = 1000
+# Number of generations in which to propose a chain swap
+
+chainSwapFileName = chain_swap.txt
+# File name in which to output data about each chain swap proposal.
+# The format of each line is [generation],[rank_1],[rank_2],[swap_accepted]
+# where [generation] is the generation in which the swap proposal was made,
+# [rank_1] and [rank_2] are the chains that were chosen, and [swap_accepted] is
+# whether the swap was made. The cold chain has a rank of 1.
+
+
+################################################################################
+# NUMERICAL AND OTHER PARAMETERS
+################################################################################
+
+minCladeSizeForShift = 1
+# Allows you to constrain location of possible rate-change events to occur
+# only on branches with at least this many descendant tips. A value of 1
+# allows shifts to occur on all branches. 
+
+segLength = 0.02
+# Controls the "grain" of the likelihood calculations. Approximates the
+# continuous-time change in diversification rates by breaking each branch into
+# a constant-rate diversification segments, with each segment given a length
+# determined by segLength. segLength is in units of the root-to-tip distance of
+# the tree. So, if the segLength parameter is 0.01, and the crown age of your
+# tree is 50, the "step size" of the constant rate approximation will be 0.5.
+# If the value is greater than the branch length (e.g., you have a branch of
+# length < 0.5 in the preceding example) BAMM will not break the branch into
+# segments but use the mean rate across the entire branch.

BAMM/template_trait.txt

+# BAMM configuration file for phenotypic analysis
+# ===============================================
+#
+# Format
+# ------
+#
+#     - Each option is specified as: option_name = option_value
+#     - Comments start with # and go to the end of the line
+#     - True is specified with "1" and False with "0"
+
+
+################################################################################
+# GENERAL SETUP AND DATA INPUT
+################################################################################
+
+modeltype = trait        
+# Specify "speciationextinction" or "trait" analysis
+                                  
+treefile = %%%%
+# File name of the phylogenetic tree to be analyzed
+
+traitfile = %%%%
+# File name of the phenotypic traits file
+
+runInfoFilename = run_info.txt
+# File name to output general information about this run
+
+sampleFromPriorOnly = 0                 
+# Whether to perform analysis sampling from prior only (no likelihoods computed)
+
+runMCMC = 1                             
+# Whether to perform the MCMC simulation. If runMCMC = 0, the program will only
+# check whether the data file can be read and the initial likelihood computed
+
+simulatePriorShifts = 1
+# Whether to simulate the prior distribution of the number of shift events,
+# given the hyperprior on the Poisson rate parameter. This is necessary to
+# compute Bayes factors
+
+loadEventData = 0                       
+# Whether to load a previous event data file
+
+eventDataInfile = event_data_in.txt
+# File name of the event data file to load, used only if loadEventData = 1
+
+initializeModel = 1                     
+# Whether to initialize (but not run) the MCMC. If initializeModel = 0, the
+# program will only ensure that the data files (e.g., treefile) can be read
+
+# seed = 12345
+# Seed for the random number generator. 
+# If not specified (or is -1), a seed is obtained from the system clock
+
+overwrite = 0
+# If True (1), the program will overwrite any output files in the current
+# directory (if present)
+
+
+################################################################################
+# PRIORS
+################################################################################
+
+expectedNumberOfShifts = 1.0
+# prior on the number of shifts in diversification
+# Suggested values: 
+#     expectedNumberOfShifts = 1.0 for small trees (< 500 tips)
+#	  expectedNumberOfShifts = 10 or even 50 for large trees (> 5000 tips) 
+
+betaInitPrior = 1.0
+# Prior (rate parameter of exponential) on the initial
+# phenotypic evolutionary rate associated with regimes
+
+betaShiftPrior = 0.05
+# Prior (std dev of normal) on the rate-change parameter
+# You cannot adjust the mean of this distribution (fixed at zero, which is
+# equal to a constant rate diversification process)
+
+useObservedMinMaxAsTraitPriors = 1
+# If True (1), will put a uniform prior density on the distribution
+# of ancestral character states, with upper and lower bounds determined
+# by the min and max of the observed data
+
+traitPriorMin = 0
+# User-defined minimum value for the uniform density on the distribution of
+# ancestral character states. Only used if useObservedMinMaxAsTraitPriors = 0.
+
+traitPriorMax = 0
+# User-defined maximum value for the uniform density on the distribution of
+# ancestral character states. Only used if useObservedMinMaxAsTraitPriors = 0.
+
+betaIsTimeVariablePrior = 1
+# Prior (probability) of the time mode being time-variable (vs. time-constant)
+
+
+################################################################################
+# MCMC SIMULATION SETTINGS & OUTPUT OPTIONS
+################################################################################
+
+numberOfGenerations = %%%%
+# Number of generations to perform MCMC simulation
+
+mcmcOutfile = mcmc_out.txt
+# File name for the MCMC output, which only includes summary information about
+# MCMC simulation (e.g., log-likelihoods, log-prior, number of processes)
+
+mcmcWriteFreq = %%%%
+# Frequency in which to write the MCMC output to a file
+
+eventDataOutfile = event_data.txt
+# The raw event data (these are the main results). ALL of the results are
+# contained in this file, and all branch-specific speciation rates, shift
+# positions, marginal distributions etc can be reconstructed from this output.
+# See R package BAMMtools for working with this output
+
+eventDataWriteFreq = %%%%
+# Frequency in which to write the event data to a file
+
+printFreq = %%%%
+# Frequency in which to print MCMC status to the screen
+
+acceptanceResetFreq = 1000
+# Frequency in which to reset the acceptance rate calculation
+# The acceptance rate is output to both the MCMC data file and the screen
+
+# outName = BAMM
+# Optional name that will be prefixed on all output files (separated with "_")
+# If commented out, no prefix will be used
+
+
+################################################################################
+# OPERATORS: MCMC SCALING OPERATORS
+################################################################################
+
+updateBetaInitScale = 1
+# Scale operator for proportional shrinking-expanding move to update
+# initial phenotypic rate for rate regimes
+
+updateBetaShiftScale = 1
+# Scale operator for sliding window move to update initial phenotypic rate
+
+updateNodeStateScale = 1
+# Scale operator for sliding window move to update ancestral states
+# at internal nodes
+
+updateEventLocationScale = 0.05
+# Scale parameter for updating LOCAL moves of events on the tree
+# This defines the width of the sliding window proposal
+ 
+updateEventRateScale = 4.0
+# Scale parameter (proportional shrinking/expanding) for updating
+# the rate parameter of the Poisson process 
+
+
+################################################################################
+# OPERATORS: MCMC MOVE FREQUENCIES
+################################################################################
+
+updateRateEventNumber = 1
+# Relative frequency of MCMC moves that change the number of events
+
+updateRateEventPosition = 1
+# Relative frequency of MCMC moves that change the location of an event
+# on the tree
+
+updateRateEventRate = 1
+# Relative frequency of MCMC moves that change the rate at which events occur 
+
+updateRateBeta0 = 1
+# Relative frequency of MCMC moves that change the initial phenotypic rate
+# associated with an event
+
+updateRateBetaShift = 1
+# Relative frequency of MCMC moves that change the exponential shift parameter
+# of the phenotypic rate associated with an event
+
+updateRateNodeState = 25
+# Relative frequency of MCMC moves that update the value of ancestral
+# character states. You have as many ancestral states as you have
+# internal nodes in your tree, so there are a lot of parameters:
+# you should update this much more often than you update the event-associated
+# parameters.
+
+updateRateBetaTimeMode = 0
+# Relative frequency of MCMC moves that flip the time mode
+# (time-constant <=> time-variable)
+
+localGlobalMoveRatio = 10.0
+# Ratio of local to global moves of events 
+
+
+################################################################################
+# INITIAL PARAMETER VALUES
+################################################################################
+
+betaInit = 0.5
+# Initial value of the phenotypic evolutionary process at the root of the tree
+
+betaShiftInit = 0
+# Initial value of the exponential change parameter for the phenotypic
+# evolutionary process at the root of the tree. A value of zero implies
+# time-constant rates
+
+initialNumberEvents = 0
+# Initial number of non-root processes
+
+
+################################################################################
+# METROPOLIS COUPLED MCMC
+################################################################################
+
+numberOfChains = 4
+# Number of Markov chains to run
+
+deltaT = 0.01
+# Temperature increment parameter. This value should be > 0
+# The temperature for the i-th chain is calculated as 1 / [1 + deltaT * (i - 1)]
+
+swapPeriod = 1000
+# Number of generations in which to propose a chain swap
+
+chainSwapFileName = chain_swap.txt
+# File name in which to output data about each chain swap proposal.
+# The format of each line is [generation],[rank_1],[rank_2],[swap_accepted]
+# where [generation] is the generation in which the swap proposal was made,
+# [rank_1] and [rank_2] are the chains that were chosen, and [swap_accepted] is
+# whether the swap was made. The cold chain has a rank of 1.

BAMM/whaletree.txt

+(((Balaena_mysticetus:8.81601900,(Eubalaena_australis:1.62202100,(Eubalaena_glacialis:0.34702900,Eubalaena_japonica:0.34702900):1.27499200):7.19399800):19.18398100,(Caperea_marginata:26.06301600,(Eschrichtius_robustus:17.89065500,(((Balaenoptera_acutorostrata:5.27807100,Balaenoptera_bonaerensis:5.27807100):9.82125300,(Balaenoptera_physalus:10.47223400,Megaptera_novaeangliae:10.47223400):4.62709000):0.96736100,(Balaenoptera_musculus:12.84739500,(Balaenoptera_omurai:11.38295800,(Balaenoptera_borealis:5.26532500,(Balaenoptera_brydei:4.32202200,Balaenoptera_edeni:4.32202200):0.94330300):6.11763300):1.46443700):3.21929000):1.82397000):8.17236100):1.93698400):7.85784400,((Physeter_catodon:22.04439100,(Kogia_breviceps:8.80301800,Kogia_simus:8.80301800):13.24137300):11.75461200,((Platanista_gangetica:0.28307000,Platanista_minor:0.28307000):32.10759100,((Tasmacetus_shepherdi:19.19566400,((Berardius_arnuxii:6.28945000,Berardius_bairdii:6.28945000):11.73396200,(Ziphius_cavirostris:15.66970200,((Indopacetus_pacificus:11.02830400,(Hyperoodon_ampullatus:8.10026600,Hyperoodon_planifrons:8.10026600):2.92803800):3.51197900,(Mesoplodon_bidens:13.04286900,(Mesoplodon_traversii:11.07929300,(Mesoplodon_ginkgodens:8.92594300,(Mesoplodon_europaeus:8.25210300,(Mesoplodon_mirus:7.67742400,((Mesoplodon_bowdoini:4.73244800,(Mesoplodon_carlhubbsi:4.17096800,Mesoplodon_layardii:4.17096800):0.56148000):2.44423200,(Mesoplodon_hectori:6.37563100,((Mesoplodon_densirostris:4.92715900,Mesoplodon_stejnegeri:4.92715900):0.86942800,(Mesoplodon_grayi:5.09638400,(Mesoplodon_perrini:4.16622600,Mesoplodon_peruvianus:4.16622600):0.93015800):0.70020200):0.57904500):0.80104900):0.50074400):0.57467900):0.67384000):2.15335000):1.96357700):1.49741400):1.12941900):2.35371000):1.17225200):12.42586500,((Lipotes_vexillifer:24.69821400,(Inia_geoffrensis:18.22641900,Pontoporia_blainvillei:18.22641900):6.47179400):1.30178600,(((Delphinapterus_leucas:5.46643200,Monodon_monoceros:5.46643200):8.59512200,((Neophocaena_phocaenoides:4.98587600,(Phocoena_phocoena:3.70627600,Phocoenoides_dalli:3.70627600):1.27960000):0.63050500,(Phocoena_sinus:4.94717000,(Phocoena_dioptrica:4.04570300,Phocoena_spinipinnis:4.04570300):0.90146700):0.66921000):8.44517400):3.87787200,(Orcinus_orca:10.70277000,((Orcaella_brevirostris:8.20905000,(Grampus_griseus:6.04703000,(Pseudorca_crassidens:5.49324100,(Feresa_attenuata:4.45272000,(Peponocephala_electra:3.04867500,(Globicephala_macrorhynchus:1.47078200,Globicephala_melas:1.47078200):1.57789300):1.40404500):1.04052100):0.55379000):2.16202000):1.22896300,(Lagenorhynchus_albirostris:8.71603900,((Lagenorhynchus_acutus:6.97518500,((Lissodelphis_borealis:1.36135800,Lissodelphis_peronii:1.36135800):3.90213700,((Cephalorhynchus_hectori:3.29116300,(Cephalorhynchus_commersonii:1.82123900,Cephalorhynchus_eutropia:1.82123900):1.46992500):1.27972900,(Lagenorhynchus_obscurus:3.79185300,(Lagenorhynchus_obliquidens:2.91977900,(Cephalorhynchus_heavisidii:2.09621900,(Lagenorhynchus_australis:1.57043300,Lagenorhynchus_cruciger:1.57043300):0.52578600):0.82356000):0.87207400):0.77904000):0.69260200):1.71169000):1.16787300,((Steno_bredanensis:5.89750600,(Sotalia_fluviatilis:3.21256100,Sotalia_guianensis:3.21256100):2.68494500):1.61688800,((Lagenodelphis_hosei:3.44536000,Stenella_longirostris:3.44536000):0.91035700,((Stenella_attenuata:3.07917000,(Tursiops_aduncus:2.19441300,Tursiops_truncatus:2.19441300):0.88475700):0.54694500,(Sousa_chinensis:2.83298000,(Stenella_clymene:1.93481200,((Stenella_coeruleoalba:1.01116300,Stenella_frontalis:1.01116300):0.49557400,(Delphinus_tropicalis:1.26811400,(Delphinus_capensis:0.92486200,Delphinus_delphis:0.92486200):0.34325200):0.23862300):0.42807500):0.89816800):0.79313500):0.72960200):3.15867700):0.62866400):0.57298100):0.72197400):1.26475700):7.23665700):8.06057400):5.62152800):0.76913200):1.40834300):2.05884100);
\ No newline at end of file

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
+

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
+

CPMD/CPMD-test.slurm

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

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
+

Cufflinks/README.md

+"Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols."
+
+Example BAM files from
+http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/
+

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

FFTW/fftw_example.c

+/* Start reading here */
+
+#include <fftw3.h>
+
+#define NUM_POINTS 64
+
+
+/* Never mind this bit */
+
+#include <stdio.h>
+#include <math.h>
+
+#define REAL 0
+#define IMAG 1
+
+void acquire_from_somewhere(fftw_complex* signal) {
+    /* Generate two sine waves of different frequencies and
+     * amplitudes.
+     */
+
+    int i;
+    for (i = 0; i < NUM_POINTS; ++i) {
+        double theta = (double)i / (double)NUM_POINTS * M_PI;
+
+        signal[i][REAL] = 1.0 * cos(10.0 * theta) +
+                          0.5 * cos(25.0 * theta);
+
+        signal[i][IMAG] = 1.0 * sin(10.0 * theta) +
+                          0.5 * sin(25.0 * theta);
+    }
+}
+
+void do_something_with(fftw_complex* result) {
+    int i;
+    for (i = 0; i < NUM_POINTS; ++i) {
+        double mag = sqrt(result[i][REAL] * result[i][REAL] +
+                          result[i][IMAG] * result[i][IMAG]);
+
+        printf("%g\n", mag);
+    }
+}
+
+
+/* Resume reading here */
+
+int main() {
+    fftw_complex signal[NUM_POINTS];
+    fftw_complex result[NUM_POINTS];
+
+    fftw_plan plan = fftw_plan_dft_1d(NUM_POINTS,
+                                      signal,
+                                      result,
+                                      FFTW_FORWARD,
+                                      FFTW_ESTIMATE);
+
+    acquire_from_somewhere(signal);
+    fftw_execute(plan);
+    do_something_with(result);
+
+    fftw_destroy_plan(plan);
+
+    return 0;
+}

FreePascal/FreePascal-test.slurm

+#!/bin/bash
+
+# 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
+
+# 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 fpc/3.0.4
+
+fpc hello.pas
+
+./hello > results.txt

GPU/README

@@ -2,8 +2,6 @@
 
 #SBATCH --partition gpgpu
 #SBATCH --account=test # Use a project ID that has access.
-#SBATCH --qos=gpgu # Note that this qos may differ if you are from a non UoM institution
-#SBATCH --gres=gpu:1 
 
 # For example if you wish to access up four GPUs in a single job use:
 

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
+

HMMER/README

+Programs part of HMMER
+======================
+
+hmmbuild	build profile from input multiple alignment
+hmmalign	make multiple sequence alignment using a profile
+hmmsearch	search profile against sequence database
+hmmscan		search sequence against profile database
+hmmpress	prepare profile database for hmmscan
+phmmer		search single sequence against sequence database
+jackhmmer	iteratively search single sequence against database
+nhmmer		search DNA query against DNA sequence database
+nhmmscan 	search DNA sequence against a DNA profile database
+hmmfetch	retrieve profile(s) from a profile file
+hmmstat		show summary statistics for a profile file
+hmmemit		generate (sample) sequences from a profile
+hmmlogo		produce a conservation logo graphic from a profile
+hmmconvert	convert between different profile file formats
+hmmpgmd search 	daemon for the hmmer.org website
+hmmpgmd_shard	sharded search daemon for the hmmer.org website
+makehmmerdb	prepare an nhmmer binary database
+hmmsim		collect score distributions on random sequences
+alimask 	add column mask to a multiple sequence alignment
+

HMMER/globins4.sto

+# STOCKHOLM 1.0
+
+HBB_HUMAN   ........VHLTPEEKSAVTALWGKV....NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVL
+HBA_HUMAN   .........VLSPADKTNVKAAWGKVGA..HAGEYGAEALERMFLSFPTTKTYFPHF.DLS.....HGSAQVKGHGKKVA
+MYG_PHYCA   .........VLSEGEWQLVLHVWAKVEA..DVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVL
+GLB5_PETMA  PIVDTGSVAPLSAAEKTKIRSAWAPVYS..TYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERII
+
+HBB_HUMAN   GAFSDGLAHL...D..NLKGTFATLSELHCDKL..HVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANAL
+HBA_HUMAN   DALTNAVAHV...D..DMPNALSALSDLHAHKL..RVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL
+MYG_PHYCA   TALGAILKK....K.GHHEAELKPLAQSHATKH..KIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDI
+GLB5_PETMA  NAVNDAVASM..DDTEKMSMKLRDLSGKHAKSF..QVDPQYFKVLAAVIADTVAAG.........DAGFEKLMSMICILL
+
+HBB_HUMAN   AHKYH......
+HBA_HUMAN   TSKYR......
+MYG_PHYCA   AAKYKELGYQG
+GLB5_PETMA  RSAY.......
+//
+

HMMER/globins45.fa

+>MYG_ESCGI 
+VLSDAEWQLVLNIWAKVEADVAGHGQDILIRLFKGHPETLEKFDKFKHLK
+TEAEMKASEDLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIP
+IKYLEFISDAIIHVLHSRHPGDFGADAQAAMNKALELFRKDIAAKYKELG
+FQG
+>MYG_HORSE 
+GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLK
+TEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIP
+IKYLEFISDAIIHVLHSKHPGNFGADAQGAMTKALELFRNDIAAKYKELG
+FQG
+>MYG_PROGU 
+GLSDGEWQLVLNVWGKVEGDLSGHGQEVLIRLFKGHPETLEKFDKFKHLK
+AEDEMRASEELKKHGTTVLTALGGILKKKGQHAAELAPLAQSHATKHKIP
+VKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKELG
+FQG
+>MYG_SAISC 
+GLSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLK
+SEDEMKASEELKKHGTTVLTALGGILKKKGQHEAELKPLAQSHATKHKIP
+VKYLELISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKELG
+FQG
+>MYG_LYCPI 
+GLSDGEWQIVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLK
+TEDEMKGSEDLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIP
+VKYLEFISDAIIQVLQNKHSGDFHADTEAAMKKALELFRNDIAAKYKELG
+FQG
+>MYG_MOUSE 
+GLSDGEWQLVLNVWGKVEADLAGHGQEVLIGLFKTHPETLDKFDKFKNLK
+SEEDMKGSEDLKKHGCTVLTALGTILKKKGQHAAEIQPLAQSHATKHKIP
+VKYLEFISEIIIEVLKKRHSGDFGADAQGAMSKALELFRNDIAAKYKELG
+FQG
+>MYG_MUSAN 
+VDWEKVNSVWSAVESDLTAIGQNILLRLFEQYPESQNHFPKFKNKSLGEL
+KDTADIKAQADTVLSALGNIVKKKGSHSQPVKALAATHITTHKIPPHYFT
+KITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEYKAANFQG
+>HBA_AILME 
+VLSPADKTNVKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHFDLSP
+GSAQVKAHGKKVADALTTAVGHLDDLPGALSALSDLHAHKLRVDPVNFKL
+LSHCLLVTLASHHPAEFTPAVHASLDKFFSAVSTVLTSKYR
+>HBA_PROLO 
+VLSPADKANIKATWDKIGGHAGEYGGEALERTFASFPTTKTYFPHFDLSP
+GSAQVKAHGKKVADALTLAVGHLDDLPGALSALSDLHAYKLRVDPVNFKL
+LSHCLLVTLACHHPAEFTPAVHASLDKFFTSVSTVLTSKYR
+>HBA_PAGLA 
+VLSSADKNNIKATWDKIGSHAGEYGAEALERTFISFPTTKTYFPHFDLSH
+GSAQVKAHGKKVADALTLAVGHLEDLPNALSALSDLHAYKLRVDPVNFKL
+LSHCLLVTLACHHPAEFTPAVHSALDKFFSAVSTVLTSKYR
+>HBA_MACFA 
+VLSPADKTNVKAAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHFDLSH
+GSAQVKGHGKKVADALTLAVGHVDDMPQALSALSDLHAHKLRVDPVNFKL
+LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
+>HBA_MACSI 
+VLSPADKTNVKDAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHFDLSH
+GSAQVKGHGKKVADALTLAVGHVDDMPQALSALSDLHAHKLRVDPVNFKL
+LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
+>HBA_PONPY 
+VLSPADKTNVKTAWGKVGAHAGDYGAEALERMFLSFPTTKTYFPHFDLSH
+GSAQVKDHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL
+LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
+>HBA2_GALCR 
+VLSPTDKSNVKAAWEKVGAHAGDYGAEALERMFLSFPTTKTYFPHFDLSH
+GSTQVKGHGKKVADALTNAVLHVDDMPSALSALSDLHAHKLRVDPVNFKL
+LRHCLLVTLACHHPAEFTPAVHASLDKFMASVSTVLTSKYR
+>HBA_MESAU 
+VLSAKDKTNISEAWGKIGGHAGEYGAEALERMFFVYPTTKTYFPHFDVSH
+GSAQVKGHGKKVADALTNAVGHLDDLPGALSALSDLHAHKLRVDPVNFKL
+LSHCLLVTLANHHPADFTPAVHASLDKFFASVSTVLTSKYR
+>HBA2_BOSMU 
+VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSH
+GSAQVKGHGAKVAAALTKAVGHLDDLPGALSELSDLHAHKLRVDPVNFKL
+LSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR
+>HBA_ERIEU 
+VLSATDKANVKTFWGKLGGHGGEYGGEALDRMFQAHPTTKTYFPHFDLNP
+GSAQVKGHGKKVADALTTAVNNLDDVPGALSALSDLHAHKLRVDPVNFKL
+LSHCLLVTLALHHPADFTPAVHASLDKFLATVATVLTSKYR
+>HBA_FRAPO 
+VLSAADKNNVKGIFGKISSHAEDYGAEALERMFITYPSTKTYFPHFDLSH
+GSAQVKGHGKKVVAALIEAANHIDDIAGTLSKLSDLHAHKLRVDPVNFKL
+LGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGNVLTAKYR
+>HBA_PHACO 
+VLSAADKNNVKGIFTKIAGHAEEYGAEALERMFITYPSTKTYFPHFDLSH
+GSAQIKGHGKKVVAALIEAVNHIDDITGTLSKLSDLHAHKLRVDPVNFKL
+LGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGTVLTAKYR
+>HBA_TRIOC 
+VLSANDKTNVKTVFTKITGHAEDYGAETLERMFITYPPTKTYFPHFDLHH
+GSAQIKAHGKKVVGALIEAVNHIDDIAGALSKLSDLHAQKLRVDPVNFKL
+LGQCFLVVVAIHHPSVLTPEVHASLDKFLCAVGNVLSAKYR
+>HBA_ANSSE 
+VLSAADKGNVKTVFGKIGGHAEEYGAETLQRMFQTFPQTKTYFPHFDLQP
+GSAQIKAHGKKVAAALVEAANHIDDIAGALSKLSDLHAQKLRVDPVNFKF
+LGHCFLVVLAIHHPSLLTPEVHASMDKFLCAVATVLTAKYR
+>HBA_COLLI 
+VLSANDKSNVKAVFAKIGGQAGDLGGEALERLFITYPQTKTYFPHFDLSH
+GSAQIKGHGKKVAEALVEAANHIDDIAGALSKLSDLHAQKLRVDPVNFKL
+LGHCFLVVVAVHFPSLLTPEVHASLDKFVLAVGTVLTAKYR
+>HBAD_CHLME 
+MLTADDKKLLTQLWEKVAGHQEEFGSEALQRMFLTYPQTKTYFPHFDLHP
+GSEQVRGHGKKVAAALGNAVKSLDNLSQALSELSNLHAYNLRVDPANFKL
+LAQCFQVVLATHLGKDYSPEMHAAFDKFLSAVAAVLAEKYR
+>HBAD_PASMO 
+MLTAEDKKLIQQIWGKLGGAEEEIGADALWRMFHSYPSTKTYFPHFDLSQ
+GSDQIRGHGKKVVAALSNAIKNLDNLSQALSELSNLHAYNLRVDPVNFKF
+LSQCLQVSLATRLGKEYSPEVHSAVDKFMSAVASVLAEKYR
+>HBAZ_HORSE 
+SLTKAERTMVVSIWGKISMQADAVGTEALQRLFSSYPQTKTYFPHFDLHE
+GSPQLRAHGSKVAAAVGDAVKSIDNVAGALAKLSELHAYILRVDPVNFKF
+LSHCLLVTLASRLPADFTADAHAAWDKFLSIVSSVLTEKYR
+>HBA4_SALIR 
+SLSAKDKANVKAIWGKILPKSDEIGEQALSRMLVVYPQTKAYFSHWASVA
+PGSAPVKKHGITIMNQIDDCVGHMDDLFGFLTKLSELHATKLRVDPTNFK
+ILAHNLIVVIAAYFPAEFTPEIHLSVDKFLQQLALALAEKYR
+>HBB_ORNAN 
+VHLSGGEKSAVTNLWGKVNINELGGEALGRLLVVYPWTQRFFEAFGDLSS
+AGAVMGNPKVKAHGAKVLTSFGDALKNLDDLKGTFAKLSELHCDKLHVDP
+ENFNRLGNVLIVVLARHFSKDFSPEVQAAWQKLVSGVAHALGHKYH
+>HBB_TACAC 
+VHLSGSEKTAVTNLWGHVNVNELGGEALGRLLVVYPWTQRFFESFGDLSS
+ADAVMGNAKVKAHGAKVLTSFGDALKNLDNLKGTFAKLSELHCDKLHVDP
+ENFNRLGNVLVVVLARHFSKEFTPEAQAAWQKLVSGVSHALAHKYH
+>HBE_PONPY 
+VHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSS
+PSAILGNPKVKAHGKKVLTSFGDAIKNMDNLKTTFAKLSELHCDKLHVDP
+ENFKLLGNVMVIILATHFGKEFTPEVQAAWQKLVSAVAIALAHKYH
+>HBB_SPECI 
+VHLSDGEKNAISTAWGKVHAAEVGAEALGRLLVVYPWTQRFFDSFGDLSS
+ASAVMGNAKVKAHGKKVIDSFSNGLKHLDNLKGTFASLSELHCDKLHVDP
+ENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALAHKYH
+>HBB_SPETO 
+VHLTDGEKNAISTAWGKVNAAEIGAEALGRLLVVYPWTQRFFDSFGDLSS
+ASAVMGNAKVKAHGKKVIDSFSNGLKHLDNLKGTFASLSELHCDKLHVDP
+ENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALSHKYH
+>HBB_EQUHE 
+VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSN
+PAAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAQLSELHCDKLHVDP
+ENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH
+>HBB_SUNMU 
+VHLSGEEKACVTGLWGKVNEDEVGAEALGRLLVVYPWTQRFFDSFGDLSS
+ASAVMGNPKVKAHGKKVLHSLGEGVANLDNLKGTFAKLSELHCDKLHVDP
+ENFRLLGNVLVVVLASKFGKEFTPPVQAAFQKVVAGVANALAHKYH
+>HBB_CALAR 
+VHLTGEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLST
+PDAVMNNPKVKAHGKKVLGAFSDGLTHLDNLKGTFAHLSELHCDKLHVDP
+ENFRLLGNVLVCVLAHHFGKEFTPVVQAAYQKVVAGVANALAHKYH
+>HBB_MANSP 
+VHLTPEEKTAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSS
+PDAVMGNPKVKAHGKKVLGAFSDGLNHLDNLKGTFAQLSELHCDKLHVDP
+ENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH
+>HBB_URSMA 
+VHLTGEEKSLVTGLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSS
+ADAIMNNPKVKAHGKKVLNSFSDGLKNLDNLKGTFAKLSELHCDKLHVDP
+ENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH
+>HBB_RABIT 
+VHLSSEEKSAVTALWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSS
+ANAVMNNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDP
+ENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH
+>HBB_TUPGL 
+VHLSGEEKAAVTGLWGKVDLEKVGGQSLGSLLIVYPWTQRFFDSFGDLSS
+PSAVMSNPKVKAHGKKVLTSFSDGLNHLDNLKGTFAKLSELHCDKLHVDP
+ENFRLLGNVLVRVLACNFGPEFTPQVQAAFQKVVAGVANALAHKYH
+>HBB_TRIIN 
+VHLTPEEKALVIGLWAKVNVKEYGGEALGRLLVVYPWTQRFFEHFGDLSS
+ASAIMNNPKVKAHGEKVFTSFGDGLKHLEDLKGAFAELSELHCDKLHVDP
+ENFRLLGNVLVCVLARHFGKEFSPEAQAAYQKVVAGVANALAHKYH
+>HBB_COLLI 
+VHWSAEEKQLITSIWGKVNVADCGAEALARLLIVYPWTQRFFSSFGNLSS
+ATAISGNPNVKAHGKKVLTSFGDAVKNLDNIKGTFAQLSELHCDKLHVDP
+ENFRLLGDILVIILAAHFGKDFTPECQAAWQKLVRVVAHALARKYH
+>HBB_LARRI 
+VHWSAEEKQLITGLWGKVNVADCGAEALARLLIVYPWTQRFFASFGNLSS
+PTAINGNPMVRAHGKKVLTSFGEAVKNLDNIKNTFAQLSELHCDKLHVDP
+ENFRLLGDILIIVLAAHFAKDFTPDSQAAWQKLVRVVAHALARKYH
+>HBB1_VAREX 
+VHWTAEEKQLICSLWGKIDVGLIGGETLAGLLVIYPWTQRQFSHFGNLSS
+PTAIAGNPRVKAHGKKVLTSFGDAIKNLDNIKDTFAKLSELHCDKLHVDP
+TNFKLLGNVLVIVLADHHGKEFTPAHHAAYQKLVNVVSHSLARRYH
+>HBB2_XENTR 
+VHWTAEEKATIASVWGKVDIEQDGHDALSRLLVVYPWTQRYFSSFGNLSN
+VSAVSGNVKVKAHGNKVLSAVGSAIQHLDDVKSHLKGLSKSHAEDLHVDP
+ENFKRLADVLVIVLAAKLGSAFTPQVQAVWEKLNATLVAALSHGYF
+>HBBL_RANCA 
+VHWTAEEKAVINSVWQKVDVEQDGHEALTRLFIVYPWTQRYFSTFGDLSS
+PAAIAGNPKVHAHGKKILGAIDNAIHNLDDVKGTLHDLSEEHANELHVDP
+ENFRRLGEVLIVVLGAKLGKAFSPQVQHVWEKFIAVLVDALSHSYH
+>HBB2_TRICR 
+VHLTAEDRKEIAAILGKVNVDSLGGQCLARLIVVNPWSRRYFHDFGDLSS
+CDAICRNPKVLAHGAKVMRSIVEATKHLDNLREYYADLSVTHSLKFYVDP
+ENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY

HTSlib/HTSlib-test.slurm

+#!/bin/bash
+
+# Partition and name
+#SBATCH --job-name=HTSlib-test.slurm
+#SBATCH -p physicaltest
+
+# 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 HTSlib/1.9-intel-2018.u4
+
+# Start the tabix binary from htslib
+tabix -p gff sample.sorted.gff.gz;
+tabix sample.sorted.gff.gz chr1:10,000,000-20,000,000;

Interact/README

@@ -10,12 +10,14 @@ ssh <username>@spartan.hpc.unimelb.edu.au -X
 sinteractive -p cloud --x11=first
 xclock
 
-# If you are running interactive jobs on GPU partitions you have to include the appropriate QOS commands.
+# If you are running interactive jobs on GPU partitions you have to include the appropriate QOS commands or account.
 
 sinteractive --x11=first --partition=shortgpgpu --gres=gpu:p100:1
 
 sinteractive --x11=first --partition=deeplearn --qos=gpgpudeeplearn --gres=gpu:v100:1
 
+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. 
 
@@ -25,4 +27,8 @@ export http_proxy=http://wwwproxy.unimelb.edu.au:8000
 export https_proxy=$http_proxy
 export ftp_proxy=$http_proxy
 
+# Or load the web_proxy module
+
+module load web_proxy
+
 

LAMMPS/accelerate/Make.list

+# desktop builds for dual hex-core Xeons and Fermi GPUs
+# use mpicxx or nvcc with its default compiler
+# use default FFT support = KISS library
+
+# build with one accelerator package
+
+cpu: -d ../.. -j 16 -p none asphere molecule kspace rigid orig -o cpu file clean mpi
+
+omp: -d ../.. -j 16 -p none asphere molecule kspace rigid omp orig -o omp file clean mpi
+
+opt: -d ../.. -j 16 -p none asphere molecule kspace rigid opt orig -o opt file clean mpi
+
+cuda_double: -d ../.. -j 16 -p none asphere molecule kspace rigid cuda orig -cuda mode=double arch=21 -o cuda_double lib-cuda file clean mpi
+
+cuda_mixed: -d ../.. -j 16 -p none asphere molecule kspace rigid cuda orig -cuda mode=mixed arch=21 -o cuda_mixed lib-cuda file clean mpi
+
+cuda_single: -d ../.. -j 16 -p none asphere molecule kspace rigid cuda orig -cuda mode=single arch=21 -o cuda_single lib-cuda file clean mpi
+
+gpu_double: -d ../.. -j 16 -p none asphere molecule kspace rigid gpu orig -gpu mode=double arch=21 -o gpu_double lib-gpu file clean mpi
+
+gpu_mixed: -d ../.. -j 16 -p none asphere molecule kspace rigid gpu orig -gpu mode=mixed arch=21 -o gpu_mixed lib-gpu file clean mpi
+
+gpu_single: -d ../.. -j 16 -p none asphere molecule kspace rigid gpu orig -gpu mode=single arch=21 -o gpu_single lib-gpu file clean mpi
+
+intel_cpu: -d ../.. -j 16 -p none asphere molecule kspace rigid intel omp orig -cc mpi wrap=icc -intel cpu -o intel_cpu file clean mpi
+
+#intel_phi: -d ../.. -j 16 -p none asphere molecule kspace rigid intel omp orig -intel phi -o intel_phi file clean mpi 
+
+kokkos_omp: -d ../.. -j 16 -p none asphere molecule kspace rigid kokkos orig -kokkos omp -o kokkos_omp file clean mpi 
+
+kokkos_cuda: -d ../.. -j 16 -p none asphere molecule kspace rigid kokkos orig -cc nvcc wrap=mpi -kokkos cuda arch=21 -o kokkos_cuda file clean mpi
+
+#kokkos_phi: -d ../.. -j 16 -p none asphere molecule kspace rigid kokkos orig -kokkos phi -o kokkos_phi file clean mpi 
+
+# build with all accelerator packages for CPU
+
+all_cpu: -d ../.. -j 16 -p asphere molecule kspace rigid none opt omp intel kokkos orig -cc mpi wrap=icc -intel cpu -kokkos omp -o all_cpu file clean mpi
+
+# build with all accelerator packages for GPU
+
+all_gpu: -d ../.. -j 16 -p none asphere molecule kspace rigid omp gpu cuda kokkos orig -cc nvcc wrap=mpi -cuda mode=double arch=21 -gpu mode=double arch=21 -kokkos cuda arch=21 -o all_gpu lib-all file clean mpi

LAMMPS/accelerate/README

+These are example scripts that can be run with any of
+the acclerator packages in LAMMPS:
+
+GPU, USER-INTEL, KOKKOS, USER-OMP, OPT
+
+The easiest way to build LAMMPS with these packages
+is via the flags described in Section 4 of the manual.
+The easiest way to run these scripts is by using the appropriate
+Details on the individual accelerator packages
+can be found in doc/Section_accelerate.html.
+
+---------------------
+
+Build LAMMPS with one or more of the accelerator packages
+
+Note that in addition to any accelerator packages, these packages also
+need to be installed to run all of the example scripts: ASPHERE,
+MOLECULE, KSPACE, RIGID.
+
+These two targets will build a single LAMMPS executable with all the
+CPU accelerator packages installed (USER-INTEL for CPU, KOKKOS for
+OMP, USER-OMP, OPT) or all the GPU accelerator packages installed
+(GPU, KOKKOS for CUDA):
+
+For any build with GPU, or KOKKOS for CUDA, be sure to set
+the arch=XX setting to the appropriate value for the GPUs and Cuda
+environment on your system.
+
+---------------------
+
+Running with each of the accelerator packages
+
+All of the input scripts have a default problem size and number of
+timesteps:
+
+in.lj = LJ melt with cutoff of 2.5 = 32K atoms for 100 steps
+in.lj.5.0 = same with cutoff of 5.0 = 32K atoms for 100 steps
+in.phosphate = 11K atoms for 100 steps
+in.rhodo = 32K atoms for 100 steps
+in.lc = 33K atoms for 100 steps (after 200 steps equilibration)
+
+These can be reset using the x,y,z and t variables in the command
+line.  E.g. adding "-v x 2 -v y 2 -v z 4 -t 1000" to any of the run
+command below would run a 16x larger problem (2x2x4) for 1000 steps.
+
+Here are example run commands using each of the accelerator packages:
+
+** CPU only
+
+lmp_cpu < in.lj
+mpirun -np 4 lmp_cpu -in in.lj
+
+** OPT package
+
+lmp_opt -sf opt < in.lj
+mpirun -np 4 lmp_opt -sf opt -in in.lj
+
+** USER-OMP package
+
+lmp_omp -sf omp -pk omp 1 < in.lj
+mpirun -np 4 lmp_omp -sf opt -pk omp 1 -in in.lj   # 4 MPI, 1 thread/MPI
+mpirun -np 2 lmp_omp -sf opt -pk omp 4 -in in.lj   # 2 MPI, 4 thread/MPI
+
+** GPU package
+
+lmp_gpu_double -sf gpu < in.lj               
+mpirun -np 8 lmp_gpu_double -sf gpu < in.lj        # 8 MPI, 8 MPI/GPU
+mpirun -np 12 lmp_gpu_double -sf gpu -pk gpu 2 < in.lj  # 12 MPI, 6 MPI/GPU
+mpirun -np 4 lmp_gpu_double -sf gpu -pk gpu 2 tpa 8 < in.lj.5.0   # 4 MPI, 2 MPI/GPU
+
+Note that when running in.lj.5.0 (which has a long cutoff) with the
+GPU package, the "-pk tpa" setting should be > 1 (e.g. 8) for best
+performance.
+
+** KOKKOS package for OMP
+
+lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half < in.lj
+mpirun -np 2 lmp_kokkos_omp -k on t 4 -sf kk < in.lj  # 2 MPI, 4 thread/MPI
+
+Note that when running with just 1 thread/MPI, "-pk kokkos neigh half"
+was specified to use half neighbor lists which are faster when running
+on just 1 thread.
+
+** KOKKOS package for CUDA
+
+lmp_kokkos_cuda -k on t 1 -sf kk < in.lj    # 1 thread, 1 GPU
+mpirun -np 2 lmp_kokkos_cuda -k on t 6 g 2 -sf kk < in.lj   # 2 MPI, 6 thread/MPI, 1 MPI/GPU
+
+** KOKKOS package for PHI
+
+mpirun -np 1 lmp_kokkos_phi -k on t 240 -sf kk -in in.lj   # 1 MPI, 240 threads/MPI
+mpirun -np 30 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj    # 30 MPI, 8 threads/MPI
+
+** USER-INTEL package for CPU
+
+lmp_intel_cpu -sf intel < in.lj
+mpirun -np 4 lmp_intl_cpu -sf intel < in.lj             # 4 MPI
+mpirun -np 4 lmp_intl_cpu -sf intel -pk omp 2 < in.lj   # 4 MPI, 2 thread/MPI
+
+** USER-INTEL package for PHI
+
+lmp_intel_phi -sf intel -pk intel 1 omp 16 < in.lc      # 1 MPI, 16 CPU thread/MPI, 1 Phi, 240 Phi thread/MPI
+mpirun -np 4 lmp_intel_phi -sf intel -pk intel 1 omp 2 < in.lc  # 4 MPI, 2 CPU threads/MPI, 1 Phi, 60 Phi thread/MPI
+
+Note that there is currently no Phi support for pair_style lj/cut in
+the USER-INTEL package.

LAMMPS/accelerate/in.lc

+# Gay-Berne benchmark
+# biaxial ellipsoid mesogens in isotropic phase
+# shape: 2 1.5 1
+# cutoff 4.0 with skin 0.8
+# NPT, T=2.4, P=8.0
+
+variable        x index 1
+variable        y index 1
+variable        z index 1
+variable        t index 100
+
+variable        i equal $x*32
+variable        j equal $y*32
+variable        k equal $z*32
+
+units	        lj
+atom_style      ellipsoid
+
+# create lattice of ellipsoids
+
+lattice	      sc 0.22
+region	      box block 0 $i 0 $j 0 $k
+create_box    1 box
+create_atoms  1 box
+
+set           type 1 mass 1.5
+set           type 1 shape 1 1.5 2
+set	      group all quat/random 982381
+
+compute	       rot all temp/asphere
+group	       spheroid type 1
+variable       dof equal count(spheroid)+3
+compute_modify rot extra/dof ${dof}
+
+velocity      all create 2.4 41787 loop geom
+
+pair_style    gayberne 1.0 3.0 1.0 4.0
+pair_coeff    1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
+
+neighbor      0.8 bin
+
+timestep      0.002
+thermo	      100
+
+# equilibration run
+
+fix	       1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
+compute_modify 1_temp extra/dof ${dof}
+run	       200
+
+# dynamics run
+
+reset_timestep 0
+unfix          1
+fix            1 all nve/asphere
+
+run	       $t

LAMMPS/accelerate/in.lj

+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+variable        t index 100
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+thermo          100
+
+run		$t

LAMMPS/accelerate/in.lj.5.0

+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+variable        t index 100
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 5.0
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+thermo          100
+
+run		$t

LAMMPS/accelerate/in.phosphate

+# GI-System
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+variable	t index 100
+
+units metal
+atom_style      charge 
+
+read_data 	data.phosphate
+
+replicate	$x $y $z
+
+pair_style      lj/cut/coul/long 15.0
+
+pair_coeff 1 1  0.0 0.29
+pair_coeff 1 2  0.0 0.29
+pair_coeff 1 3  0.000668 2.5738064
+pair_coeff 2 2  0.0 0.29
+pair_coeff 2 3  0.004251 1.91988674
+pair_coeff 3 3  0.012185 2.91706967
+
+kspace_style    pppm 1e-5
+
+neighbor	2.0 bin
+
+thermo          100
+timestep        0.001
+
+fix 		1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
+
+run 		$t

LAMMPS/accelerate/in.rhodo

+# Rhodopsin model
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+variable	t index 100
+
+units           real  
+neigh_modify    delay 5 every 1   
+
+atom_style      full  
+bond_style      harmonic 
+angle_style     charmm 
+dihedral_style  charmm 
+improper_style  harmonic 
+pair_style      lj/charmm/coul/long 8.0 10.0 
+pair_modify     mix arithmetic 
+kspace_style    pppm 1e-4 
+
+read_data       ../../bench/data.rhodo
+
+replicate	$x $y $z
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+fix             2 all npt temp 300.0 300.0 100.0 &
+		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+ 
+thermo          100
+thermo_style    multi 
+timestep        2.0
+
+run	        $t

LAMMPS/accelerate/log.cite

+This LAMMPS simulation made specific use of work described in the
+following references.  See http://lammps.sandia.gov/cite.html
+for details.
+
+GPU package (short-range, long-range and three-body potentials):
+
+@Article{Brown11,
+ author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},
+ title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},
+ journal = {Comp.~Phys.~Comm.},
+ year =    2011,
+ volume =  182,
+ pages =   {898--911}
+}
+
+@Article{Brown12,
+ author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},
+ title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},
+ journal = {Comp.~Phys.~Comm.},
+ year =    2012,
+ volume =  183,
+ pages =   {449--459}
+}
+
+@Article{Brown13,
+ author = {W. M. Brown, Y. Masako},
+ title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},
+ journal = {Comp.~Phys.~Comm.},
+ year =    2013,
+ volume =  184,
+ pages =   {2785--2793}
+}
+

LAMMPS/accelerate/log.lammps

+LAMMPS (11 Aug 2017)
+package gpu 1
+package gpu 2
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+variable        t index 100
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+thermo          100
+
+run		$t
+run		100
+Per MPI rank memory allocation (min/avg/max) = 4.811 | 4.811 | 4.811 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733682            0   -4.6134357   -5.0197069 
+     100   0.75745332   -5.7585059            0   -4.6223615   0.20726081 
+Loop time of 0.0620875 on 2 procs for 100 steps with 32000 atoms
+
+Performance: 695791.827 tau/day, 1610.629 timesteps/s
+91.4% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.022442   | 0.022491   | 0.022539   |   0.0 | 36.22
+Neigh   | 9.5367e-07 | 1.9073e-06 | 2.861e-06  |   0.0 |  0.00
+Comm    | 0.019505   | 0.0196     | 0.019695   |   0.1 | 31.57
+Output  | 4.7922e-05 | 5.4002e-05 | 6.0081e-05 |   0.0 |  0.09
+Modify  | 0.015807   | 0.015847   | 0.015887   |   0.0 | 25.52
+Other   |            | 0.004095   |            |       |  6.59
+
+Nlocal:    16000 ave 16001 max 15999 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    13632.5 ave 13635 max 13630 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

LAMMPS/accelerate/log.lj.1Feb14.gpu.1

+LAMMPS (1 Feb 2014)
+# 3d Lennard-Jones melt
+
+newton          off
+package 	gpu force/neigh 0 1 1
+
+variable	x index 2
+variable	y index 2
+variable	z index 2
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*2
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 40
+create_box	1 box
+Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 256000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut/gpu 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+thermo 		100
+run		1000
+Memory usage per processor = 46.8462 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733683            0   -4.6133768   -5.0196737 
+     100   0.75865617    -5.760326            0   -4.6223462   0.19586079 
+     200   0.75643086   -5.7572859            0   -4.6226441   0.22641241 
+     300   0.74927423   -5.7463997            0   -4.6224927   0.29737707 
+     400   0.74049393   -5.7329259            0   -4.6221893    0.3776681 
+     500   0.73092107   -5.7182622            0   -4.6218849   0.46900655 
+     600   0.72320925   -5.7064076            0   -4.6215979   0.53444495 
+     700   0.71560947   -5.6946702            0   -4.6212602   0.59905402 
+     800   0.71306623   -5.6906095            0   -4.6210143   0.62859381 
+     900   0.70675364   -5.6807352            0   -4.6206089   0.68471945 
+    1000    0.7044073   -5.6771664            0   -4.6205596   0.70033364 
+Loop time of 21.016 on 1 procs for 1000 steps with 256000 atoms
+
+Pair  time (%) = 13.4638 (64.0646)
+Neigh time (%) = 6.74725e-05 (0.000321052)
+Comm  time (%) = 1.09447 (5.20779)
+Outpt time (%) = 0.0103211 (0.0491108)
+Other time (%) = 6.44732 (30.6781)
+
+Nlocal:    256000 ave 256000 max 256000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    69917 ave 69917 max 69917 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 50
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+

LAMMPS/accelerate/log.lj.1Feb14.gpu.4

+LAMMPS (1 Feb 2014)
+# 3d Lennard-Jones melt
+
+newton          off
+package 	gpu force/neigh 0 1 1
+
+variable	x index 2
+variable	y index 2
+variable	z index 2
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*2
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 40
+create_box	1 box
+Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 256000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut/gpu 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+thermo 		100
+run		1000
+Memory usage per processor = 14.5208 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733683            0   -4.6133768   -5.0196737 
+     100   0.75865617    -5.760326            0   -4.6223462   0.19586079 
+     200   0.75643087   -5.7572859            0   -4.6226441    0.2264124 
+     300   0.74927423   -5.7463997            0   -4.6224927   0.29737713 
+     400    0.7404939   -5.7329258            0   -4.6221893   0.37766836 
+     500   0.73092104   -5.7182626            0   -4.6218853   0.46900587 
+     600   0.72320865   -5.7064076            0   -4.6215989   0.53444677 
+     700   0.71560468   -5.6946635            0   -4.6212607   0.59907258 
+     800    0.7130474   -5.6905859            0    -4.621019   0.62875333 
+     900   0.70683795    -5.680864            0   -4.6206112    0.6839564 
+    1000   0.70454326   -5.6773491            0   -4.6205384   0.69975744 
+Loop time of 8.72938 on 4 procs for 1000 steps with 256000 atoms
+
+Pair  time (%) = 5.30046 (60.7198)
+Neigh time (%) = 5.78761e-05 (0.000663004)
+Comm  time (%) = 1.62433 (18.6076)
+Outpt time (%) = 0.0129588 (0.14845)
+Other time (%) = 1.79157 (20.5235)
+
+Nlocal:    64000 ave 64066 max 63924 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost:    30535 ave 30559 max 30518 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 50
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+

LAMMPS/accelerate/log.lj.1Feb14.kokkos.cuda.1

+LAMMPS (27 May 2014)
+KOKKOS mode is enabled (../lammps.cpp:468)
+  using 6 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Memory usage per processor = 16.9509 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 0.57192 on 6 procs (1 MPI x 6 OpenMP) for 100 steps with 32000 atoms
+
+Pair  time (%) = 0.205416 (35.917)
+Neigh time (%) = 0.112468 (19.665)
+Comm  time (%) = 0.174223 (30.4629)
+Outpt time (%) = 0.000159025 (0.0278055)
+Other time (%) = 0.0796535 (13.9274)
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19657 ave 19657 max 19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2405666
+Ave neighs/atom = 75.1771
+Neighbor list builds = 5
+Dangerous builds = 0

LAMMPS/accelerate/log.lj.1Feb14.kokkos.cuda.2

+LAMMPS (27 May 2014)
+KOKKOS mode is enabled (../lammps.cpp:468)
+  using 6 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Memory usage per processor = 8.95027 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 0.689608 on 12 procs (2 MPI x 6 OpenMP) for 100 steps with 32000 atoms
+
+Pair  time (%) = 0.210953 (30.5903)
+Neigh time (%) = 0.122991 (17.8349)
+Comm  time (%) = 0.25264 (36.6353)
+Outpt time (%) = 0.000259042 (0.0375636)
+Other time (%) = 0.102765 (14.9019)
+
+Nlocal:    16000 ave 16001 max 15999 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    13632.5 ave 13635 max 13630 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+FullNghs:  1.20283e+06 ave 1.20347e+06 max 1.2022e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 2405666
+Ave neighs/atom = 75.1771
+Neighbor list builds = 5
+Dangerous builds = 0

LAMMPS/accelerate/log.lj.1Feb14.kokkos.omp.1

+LAMMPS (27 May 2014)
+KOKKOS mode is enabled (../lammps.cpp:468)
+  using 1 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+package         kokkos neigh half
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Memory usage per processor = 7.79551 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 2.29105 on 1 procs (1 MPI x 1 OpenMP) for 100 steps with 32000 atoms
+
+Pair  time (%) = 1.82425 (79.6249)
+Neigh time (%) = 0.338632 (14.7806)
+Comm  time (%) = 0.0366232 (1.59853)
+Outpt time (%) = 0.000144005 (0.00628553)
+Other time (%) = 0.0914049 (3.98965)
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19657 ave 19657 max 19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1202833
+Ave neighs/atom = 37.5885
+Neighbor list builds = 5
+Dangerous builds = 0

LAMMPS/accelerate/log.lj.1Feb14.kokkos.omp.4

+LAMMPS (27 May 2014)
+KOKKOS mode is enabled (../lammps.cpp:468)
+  using 4 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+run		100
+Memory usage per processor = 13.2888 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+Loop time of 0.983697 on 4 procs (1 MPI x 4 OpenMP) for 100 steps with 32000 atoms
+
+Pair  time (%) = 0.767155 (77.9869)
+Neigh time (%) = 0.14734 (14.9782)
+Comm  time (%) = 0.041466 (4.21532)
+Outpt time (%) = 0.000172138 (0.0174991)
+Other time (%) = 0.0275636 (2.80204)
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    19657 ave 19657 max 19657 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  2.40567e+06 ave 2.40567e+06 max 2.40567e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2405666
+Ave neighs/atom = 75.1771
+Neighbor list builds = 5
+Dangerous builds = 0

LAMMPS/accelerate/log.lj.5.0.1Feb14.gpu.1

+LAMMPS (1 Feb 2014)
+# 3d Lennard-Jones melt
+
+newton          off
+package 	gpu force/neigh 0 1 1 threads_per_atom 8
+
+variable	x index 2
+variable	y index 2
+variable	z index 2
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*2
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 40
+create_box	1 box
+Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 256000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut/gpu 5.0
+pair_coeff	1 1 1.0 1.0 5.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+thermo 		100
+run		1000
+Memory usage per processor = 58.5717 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -7.1616931            0   -5.0017016   -5.6743465 
+     100   0.75998441   -6.1430228            0   -5.0030506  -0.43702263 
+     200   0.75772859   -6.1397321            0   -5.0031437  -0.40563811 
+     300   0.75030002   -6.1286578            0   -5.0032122  -0.33104717 
+     400   0.73999054   -6.1132463            0   -5.0032649  -0.24001424 
+     500   0.73224838   -6.1016938            0   -5.0033255  -0.16524979 
+     600   0.72455889   -6.0902001            0    -5.003366 -0.099949772 
+     700   0.71911385   -6.0820798            0   -5.0034133 -0.046759186 
+     800   0.71253787   -6.0722342            0   -5.0034316 0.0019671065 
+     900   0.70835425   -6.0659819            0   -5.0034546  0.037482543 
+    1000   0.70648171   -6.0631852            0   -5.0034668  0.057159495 
+Loop time of 53.1575 on 1 procs for 1000 steps with 256000 atoms
+
+Pair  time (%) = 45.4859 (85.5682)
+Neigh time (%) = 7.9155e-05 (0.000148907)
+Comm  time (%) = 1.40304 (2.63941)
+Outpt time (%) = 0.00999498 (0.0188026)
+Other time (%) = 6.25847 (11.7734)
+
+Nlocal:    256000 ave 256000 max 256000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    141542 ave 141542 max 141542 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 50
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+

LAMMPS/accelerate/log.lj.5.0.1Feb14.gpu.4

+LAMMPS (1 Feb 2014)
+# 3d Lennard-Jones melt
+
+newton          off
+package 	gpu force/neigh 0 1 1 threads_per_atom 8
+
+variable	x index 2
+variable	y index 2
+variable	z index 2
+
+variable	xx equal 20*$x
+variable	xx equal 20*2
+variable	yy equal 20*$y
+variable	yy equal 20*2
+variable	zz equal 20*$z
+variable	zz equal 20*2
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 40 0 ${yy} 0 ${zz}
+region		box block 0 40 0 40 0 ${zz}
+region		box block 0 40 0 40 0 40
+create_box	1 box
+Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 256000 atoms
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut/gpu 5.0
+pair_coeff	1 1 1.0 1.0 5.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+thermo 		100
+run		1000
+Memory usage per processor = 20.382 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -7.1616931            0   -5.0017016   -5.6743465 
+     100   0.75998441   -6.1430228            0   -5.0030506  -0.43702263 
+     200   0.75772859   -6.1397321            0   -5.0031437  -0.40563811 
+     300   0.75030002   -6.1286578            0   -5.0032122  -0.33104718 
+     400   0.73999055   -6.1132463            0   -5.0032649  -0.24001425 
+     500   0.73224835   -6.1016938            0   -5.0033256  -0.16524973 
+     600   0.72455878      -6.0902            0   -5.0033661 -0.099949172 
+     700   0.71911606   -6.0820833            0   -5.0034134 -0.046771469 
+     800   0.71253754   -6.0722337            0   -5.0034316 0.0019725827 
+     900   0.70832904   -6.0659437            0   -5.0034543   0.03758241 
+    1000   0.70634002    -6.062973            0   -5.0034671  0.057951142 
+Loop time of 26.0448 on 4 procs for 1000 steps with 256000 atoms
+
+Pair  time (%) = 18.6673 (71.674)
+Neigh time (%) = 6.55651e-05 (0.00025174)
+Comm  time (%) = 5.797 (22.2578)
+Outpt time (%) = 0.0719919 (0.276416)
+Other time (%) = 1.50839 (5.79152)
+
+Nlocal:    64000 ave 64092 max 63823 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost:    64384.2 ave 64490 max 64211 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 50
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+

LAMMPS/accelerate/log.phosphate.1Feb14.gpu.1

+LAMMPS (1 Feb 2014)
+# GI-System
+
+units metal
+newton off
+package		gpu force/neigh 0 1 1
+
+atom_style      charge
+read_data 	data.phosphate
+  orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  10950 atoms
+  reading velocities ...
+  10950 velocities
+
+replicate 	3 3 3
+  orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
+  1 by 1 by 1 MPI processor grid
+  295650 atoms
+
+pair_style      lj/cut/coul/long/gpu 15.0
+
+pair_coeff 1 1  0.0 0.29
+pair_coeff 1 2  0.0 0.29
+pair_coeff 1 3  0.000668 2.5738064
+pair_coeff 2 2  0.0 0.29
+pair_coeff 2 3  0.004251 1.91988674
+pair_coeff 3 3  0.012185 2.91706967
+
+kspace_style    pppm/gpu 1e-5
+
+neighbor	2.0 bin
+
+thermo 100
+
+timestep 0.001
+
+fix 		1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
+run 		200
+PPPM initialization ...
+  G vector (1/distance) = 0.210051
+  grid = 108 108 108
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000178801
+  estimated relative force accuracy = 1.24171e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 1520875 1259712
+Memory usage per processor = 266.927 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0    400.30257   -2381941.6            0   -2366643.8   -449.96842    4242016.4 
+     100    411.69681   -2392428.5            0   -2376695.3     7046.698    4308883.5 
+     200    401.28392   -2394152.5            0   -2378817.2    3243.2685    4334284.4 
+Loop time of 154.943 on 1 procs for 200 steps with 295650 atoms
+
+Pair  time (%) = 12.0178 (7.75625)
+Kspce time (%) = 80.3771 (51.8753)
+Neigh time (%) = 0.0138304 (0.00892614)
+Comm  time (%) = 0.348981 (0.225232)
+Outpt time (%) = 0.00180006 (0.00116176)
+Other time (%) = 62.1834 (40.1331)
+
+FFT time (% of Kspce) = 56.9885 (70.9013)
+FFT Gflps 3d (1d only) = 1.24196 3.00739
+
+Nlocal:    295650 ave 295650 max 295650 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    226982 ave 226982 max 226982 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 6
+Dangerous builds = 0
+unfix 		1
+
+Please see the log.cite file for references relevant to this simulation
+

LAMMPS/accelerate/log.phosphate.1Feb14.gpu.4

+LAMMPS (1 Feb 2014)
+# GI-System
+
+units metal
+newton off
+package		gpu force/neigh 0 1 1
+
+atom_style      charge
+read_data 	data.phosphate
+  orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  10950 atoms
+  reading velocities ...
+  10950 velocities
+
+replicate 	3 3 3
+  orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
+  2 by 1 by 2 MPI processor grid
+  295650 atoms
+
+pair_style      lj/cut/coul/long/gpu 15.0
+
+pair_coeff 1 1  0.0 0.29
+pair_coeff 1 2  0.0 0.29
+pair_coeff 1 3  0.000668 2.5738064
+pair_coeff 2 2  0.0 0.29
+pair_coeff 2 3  0.004251 1.91988674
+pair_coeff 3 3  0.012185 2.91706967
+
+kspace_style    pppm/gpu 1e-5
+
+neighbor	2.0 bin
+
+thermo 100
+
+timestep 0.001
+
+fix 		1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
+run 		200
+PPPM initialization ...
+  G vector (1/distance) = 0.210051
+  grid = 108 108 108
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000178801
+  estimated relative force accuracy = 1.24171e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 427915 314928
+Memory usage per processor = 80.0769 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0    400.30257   -2381941.6            0   -2366643.8   -449.96842    4242016.4 
+     100    411.69681   -2392428.5            0   -2376695.3     7046.698    4308883.5 
+     200    401.28392   -2394152.5            0   -2378817.2    3243.2685    4334284.4 
+Loop time of 56.1151 on 4 procs for 200 steps with 295650 atoms
+
+Pair  time (%) = 4.55937 (8.12503)
+Kspce time (%) = 34.5442 (61.5596)
+Neigh time (%) = 0.00624901 (0.0111361)
+Comm  time (%) = 0.470437 (0.838343)
+Outpt time (%) = 0.000446558 (0.000795789)
+Other time (%) = 16.5344 (29.4651)
+
+FFT time (% of Kspce) = 22.6526 (65.5758)
+FFT Gflps 3d (1d only) = 3.12448 11.5533
+
+Nlocal:    73912.5 ave 74223 max 73638 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Nghost:    105257 ave 105797 max 104698 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 6
+Dangerous builds = 0
+unfix 		1
+
+Please see the log.cite file for references relevant to this simulation
+

LAMMPS/accelerate/log.rhodo.1Feb14.gpu.1

+LAMMPS (1 Feb 2014)
+# Rhodopsin model
+
+newton off
+package 	gpu force/neigh 0 1 1
+
+variable	x index 2
+variable	y index 2
+variable	z index 2
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long/gpu 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm/gpu 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  18 = max angles/atom
+  scanning dihedrals ...
+  40 = max dihedrals/atom
+  scanning impropers ...
+  4 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+replicate	$x $y $z
+replicate	2 $y $z
+replicate	2 2 $z
+replicate	2 2 2
+  orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
+  1 by 1 by 1 MPI processor grid
+  256000 atoms
+  221784 bonds
+  323736 angles
+  454632 dihedrals
+  8272 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  12936 = # of size 2 clusters
+  29064 = # of size 3 clusters
+  5976 = # of size 4 clusters
+  33864 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          100
+thermo_style    multi
+timestep        2.0
+
+run		200
+PPPM initialization ...
+  G vector (1/distance) = 0.245959
+  grid = 48 64 60
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0410392
+  estimated relative force accuracy = 0.000123588
+  using double precision FFTs
+  3d grid and FFT values/proc = 237705 184320
+Memory usage per processor = 760.048 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    157024.0504 KinEng   =    172792.6155 Temp     =       301.1796 
+PotEng   =    -15768.5651 E_bond   =     28164.9917 E_angle  =    117224.0742 
+E_dihed  =     61174.8491 E_impro  =      3752.0273 E_vdwl   =     10108.6323 
+E_coul   =   1894295.6635 E_long   =  -2130488.8032 Press    =      9562.1557 
+Volume   =   2457390.7959 
+---------------- Step      100 ----- CPU =     36.3779 (sec) ----------------
+TotEng   =   -233301.6813 KinEng   =    123222.9259 Temp     =       214.7790 
+PotEng   =   -356524.6072 E_bond   =     13098.4672 E_angle  =     56766.9111 
+E_dihed  =     45556.8240 E_impro  =      1313.9378 E_vdwl   =    -40863.9278 
+E_coul   =   1705084.7672 E_long   =  -2137481.5867 Press    =     -1634.3912 
+Volume   =   2522232.6302 
+---------------- Step      200 ----- CPU =     70.7784 (sec) ----------------
+TotEng   =   -308342.0030 KinEng   =    108937.4160 Temp     =       189.8792 
+PotEng   =   -417279.4189 E_bond   =      9579.0134 E_angle  =     47373.6274 
+E_dihed  =     39847.4817 E_impro  =       967.6755 E_vdwl   =    -23635.2960 
+E_coul   =   1646633.4711 E_long   =  -2138045.3918 Press    =     -1185.9327 
+Volume   =   2554683.1533 
+Loop time of 70.7784 on 1 procs for 200 steps with 256000 atoms
+
+Pair  time (%) = 10.0374 (14.1815)
+Bond  time (%) = 27.2471 (38.4963)
+Kspce time (%) = 7.19169 (10.1608)
+Neigh time (%) = 5.43951 (7.68527)
+Comm  time (%) = 0.681534 (0.962912)
+Outpt time (%) = 0.00139809 (0.0019753)
+Other time (%) = 20.1798 (28.5112)
+
+FFT time (% of Kspce) = 5.17983 (72.0253)
+FFT Gflps 3d (1d only) = 1.72575 2.95071
+
+Nlocal:    256000 ave 256000 max 256000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    161662 ave 161662 max 161662 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 31
+Dangerous builds = 12
+
+Please see the log.cite file for references relevant to this simulation
+

LAMMPS/accelerate/log.rhodo.1Feb14.gpu.4

+LAMMPS (1 Feb 2014)
+# Rhodopsin model
+
+newton off
+package 	gpu force/neigh 0 1 1
+
+variable	x index 2
+variable	y index 2
+variable	z index 2
+
+units           real
+neigh_modify    delay 5 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long/gpu 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm/gpu 1e-4
+
+read_data       data.rhodo
+  orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  32000 atoms
+  reading velocities ...
+  32000 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  18 = max angles/atom
+  scanning dihedrals ...
+  40 = max dihedrals/atom
+  scanning impropers ...
+  4 = max impropers/atom
+  reading bonds ...
+  27723 bonds
+  reading angles ...
+  40467 angles
+  reading dihedrals ...
+  56829 dihedrals
+  reading impropers ...
+  1034 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+replicate	$x $y $z
+replicate	2 $y $z
+replicate	2 2 $z
+replicate	2 2 2
+  orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
+  1 by 2 by 2 MPI processor grid
+  256000 atoms
+  221784 bonds
+  323736 angles
+  454632 dihedrals
+  8272 impropers
+  4 = max # of 1-2 neighbors
+  12 = max # of 1-3 neighbors
+  24 = max # of 1-4 neighbors
+  26 = max # of special neighbors
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+  12936 = # of size 2 clusters
+  29064 = # of size 3 clusters
+  5976 = # of size 4 clusters
+  33864 = # of frozen angles
+fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          100
+thermo_style    multi
+timestep        2.0
+
+run		200
+PPPM initialization ...
+  G vector (1/distance) = 0.245959
+  grid = 48 64 60
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0410392
+  estimated relative force accuracy = 0.000123588
+  using double precision FFTs
+  3d grid and FFT values/proc = 68635 46080
+Memory usage per processor = 250.358 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =    157024.0504 KinEng   =    172792.6155 Temp     =       301.1796 
+PotEng   =    -15768.5651 E_bond   =     28164.9917 E_angle  =    117224.0742 
+E_dihed  =     61174.8491 E_impro  =      3752.0273 E_vdwl   =     10108.6323 
+E_coul   =   1894295.6635 E_long   =  -2130488.8032 Press    =      9562.1557 
+Volume   =   2457390.7959 
+---------------- Step      100 ----- CPU =     12.3409 (sec) ----------------
+TotEng   =   -233301.6797 KinEng   =    123222.9259 Temp     =       214.7790 
+PotEng   =   -356524.6057 E_bond   =     13098.4672 E_angle  =     56766.9111 
+E_dihed  =     45556.8240 E_impro  =      1313.9378 E_vdwl   =    -40863.9278 
+E_coul   =   1705084.7688 E_long   =  -2137481.5867 Press    =     -1634.3910 
+Volume   =   2522232.6302 
+---------------- Step      200 ----- CPU =     23.6590 (sec) ----------------
+TotEng   =   -308341.9699 KinEng   =    108937.4196 Temp     =       189.8792 
+PotEng   =   -417279.3895 E_bond   =      9579.0134 E_angle  =     47373.6274 
+E_dihed  =     39847.4807 E_impro  =       967.6755 E_vdwl   =    -23635.2996 
+E_coul   =   1646633.5046 E_long   =  -2138045.3916 Press    =     -1185.9299 
+Volume   =   2554683.1519 
+Loop time of 23.6591 on 4 procs for 200 steps with 256000 atoms
+
+Pair  time (%) = 4.81669 (20.3587)
+Bond  time (%) = 6.52579 (27.5826)
+Kspce time (%) = 4.48765 (18.968)
+Neigh time (%) = 1.3238 (5.5953)
+Comm  time (%) = 0.490551 (2.07342)
+Outpt time (%) = 0.000454485 (0.00192098)
+Other time (%) = 6.01414 (25.42)
+
+FFT time (% of Kspce) = 1.77734 (39.6051)
+FFT Gflps 3d (1d only) = 5.02949 11.6654
+
+Nlocal:    64000 ave 64001 max 63999 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:    70656.5 ave 70660 max 70654 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Ave special neighs/atom = 7.43187
+Neighbor list builds = 31
+Dangerous builds = 12
+
+Please see the log.cite file for references relevant to this simulation
+

LAMMPS/accelerate/slurm-13027206.out

+LAMMPS (11 Aug 2017)
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 1 by 2 MPI processor grid
+Created 32000 atoms
+
+--------------------------------------------------------------------------
+- Using acceleration for lj/cut:
+-  with 1 proc(s) per device.
+--------------------------------------------------------------------------
+Device 0: Tesla P100-PCIE-12GB, 56 CUs, 12/12 GB, 1.3 GHZ (Mixed Precision)
+Device 1: Tesla P100-PCIE-12GB, 56 CUs, 1.3 GHZ (Mixed Precision)
+--------------------------------------------------------------------------
+
+Initializing Device and compiling on process 0...Done.
+Initializing Devices 0-1 on core 0...Done.
+
+Setting up Verlet run ...
+  Unit style    : lj
+  Current step  : 0
+  Time step     : 0.005
+Per MPI rank memory allocation (min/avg/max) = 4.811 | 4.811 | 4.811 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733682            0   -4.6134357   -5.0197069 
+     100   0.75745332   -5.7585059            0   -4.6223615   0.20726081 
+Loop time of 0.0620875 on 2 procs for 100 steps with 32000 atoms
+
+Performance: 695791.827 tau/day, 1610.629 timesteps/s
+91.4% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.022442   | 0.022491   | 0.022539   |   0.0 | 36.22
+Neigh   | 9.5367e-07 | 1.9073e-06 | 2.861e-06  |   0.0 |  0.00
+Comm    | 0.019505   | 0.0196     | 0.019695   |   0.1 | 31.57
+Output  | 4.7922e-05 | 5.4002e-05 | 6.0081e-05 |   0.0 |  0.09
+Modify  | 0.015807   | 0.015847   | 0.015887   |   0.0 | 25.52
+Other   |            | 0.004095   |            |       |  6.59
+
+Nlocal:    16000 ave 16001 max 15999 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    13632.5 ave 13635 max 13630 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5
+Dangerous builds not checked
+
+
+---------------------------------------------------------------------
+      Device Time Info (average): 
+---------------------------------------------------------------------
+Data Transfer:   0.0096 s.
+Data Cast/Pack:  0.0120 s.
+Neighbor copy:   0.0000 s.
+Neighbor build:  0.0029 s.
+Force calc:      0.0056 s.
+Device Overhead: 0.0029 s.
+Average split:   1.0000.
+Threads / atom:  4.
+Max Mem / Proc:  22.78 MB.
+CPU Driver_Time: 0.0031 s.
+CPU Idle_Time:   0.0047 s.
+---------------------------------------------------------------------
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

LAMMPS/accelerate/submit_gpu

+#!/bin/bash
+
+#SBATCH --account=hpcadmingpgpu # Use a project ID that has access.
+#SBATCH --partition=gpgputest
+#SBATCH --gres=gpu:2 
+#SBATCH --time=0:10:00
+#SBATCH --ntasks=2
+#SBATCH --cpus-per-task=2
+#SBATCH --mem-per-cpu=4G
+
+module load LAMMPS/20170811-intel-2017.u2-GCC-6.2.0-CUDA9.1
+
+mpiexec lmp_intel_gpu -sf gpu -pk gpu 2 -in in.lj 
+
+

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

Mathematica/test.m

+Print["Hello, starting plots!"]
+SetOptions[DensityPlot,DisplayFunction->Identity]
+a=Table[DensityPlot[Sin[Sqrt[x^2 + y^2]]^2/(.001 + x^2 + y^2), {x, -13, 13}, {y, -13, 13}\
+, Mesh ->  False, PlotPoints -> 300], {i, 1, 20}]
+Do[Export["a"<>ToString[i]<>".eps",a[[i]]],{i,1,20}]
+Exit[]

README

@@ -31,7 +31,7 @@ We use LMod to manage existing software installations. Because Spartan is a gene
 This is particularly true of applications that are a language in their own right (e.g. Python, R, Matlab) or that need to be matched to those types of applications (e.g. Tensorflow needs to be compiled against a specific Python version, which then needs to be loaded alongside it when it is used).
 LMod allows us to assert that certain modules are necessary to make other modules run, and then load them automatically. As such, you can (in almost all standard cases) simply load the application you wish to use and all required components will be loaded as part of that.
 
-Typing `module avail` will show a complete list of currently installed software. You can do a simple search with this command by adding the search term to the end (e.g. `module avail Tensorflow`), or can do basic regex searches with the '-r' flag (e.g. `module -r avail '^Python'`).
+Typing `module avail` will show a complete list of currently installed software. You can do a simple search with this command by adding the search term to the end (e.g. `module avail Tensorflow`), or can do basic regex searches with the '-r' flag (e.g. `module -r avail '^Python'`). Note that this is limited to your compiler options. To view all available software and adopt a mix of compilers you will need to source the old configuration system (`source /usr/local/module/spartan_old.sh`).
 
 Typing `module list` will show a complete list of software currently loaded into your user environment. We load a few little modules into your environment when you log in by default, none of these are specifically necessary to use the cluster.
 

RegEx/basicsed.md

@@ -58,8 +58,8 @@ Adding the `w` option will print out the selection line to a new file.
 
 sed 's/ELM/LUV/gw selection.txt' gattaca.txt
 
-Quoting
-=======
+Quoting & Variables
+===================
 
 Generally strong quotes are recommended for regular expressions. However, sed often wants to use weak quotes to include (for example) variable substitution.
 
@@ -114,6 +114,10 @@ One can add new material to a file in such a manner with the insert option:
 
 `sed '1,2 i\foo' file` or `sed '1,2i foo' file` 
 
+Select duplicate words in a line and remove.
+
+`sed -e 's/\b\([a-z]\+\)[ ,\n]\1/\1/g' file`
+
 Multiple Commands
 =================
 

RegEx/python.md

 The re Package and Metacharacters
 =================================
 
-Python's re package can be used for regular expressions, and can be tested with similar metacharacters to those used in POSIX.
-
-```
-import re
-string1 = "The quick brown fox jumps over the lazy dog"
-startend = re.search("^The.*dog$", string1)
-
-if (startend):
-	print("String starts with 'The' and ends with 'dog'")
-else:
-	print("String does not start with 'The' and end with 'dog'")
-```
+Python's re package can be used for regular expressions, and can be tested with similar metacharacters to those used in POSIX. See `startend.py`
 
 The following is a list of the most common metacharacters used in `re`.
 
 Metacharacter	| Meaning
 :---------------|----------------------------------------------------------:
-	.			Any character except new line.
-	^			Start of a string.
-	$			End of a string
-	*			Zero or more repetitions of the preceeding RegEx.
-	?			Zero or one repetitions of the preceeding RegEx; ab? will match either ‘a’ or ‘ab’
-	+			Matches one or more repetitions of the preceeding RegEx; ab+ will match ‘a’ followed by any non-zero number of ‘b’s; it will not match just ‘a’
-	*?, +?, ??	The '*', '+', and '?' qualifiers are all greedy; they match as much text as possible. Adding ? after the qualifier makes it perform the match in a minimal fashion with as few characters as possible will be matched.
-	{m}			Specifies exactly m copies of the previous RegEx are matched.
-	{m,n}    	Match from m to n repetitions of the preceding RegEx, attempting to match as many repetitions as possible. For example, a{3,5} will match from 3 to 5 'a' characters. 
-	{m,n}?    	Match from m to n repetitions of the preceding RegEx, with as few repetitions as possible. 	
-	\ 			Either escapes special characters (permitting you to match characters like '*', '?', etc), or signals a special sequence.
-	[]			Used to indicate a set of characters, either individually (e.g., [ACGT]) or a range [A-Z]. Special characters lose their meaning in sets (e.g., [(+*)] will literally match (, +, *, or ). Characters that are not within a range can be matched by complementing the set with an initial ^ (e.g., [^5], not 5).To match a ']' inside a set, precede with a backslash or place at the beginning of the set.
-	|			In A|B in a RegEx, match either A or B. 
-	(...)		Match RegEx inside parantheses as a group. Use \ to escape and match literal parantheses. or enclose them in a class.
+.		Any character except new line.
+^		Start of a string.
+$		End of a string
+*		Zero or more repetitions of the preceeding RegEx.
+?		Zero or one repetitions of the preceeding RegEx; ab? will match either ‘a’ or ‘ab’
++		Matches one or more repetitions of the preceeding RegEx; ab+ will match ‘a’ followed by any non-zero number of ‘b’s; it will not match just ‘a’
+*?, +?, ??	The '*', '+', and '?' qualifiers are all greedy; they match as much text as possible. Adding ? after the qualifier makes it perform the match in a minimal fashion with as few characters as possible will be matched.
+{m}		Specifies exactly m copies of the previous RegEx are matched.
+{m,n}    	Match from m to n repetitions of the preceding RegEx, attempting to match as many repetitions as possible. For example, a{3,5} will match from 3 to 5 'a' characters. 
+{m,n}?    	Match from m to n repetitions of the preceding RegEx, with as few repetitions as possible. 	
+\ 		Either escapes special characters (permitting you to match characters like '*', '?', etc), or signals a special sequence.
+[]		Used to indicate a set of characters, either individually (e.g., [ACGT]) or a range [A-Z]. Special characters lose their meaning in sets (e.g., [(+*)] will literally match (, +, *, or ). Characters that are not within a range can be matched by complementing the set with an initial ^ (e.g., [^5], not 5).To match a ']' inside a set, precede with a backslash or place at the beginning of the set.
+|		In A|B in a RegEx, match either A or B. 
+(...)		Match RegEx inside parantheses as a group. Use \ to escape and match literal parantheses. or enclose them in a class.
 
 Special Sequences
 
 The following is a list of common special sequences
 
-	\d			Matches any decimal digit, equivalent to the class [0-9].
-	\D			Matches any non-digit character, equivalent to the class [^0-9].
-	\s    		Matches any whitespace character, equivalent to the class [ \t\n\r\f\v].
-	\S			Matches any non-whistespace.
-	\w			Matches any alphanumeric,  equivalent to the class [a-zA-Z0-9_].	\W			Matches any non-alphanumeric
+\d		Matches any decimal digit, equivalent to the class [0-9].
+\D		Matches any non-digit character, equivalent to the class [^0-9].
+\s    		Matches any whitespace character, equivalent to the class [ \t\n\r\f\v].
+\S		Matches any non-whistespace.
+\w		Matches any alphanumeric,  equivalent to the class [a-zA-Z0-9_].
+\W		Matches any non-alphanumeric
 
 
 Pattern Objects
@@ -58,7 +48,7 @@ print regexsearch
 Backslash Issues in Python
 ==========================
 
-As the norm with out RegExes, the backslash is used to escape metacharaters, and a double backslash is used to for a literal backslash. However, Python uses the same character for the same purpose in string literals.
+As the norm with RegExes, the backslash is used to escape metacharaters, and a double backslash is used to for a literal backslash. However, Python uses the same character for the same purpose in string literals.
 
 Thus, in Python, to have a regular expression that matches, say, \documentclass (used in LaTeX), the backslash has to be escaped for re.compile() and then both backslashes have to be escaped for a string literal - resulting in *four* backslashes.
 
@@ -145,6 +135,9 @@ splitseq = re.split("", contents, 1)
 print(splitseq)
 ```
 
+
+
+
 References
 ==========
 

SSH/REAME

+=================
+TABLE OF CONTENTS
+=================
+
+1. Accessing Spartan
+2. Passwordless SSH
+3. SSH Config Files
+
+
+1. Accessing Spartan
+====================
+
+Access to Spartan is with SSH (secure shell). This allows remote accesss to computer systems that are more secure than previous protocols, such as rlogin and telnet which sent passwords over the network in plain-text.
+
+SSH can be used with other networking services for file transfers, remote mounts, etc.
+
+To access Spartan, you will need an SSH client. This is available on nearly all distributions of Linux and MacOS X. For MS-Windows you may need to download a client (e.g., PuTTY from http://putty.org)
+
+From a terminal client use the command ...
+
+$ ssh username@spartan.hpc.unimelb.edu.au
+
+... and enter your password when prompted.
+
+
+2. Passwordless SSH
+====================
+
+A passwordless SSH for Spartan will make your life easier. You won't even need to remember your password!
+
+If you have a *nix system (e.g., UNIX, Linux, MacOS X) open up a terminal on your local system (not Spartan) and generate a keypair.
+
+$ ssh-keygen -t rsa
+Generating public/private rsa key pair.
+Enter file in which to save the key (/home/user/.ssh/id_rsa): 
+Created directory '/home/user/.ssh'.
+Enter passphrase (empty for no passphrase): 
+Enter same passphrase again: 
+Your identification has been saved in /home/user/.ssh/id_rsa.
+Your public key has been saved in /home/user/.ssh/id_rsa.pub.
+The key fingerprint is:
+43:51:43:a1:b5:fc:8b:b7:0a:3a:a9:b1:0f:66:73:a8 user@localhost
+
+Now append the new public key to ~/.ssh/authorized_keys on Spartan (you'll be asked for your password one last time).
+
+$ cat .ssh/id_rsa.pub | ssh username@spartan.hpc.unimelb.edu.au 'cat >> .ssh/authorized_keys'
+
+Depending on your version of SSH you might also have to do the following changes:
+
+    Put the public key in .ssh/authorized_keys2
+    Change the permissions of .ssh to 700
+    Change the permissions of .ssh/authorized_keys2 to 640
+
+You can now SSH to Spartan without having to enter your password!
+
+3. SSH Config Files
+===================
+
+An SSH config file will also make your life easier. It allows you to create alises (i.e. shortcuts) for a given hostname.
+
+Create the text file in your ~/.ssh directory with your preferred text editor, for example, nano.
+
+nano .ssh/config
+
+Enter the following (replacing username with your actual username of course!):
+
+Host *
+ServerAliveInterval 120
+Host spartan
+       Hostname spartan.hpc.unimelb.edu.au
+       User username
+
+Now to connect to Spartan, you need only type ssh spartan.
+
+

Tcl/Tcl-test.slurm

+#!/bin/bash
+
+# Partition and name
+#SBATCH --job-name=Tcl-test.slurm
+#SBATCH -p cloud
+
+# Run on single CPU
+#SBATCH --ntasks=1
+
+# set your minimum acceptable walltime=days-hours:minutes:seconds
+#SBATCH -t 0:05:00
+
+# 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 Tcl/8.6.9-GCC-8.2.0
+
+# Print "Hello World" as an array
+tclsh hello.tcl >> results.txt
+

Tcl/hello.tcl

+puts "Hello, world!"

Trimmomatic/trim.slurm

+#!/bin/bash
+#SBATCH --job-name="trimm_sample"
+#SBATCH --partition=cloud
+# A multithreaded application
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --time=0:15:00
+
+module load Trimmomatic/0.36-Java-1.8.0_152 
+
+java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar PE -threads 4 SRR2589044_1.fastq.gz SRR2589044_2.fastq.gz \
+                SRR2589044_1.trim.fastq.gz SRR2589044_1un.trim.fastq.gz \
+                SRR2589044_2.trim.fastq.gz SRR2589044_2un.trim.fastq.gz \
+                SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15

Trimmomatic/trimloop.slurm

+#!/bin/bash
+#SBATCH --job-name="trimmloop_sample"
+#SBATCH --partition=cloud
+# A multithreaded application
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --time=0:15:00
+
+module load Trimmomatic/0.36-Java-1.8.0_152 
+
+for infile in ./*_1.fastq.gz
+do
+	base=$(basename ${infile} _1.fastq.gz)
+	java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar PE -threads 4 ${infile} ${base}_2.fastq.gz \
+	${base}_1.trim.fastq.gz ${base}_1un.trim.fastq.gz \
+	${base}_2.trim.fastq.gz ${base}_2un.trim.fastq.gz \
+	SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15
+done	

web_proxy/README.md

+Archtitecture Considerations
+============================
+
+Spartan login nodes have connection to the public Internet.
+
+Spartan compute nodes do not have connection to the public Internet.
+
+When trying to connect to the public Internet via a compute node, whether as part of a Slurm script or an interactive job, the task will fail.
+
+e.g.,
+[lev@spartan-rc035 ~]$ wget https://upload.wikimedia.org/wikipedia/commons/thumb/5/5b/Linux_kernel_map.png/800px-Linux_kernel_map.png
+--2019-11-25 10:56:06--  https://upload.wikimedia.org/wikipedia/commons/thumb/5/5b/Linux_kernel_map.png/800px-Linux_kernel_map.png
+Resolving upload.wikimedia.org (upload.wikimedia.org)... 103.102.166.240, 2001:df2:e500:ed1a::2:b
+Connecting to upload.wikimedia.org (upload.wikimedia.org)|103.102.166.240|:443... failed: No route to host.
+Connecting to upload.wikimedia.org (upload.wikimedia.org)|2001:df2:e500:ed1a::2:b|:443... failed: Network is unreachable.
+
+In contrast, if the module web_proxy is loaded a proxy environment path will be established which allows connection to the public Internet.
+
+Try:
+
+sbatch fail.slurm
+sbatch succeed.slurm
+
+Run an interactive job and compare the the environment.
+
+[lev@spartan-login1 ~]$ sinteractive
+srun: job 12960294 queued and waiting for resources
+srun: job 12960294 has been allocated resources
+[lev@spartan-rc035 ~]$ module load web_proxy
+[lev@spartan-rc035 ~]$ env | grep 'proxy=http'
+[lev@spartan-rc035 ~]$ env | grep 'proxy=http'
+http_proxy=http://wwwproxy.unimelb.edu.au:8000
+ftp_proxy=http://wwwproxy.unimelb.edu.au:8000
+https_proxy=http://wwwproxy.unimelb.edu.au:8000
+

web_proxy/fail.slurm

+#!/bin/bash
+
+#SBATCH --partition=cloud
+#SBATCH --time=0:2:00
+
+wget https://upload.wikimedia.org/wikipedia/commons/thumb/5/5b/Linux_kernel_map.png/800px-Linux_kernel_map.png
+

web_proxy/succeed.slurm

+#!/bin/bash
+
+#SBATCH --partition=cloud
+#SBATCH --time=0:2:00
+
+module load web_proxy
+
+wget https://upload.wikimedia.org/wikipedia/commons/thumb/5/5b/Linux_kernel_map.png/800px-Linux_kernel_map.png
+