Software on M3

M3 uses a modular system to manage software.

Modules

Modules is software installed on M3 that provides an easy mechanism for updating your environment variables, so that your environment uses the correct version of software and libraries installed on M3.

Installed software modules

Jump to software beginning with A B C D E F G H I J K L M N O P Q R S T U V W X Y Z.

Attention

Some software packages on M3 have license conditions that restrict access to the software to certain user groups. These software packages are marked with the restricted keyword. To apply for access to restricted software, log in to the HPC ID system and navigate to the Software section of your profile. To enquire about restricted software contact the MASSIVE Help Desk

Note

Software packages with a version named ansto are copies of the software installed on the ASCI facility

Note

The Monash Bioinformatics Platform (MBP) maintains a software stack on M3. More information, including how to access this software stack, can be found on the Bioinformatics community page.

Software

Version(s)

3daprecon restricted

0.0.1, 1.0

3depict restricted

0.0.15

3dslicer

4.10.2, 4.6.0, 4.8.1

A

abaqus restricted

6.14

abinit

8.8.3

abricate

0.8.13

abyss

2.0.2

adapterremoval

2.3.1

adf

2019.104

adxv

1.9.12

afni

16.2.16, 17.0.11

align2rawsignal

2.0

allpathslg

52488

amber restricted

18-multi-gpus, 18-parallel, 18-serial, 18-single-gpu

amira restricted

6.3.0, 6.4.0, 6.5.0

anaconda

2018.12-Python3.7-gcc6, 2019.03-Python3.7-gcc5, 4.3.1-Python3.5, 4.3.1-Python3.5-gcc5, 5.0.1-Python2.7-gcc5, 5.0.1-Python3.5-gcc5, 5.0.1-Python3.6-gcc5, 5.1.0-Python3.6-gcc5

analyze restricted

12.0

analyze-temp

12.0

ansys restricted

18.1, 19.1, 19.2

ants

1.9.v4, 20190910, 2.2.0, 2.3.1

apex

latest

apr

1.6.5

apr-util

1.6.1

argos

3.0.0-beta52

ariba

2.12.1

armadillo

9.200-rc1

arpack

2.1, 3.1.3-2

ascp

3.5.4

ashs

1.0.0

atlas

3.10.2-gcc4, 3.10.2-gcc5

atom

1.39.1

atomprobedevcode restricted

1.0.0(default)

attr

2.4.46-12

augustus

3.3.3

autodock_vina

1.1.2

automake

1.16.1, 1.4-p6

autometa

2019-09

avizo restricted

9.0.1, 9.3.0, 9.3.0.1, 9.4.0, 9.5.0, 9.7

axel

2.12

B

bamsurgeon

1.2

bamtools

2.4.1

barrnap

0.9

bart

0.4.04, 0.4.04-cuda9.0

bayenv

2.0

bayesass

1.3, 3.04

bayescan

2.1

bbcp

17.12

bcbtoolkit

4.0.0

bcftools

1.6, 1.7, 1.8

bcl2fastq

2.19.1

beagle

2.1.2, 3.1.2

beast1

1.10.0, 1.8.4

beast2

2.4.7, 2.4.8, 2.5.0

bedtools

2.26.0, 2.26.0-gcc5, 2.27.1-gcc5

bgen

1.1.4

bids-validator

1.3.1, 2019.01

bidscoin

2.2

bigdatascript

v0.99999e

bigwigtowig

377-0

bilm-tf

1.0

biscuit

0.2.2, 0.3.8.20180515

bismark

v0.19.1

bison

2.7.1

blas

3.8.0-gcc5, 3.8.0-gcc5-pic

blast

2.2.30, 2.3.0, 2.7.1(default)

blast+

2.9.0

blender

2.81

bolt-lmm

2.3.2, 2.3.4

boost

1.46.0-gcc5, 1.46.1-gcc5, 1.52.0-gcc5, 1.58.0, 1.58.0-gcc5, 1.62.0, 1.62.0-gcc4, 1.67.0-gcc5

bowtie

1.1.2

bowtie2

2.2.9, 2.3.5

bracken

2.5

brain_age

v1.0_18Jan2018

breseq

0.29.0, 0.33.2

bsoft

1.9.2, 2.0(default)

busco

3.0.2

buster

20170508

bwa

0.7.12, 0.7.17-gcc5

bwa-meth

0.2.2

bzip2

1.0.6

C

caffe

1.0.0, 1.0.0-protbuf32, caffe-matlab, caffe-tsn, deepvistool, latest(default), rc4

caffe2

0.8.1

caffe_enet

1.0

caffe_unet

1.0, 18.04, 2.0

canu

1.7.1

caret

5.65

caw restricted

0.2.4(default)

cblas

20032302-gcc5

ccp-em

1.3.0

ccp4

7.0, 7.0.072, ccp4i, ccp4i2, ccp4mg, coot

cdhit

4.8.1

cellprofiler

2.2.0, 3.1.5

cellprofileranalyst

2.2.0

cellranger

2.0.1, 3.0.2

centrifuge

1.0.4-beta

chimera

1.10.2, 1.11, 1.13

chimerax

0.6, 0.8

chrome

68, 69, 75, 77, 78, default

chuffed

0.10.3

circos

0.69-6

cistem

1.0.0-beta

clairvoyante

1.02

clamms

1.1

clonalframeml

1.11

cloudstor

2.3.1-1.1, 2.4.1, 2.4.2

cmake

2.8.12.2, 2.8.12.2-gcc5, 3.10.2-gcc4, 3.10.2-gcc4-system, 3.10.2-gcc5, 3.15.1-gcc4-system, 3.15.1-gcc5, 3.15.4-gcc8, 3.5.2, 3.5.2-gcc4, 3.5.2-gcc5

cmkl

9.1.023

cnvkit

0.9.5

colmap

3.6

comsol restricted

5.2a, 5.4

connectome

1.2.3

convert3d

1.0.0

coot

0.8.9.1

coventormp

1.002

cp2k

5.1.0, 6.1.0

cplex restricted

12.6, 12.6.3, 12.7.1, 12.8.0

cpmd

3.17.1, 4.3

crisprcasfinder

1.05

crispresso

1.0.13-gcc5

crossmap

0.3.5, 0.3.6

cryo-em-processing-tool

0.1

cryoef

1.1.0

cryolo

1.0.0, 1.1.3, 1.3.1, 1.4.0, 1.4.1, 1.5.3

cryosparc

beta, cryosparc-cluster, v2

crystallography restricted

0.0.3(default)

cst

2017

ctffind

4.0.17, 4.1.10, 4.1.13, 4.1.3, 4.1.4, 4.1.8

ctftilt

latest

cuda

10.0, 10.1, 4.1, 4.1.bajk, 6.0, 7.0, 7.5, 8.0, 8.0.61, 8.0-DL, 9.0, 9.1

cudadeconv

1.0

cudalibs8to9

0.1

cudnn

5.1, 5.1-DL, 7.1.2-cuda8, 7.1.3-cuda9, 7.3.0-cuda9, 7.6.5-cuda10.1

cufflinks

2.2.1

cunit

2.1.3

cutadapt

0.16, 2.5, 2.7

cytoscape

3.4.0

D

daris-utils

1.0

darknet

alexey, darknet_yolo_v3, latest

dcm2niix

latest

dcmtk

3.6.3

deep-complex-networks

2017

deepmedic

0.6.1, 0.7.0

deeptools

3.1.2, 3.1.3

deepvariant

0.8-cpu, 0.8-gpu

dense3dcrf

20160527

detectron

20180322

dftbplus

18.2

dials

1.12.1, 1.5.1

diamond

0.9.22

dicomnifti

2.32.1

diyabc

2.1.0

dmtcp

2.5.2

dominate

2.3.5

dos2unix

7.4.0

dragondisk

1.0.5

drishti

2.6.3, 2.6.4, ansto

drmaa

1.0.7, 1.1.0

dti-tk

2.3.1

dtk

0.6.4.1

dynamo

1.1.178(default), 1.1.451

dynet

2.1-cpu, 2.1-gpu

E

ea-utils

1.1.2, 1.1.2-gcc5

eclipse

4.7.3a, 4.8

effoff restricted

0.2.1(default)

eigen

2.0.17, 3.2.9, 3.3.0, 3.3.7

eigensoft

7.2.1

eiger2cbf

1.0

elf

1.0

eman

2.12, 2.2, 2.22, 2.3, 2.3.1

emap-galaxy-shortcut

1.0.0(default)

emap-mytardis-shortcut

1.0.0(default)

emap-wiki-shortcut

0.0.1(default)

emapaccess

1.0(default)

emboss

6.6.0

emclarity

1.0.0

emspring

spring_v0-84-1470, spring_v0-84-1470_mlx

epacts

3.3.2

exciting

nitrogen

exonerate

2.4.0

exploredti

4.8.6

F

fastani

1.1

fastml

3.1, 3.11

fastp

0.20.0

fastqc

0.11.7

fastQValidator

0.1.1a

fastspar

0.0.7

fasttree

2.1.10

fastx-toolkit

0.0.13

fcsalyzer

0.9.12

fdtd

2020a-r1, 8.21.1933

feedback

1.0.1(default)

ffmpeg

3.4.2

fftw

3.3.4-gcc, 3.3.5-gcc, 3.3.5-gcc5

fgbio

0.9.0

figtree

1.4.3

fiji

20160808, 20170223, 20170530, current, current.bak, MMI-MHTP

fix

1.064, 1.068

flash

1.2.11-gcc5

flashpca

2.0

flexbar

3.4.0

flye

2.3.5

fmriprep

1.0.15, 1.1.1, 1.2.5, 1.3.0_post2, 1.4.0, 1.4.1

foma

0.9.18

fooof

0.1.3

fouriertransform restricted

0.2.3(default)

freebayes

0.9.9

freesurfer

20160922, 5.3, 6.0, 6.0-patch, devel-20171013, devel-20180612, devel-20190128

frustum

xflx1992

fsl restricted

5.0.11, 5.0.9, 6.0.0, 6.0.1, 6.0.3

fsleyes

0.22.4, 0.23.0, 0.24.3, 0.32.0

ftgl

2.1

fxtract

2.3

G

gamess

16srs1, 16srs1-v2, 2018r3

gap

4.8.10

gatan

free, uwa

gatk

3.4, 3.7, 4.0.1.1, 4.0.11.0, 4.1.2.0

gatktool

0.0.1

gauss restricted

11.0, 9.0

gaussian restricted

g16a03

gautomatch

0.53, 0.56

gcat

e48bf8b

gcc

4.9.3, 5.4.0, 6.1.0, 8.1.0

gcta

1.92.2beta

gctf

0.50, 0.66, 1.06, 1.06_cuda8, 1.06_cuda8-uow, 1.08_cuda8, 1.18, 1.18_b2, 1.18_b2_cuda9, 1.18_cuda8, 1.18_cuda8-uow, 1.18_cuda91

gd-devel

2.0.35

gdal

2.2.4, 2.3.1, 3.0.2

gdb

8.2.1

gdcm

2.6.6-gcc4, 2.6.6-gcc5

geant4

10.02.p03, 10.03.p01

gem

3.3

gemini

0.30.1

gengetopt

2.10

genotypeharmonizer

1.4.20

genrich

v0.6

geos

3.6, 3.7.2

gephi

0.9.2

gflags

master, master-gcc4

ghostscript

9.26

gimp

2.8, 2.8.22

gingerale

2.3.6

git

2.17.0, 2.19.0, 2.8.1

git-annex

6.20180227

glew

2.0-gcc4, 2.0-gcc5

glm

0.9.9.5

glog

master, master-gcc4

glpk

4.60

gmp

6.1.2

gmsh

3.0.3

gnuparallel

20160822, 20190122

gnuplot

5.2.1

go

1.11.1

goctf

1.1.0

gpu_burn

0.9, 1.0

gpucomputingsdk

4.0.17

graphviz

2.30.1, 2.40.1

gromacs

2016.3-openmpi-cuda8.0, 2016.4-openmpi-cuda8.0, 2016.5-openmpi-cuda8.0-plumed, 2018.4-openmpi-cuda8.0, 2018.7-openmpi-cpu-only, 2018.7-openmpi-cuda-plumed, 2018-openmpi-cuda8.0, 2018-openmpi-cuda8.0-NVML(default), 2019.4-openmpi-cuda10.0, 5.1.4

gsl

1.15.13-system, 2.2-gcc4(default), 2.2-gcc5, 2.2-system, 2.5-gcc4

gst-devel

1.4.5

gst-libav

1.10.4, 1.4.5

gtdb-tk

0.3.2

gubbins

2.3.2

guppy

3.1.5-1, 3.2.4, container

gurobi restricted

7.5.1, 8.0.0, 9.0.0

gvcftools

0.17.0

H

h5toxds

1.1.0

haplomerger2

20180603

haystack_bio

0.5.5

hdf5

1.10.0-patch1, 1.10.5

hdfview

3.0

heudiconv

0.5.4

hisat2

2.1.0

hmmer

2.4i, 3.2.1

horovod

0.16.4

hotspot

4.0.0

hpcx

2.5.0

htop

2.0.1

htseq

0.10.0

htslib

1.7, 1.9, 1.9-gcc5

huygens

16.10.1-p1

hyperspy

1.4

hyphy

2.5.0

hypre

2.11.2, 2.15.0

I

icm restricted

3.7-3b, 3.8.7

idl

8.6

idr

2.0.3

igv

2.3.81, 2.4.19

ihrsr++

v1.5

ilastik

1.2.0, 1.3.3

illumina-utils

2.6, 2.6-python3.7

imagej

20160205

imagemagick

7.0.5-7, 7.0.8-23, 7.0.8.23-native

imagescope

11.2.0.780

imblproc

20190405

imod

4.8.54, 4.9.12, 4.9.9

imod-raza

4.7.12

imosflm

7.2.1, 7.2.2

impute2

2.3.1

intel

2015.0.090, 2016, 2017u4, 2018test, 2018u3

iqtree

1.5.3, 1.6.10, 1.6.2, 2.0-rc1

ismapper

2.0

itk

4.10.0-gcc4, 4.10.0-gcc5, 4.10.0-gcc5-p1, 4.13.0-gcc4, 4.13.1-gcc4, 4.8.2-gcc4, 4.8.2-gcc5, ansto

itksnap

3.3.x(default), 3.8.0, 3.8.0-beta

J

jags

3.3.0, 3.4.0, 4.3.0

java

1.7.0_67, 1.8.0_77(default)

jdk

10-20180320, 14

jellyfish

1.1.12, 2.3.0(default), 2.3.0-gcc5

jspr

2017-7-20

juicer

1.6.2

julia

0.6.4

K

kallisto

0.43.0

kaptive

0.5.1

kilosort

1.0

king

2.1.6

kleborate

0.2.0, 0.3.0

kraken

1.1.1

kraken2

2.0.7-beta

krakenuniq

0.5.8

kronatools

2.7.1

L

lammps

20180510(default), 20181212

lapack

3.6.1-gcc4, 3.6.1-gcc4-opt, 3.6.1-gcc5, 3.8.0-gcc5, 3.8.0-gcc5-pic

ldmap

28apr15

ldpred

1.0.6

leveldb

master, master-gcc4

levelset restricted

0.0.2(default)

libertem

20190521

libffi

3.2.1

libffi-devel

3.0.13

libfuse

3.6.1

libgd

2.2.4

libgeotiff

1.4.2

libharu

2.2.1

libint

1.1.4

libjpeg-turbo

1.4.2, 1.5.1, 1.5.1-shared

libsmm

20150702

libtiff

3.9.7, 4.0.10

libunwind

1.3.1

libuuid

2.23.2-43

libxc

4.1.0

libxsmm

1.9

libzip

0.10.1-8

lighter

1.1.2

lkh

2.0.9

lmdb

latest

locuszoom

1.4

lofreq

2.1.3.1

lsd

0.3beta

M

macs2

2.1.1.20160309

mafft

7.310

magic-impute

1.5.5

magma

1.6.1, 2.0.2

mainmast

1.0

mango

4.0.1

manta

1.5.0-gcc5

mantid

3.13.0, 3.8.0, 3.9.0

mapdamage

2.0.9(default), 2.0.9-u1

mash

2.1(default), 2.1.1

materialsstudio

18.1.0

mathematica

11.0.1, 12.0.0

mathgl

1.11.2, 2.0.3(default), 2.3.3

matlab

r2012b, r2014a, r2014b, r2015b, r2016a, r2017a, r2017b, r2017b-caffe, r2018a, r2019a

mauve

20150213

maven

3.3.9

maxquant

1.6.5.0

mc

4.8.21

mcl

11-294

mcr2010b

1.0

megahit

1.1.3, 1.2.4-beta, 1.2.9

meld

0.4.14

meme

5.0.1

merantk

1.2.1

mercurial

4.7.1

mesa

13.0.5, default

meshlab

2016.12-gcc5, 2019.03

meson

0.51.0

metal

2011

metaplotr

2018_09

metawrap

1.1.3

mevislab

2.8.1-gcc-64bit

miakat restricted

4.2.6

minc-lib

2.2-git-gcc4

minc-tools

2.2

miniconda3

4.1.11-python3.5

minimap2

2.17-r954-dirty

minizinc

2, 2.3.1

mixcr

3.0.7

mkl

2018u3

mlst

2.15

mne

TF-201804

molden

5.7

mono

5.20.1.19

moose

1.0

morphind

1.4

motioncor2

20180924, 20181020, 20181020-cuda91, 2.1, 2.1.10-cuda8, 2.1.10-cuda9.1, 2.1.3.0-cuda101, 2.1.3.0-cuda80

motioncorr

2.1

motioncorr2

20160822

mpfr

3.1.5

mpifileutils

20170922

mpip

3.4.1

mrbayes

3.2.6, 3.2.6-mpi

mrf restricted

0.2.2(default)

mriconvert

2.1.0

mricrogl

1.0.20170207, 20180623

mricron

06.2013, 30apr2016

mriqc

0.14.2, 0.9.7

mrtrix

0.3.15-gcc4, 0.3.15-gcc5, 0.3.16, 20170712, 3.0_rc3, 3.0_rc3_latest

mrtrix3tissue

5.2.8

msm_hocr

3.0

mummer

3.23-gcc5, 4.0.0.beta2-gcc5

muscle

3.8.31

mustem

5.3

mxtools

0.1

mytardis

0.1(default)

N

namd

2.12-ibverbs-smp-cuda, 2.12-multicore, 2.13-multicore-CUDA

nanofilt

201807

nanopolish

0.10.1, 0.11.1

nccl

2.4.7-cuda10.0, 2.4.7-cuda9.1, master, master-gcc4

netcdf

4.4.1.1(default), 4.4.1.1-openmpi-1.10.7-mlx, 4.7.0, 4.7.1-intel

neuro-workshop

20191115

neuro_workflow

2017v2

new-fugue

2010-06-02

newick-utils

1.6

nextgenmap

0.5.5

ngsqctoolkit

2.3.3

nibabel

2.3.3

niftilib

2.0.0

nighres

1.1.0b1

niistat

9.oct.2016

ninja

1.9.0

nis-elements-viewer

4.20

nlopt

2.6.1

nn restricted

0.2.4(default)

novactf

03.2018

nullarbor

2.0.20181010

O

objexport restricted

0.0.4(default)

octave

4.2.2

octopus

8.4, 8.4-parallel

openbabel

2.4.1

openblas

0.2.20

opencv

3.4.1, 3.4.1-gcc4, 4.1.0

openfoam

4.1, 5-paraview54, 5.x

openjpeg

2.3.0

openmpi

1.10.3-gcc4-mlx, 1.10.3-gcc4-mlx-cuda75, 1.10.3-gcc4-mlx-verbs, 1.10.3-gcc4-mlx-verbs-cuda75, 1.10.3-gcc5, 1.10.3-gcc5-mlx, 1.10.7-1.mlx, 1.10.7-intel, 1.10.7-mlx(default), 1.10.7-mlx-intel, 3.1.4-mlx

opennmt-py

0.7.0

openrefine

3.1

orange3

ansto

orca

4.0.1(default), 4.2.1

orfm

v0.7.1

P

packer

1.3.5

paleomix

1.2.13.4-python2

paml

4.9

pandoc

2.7.3

paraview

4.0.1, 5.6.0, ansto

partitionfinder2

2.1.1

pastml

1.0

pbzip2

1.1.13

peakseq

1.3.1

perl

5.24.0, 5.28.0(default), 5.30.1

petsc

3.10.1-gcc5, 3.12.1

pgap

3958

pgi

19.4, 2019

phate

0.4.4

phenix restricted

1.11.1, 1.15.1, 1.15.2

phreeqc

3.5.0

phyml

3.1

picard

2.19.0, 2.9.2

picrust2

2.1.4_b(default), 2.2.0_b

pigz

2.3.3, 2.3.4

pilon

1.22

pindel

0.6.3-gcc5

plink

1.7, 1.9, 1.90b6.10, 2.0-alpha

plinkseq

0.10

plumed

2.5.0

pmix

4.0.0, v2.2

pointless

1.10.28

posgen restricted

0.0.1(default)

posminus restricted

0.2.3(default)

pplacer

v1.1.alpha19

prank

170427

prismatic

1.1

prismatic-cpu

1.1

prodigal

2.6.3

proj

4.9.3, 5.1.0, 6.2.1

prokka

1.13.3(default), 1.14.5

protobuf

master, master-gcc4

protomo

2.4.2

psi4

v1.1

pulchra

3.06

purge_haplotigs

1.1.0

pv

1.6.6

py4dstem

0.3

pybids

0.9.1

pycharm

2018.3.3

pydeface

1.1.0

pyem

v0.1, v0.1-201806, v0.3

pymol

1.8.2.1, 1.8.6, 2.4.0a0

pyprismatic

1.1.16

pypy

7.0.0-3.6

pysam

0.15.2-python2

python

2.7.11-gcc, 2.7.12-gcc4(default), 2.7.12-gcc5, 2.7.15-gcc5, 2.7.17-gcc8, 3.5.2-gcc, 3.5.2-gcc4, 3.5.2-gcc5, 3.6.2, 3.6.2-static, 3.6.6-gcc5, 3.7.2-gcc6, 3.7.3-system

pytom

0.971

pytorch

1.0-cuda10, 1.1-cuda10(default), 1.3-cuda10

pyxnat

1.1.0.2, 20170308

Q

qatools

1.2

qctools

v2.0-beta

qgis

3.9.0

qhull

2003.1, 2015.2

qiaseq-dna

1.0(default), 14.1

qiime1

1.9.1

qiime2

2017.9, 2018.11, 2018.2, 2018.4, 2019.1, 2019.4, 2019.7-q2_scnic, 2019.7-q2_scnic_2

qt

5.7.1-gcc5

qt5-qtwebkit

5.9.1

quicktree

2.0, 2.5

quit

1.1, 2.0.2

qupath

0.2.0-m4

R

3.3.1, 3.4.3, 3.5.0, 3.5.1, 3.5.2-openblas, 3.5.3-mkl, 3.6.0-mkl

R

r-launcher

0.0.1(default)

racon

1.3.1

raremetal

4.15.1

raxml

8.2.12, 8.2.9

razers3

3.5.8

rclone

1.49.3

rdf-kd restricted

0.0.1(default)

rdkit

2019.03.3.0

relion

1.4, 2.02, 2.0.6, 2.0beta, 2.1(default), 2.1.b1, 2.1.b2, 2.1-openmpi-1.10.7-mlx, 3.0-20181109-cuda80, 3.0-20181109-cuda91, 3.0-20190115, 3.0.5, 3.0.5-uow, 3.0.6, 3.0.6-uow, 3.0.7, 3.0.7-uow, 3.0.7-uow-cuda10.1, 3.0.7-uow-mc2.1.3.0, 3.0-beta, 3.0-stable, 3.0-stable-cuda91, 3.0-stable-uow, 3.0-uow-20180904, 3.0-uow-20180917, 3.0-uow-20181109-cuda80, 3.0-uow-20181109-cuda91, 3.0-uow-20190115, 3.1_beta, 3.1_beta-20191105, 3.1_beta-20191113, 3.1_beta-latest

resmap

1.1.4, 1.1.5, 1.9.5

rest

1.8, 1.8-matlab2017a.r6685

rings

1.3.3

rnammer

1.2

roary

3.11.2(default), 3.12.0

robex

1.2

root

5.34.32

rosetta restricted

2018.09

rsem

1.3.0

rseqc

3.0.0

rstudio

1.0.143, 1.0.44, 1.1.414, 1.1.463, 1.1.463-r3.5.3-mkl, 1.1.463-r3.6.0-mkl

rstudioserver_epigenetics

1.0, 1.0-20171101

rsync

3.1.3

rtk

ansto

S

saintexpress

3.6.3

salmon

0.14.1

salome

9.2.0

samclip

0.2

samtools

0.1.18, 1.3.1, 1.6, 1.7, 1.7-gcc5, 1.9, 1.9-gcc5

sas

9.4

sbt

0.13.15, 1.2.1

scalapack

2.0.2

scipion

2.0, devel, devel-20170327, v1.0.1_2016-06-30, v1.1, v1.1.1, v1.2, v1.2.1, v1.2.1_2018-10-01

scrappie

1.4.1

sdm_1d_calculate restricted

2.0.2(default)

sdm_1d_plot restricted

0.0.4(default)

sdm_2d_calculate restricted

2.0.2(default)

sdm_2d_plot restricted

0.0.4(default)

segadapter

1.9

seqgen

1.3.4

seqtk

1.3

shapeit

v2_r837, v2_r904

shovill

1.0.4

simnibs

2.0.1g

simple

2.1, 2.5

simul-atrophy

12-09-2017

singlem

0.12.1

singularity

2.3.1, 2.4.2, 2.4.5, 2.5.2, 3.0, 3.0.1, 3.0.2, 3.1.0, 3.2.0, 3.2.1(default), 3.4.0, d3d0f3fdc4390c7e14a6065543fc85dd69ba42b7

situs

3.1

ska

1.0-e1968f0

skesa

2.2.1, 2.3

skewer

20170212

slamdunk

latest

slim

3.2

slurm

17.11.4

smafa

0.5.0

smcounter

10apr2017

smux

0.0.1

snappy

master, master-gcc4

snippy

4.3.8

snp-dists

0.6.3

snpeff

4.3t

snpm

13

soapdenovo2

2.04-r241

sourcetracker

2.0.1

spades

3.12.0, 3.13.1

sparseassembler

1.0

sparsehash

2.0.3

spectra

0.8.1

spider

21.11

spm12

matlab2015b.r6685, matlab2018a.r6685, matlab2018a.r7487

spm8

matlab2015b.r6685, matlab2017a.r6685

sqlite3

3.30.1

squashfs-tools

4.3-0.21

squashfuse

0.1.103

sra-tools

2.7.0, 2.9.2, 2.9.4, 2.9.6

srst2

0.2.0, 0.2.0-2019

stacks

2.4

star

2.5.2b

stata restricted

14(default), 14.2, 16

stisuite

3.0

strelka

2.8.4

stringtie

1.3.5, 1.3.6

structure

2.3.4

subread

1.5.1

subversion

1.9.5

suitesparse

5.4.0

superlu

3.1

surfice

7_feb_2017

svd

1.4

swig

3.0.12, 4.0.1

synopsys

3.1(default)

T

tannertools

2016.1, 2016.2

tapsim

v1.0b_r766

tbb

20180312oss

tempest

1.5

tensorflow

1.0.0-python2.7.12-gcc5, 1.10.0-pytorch, 1.10.0-pytorch-all, 1.10.0-pytorch-keras, 1.12.0-python2.7.12-gcc5, 1.12.0-python3.6-gcc5, 1.13.1-gdal, 1.14.0-keras, 1.14.0-keras-pydicom, 1.3.0-python2.7.12-gcc5, 1.4.0-python2.7.12-gcc5, 1.4.0-python3.6-gcc5, 2.0.0-beta1, 2.0.0-gpu

terastitcher

20171106

texlive

2017

tiff

4.0.8

tigervnc

1.8.0

tmap

3.0.1

toothmaker

0.64

topaz

1.0, latest

tophat

2.1.1

tracer

1.6

trackvis

0.6.1

tractseg

2.0

transdecoder

5.5.0

trim_galore

0.4.5, 0.5.0

trimmomatic

0.38

trinity

2.8.5(default), 2.8.5-gcc5

turbovnc

2.0.2(default), 2.1.0

tvips-tools

0.0.3

U

ucsc-genome-tools

201806

ucx

1.6.1

udunits2

2.2.20-2

ufo-kit

ansto

umap

0.3.8

umi-tools

0.5.5-python2, 0.5.5-python3

unblur

1.0.2

underworld

2.3.0, 2.8.0b

unicycler

0.4.7

unimelb-mf-clients

0.2.7, 0.3.2

unrar

5.0

V

valgrind

3.13

varscan

2.3.9

vasp restricted

5.4.4

vcftools

0.1.15

vdjtools

1.2.1

vegas2

v02

velvet

1.2.10, 1.2.10-modified

vep

90(default), 94

vigra

1.9.0

vim

8.0.0596

viptreegen

1.1.2

virtualgl

2.5.0(default), 2.5.2, 2.6.2

visit

2.12.3

vmd

1.9.3, 1.9.4

volview

3.4

voro++

0.4.6

vscode

1.39.2

vsearch

2.13.6

vt

0.57

vtk

5.10.1, 5.10.1-gcc4, 7.0.0, 7.0.0-gcc5

W

wasp

0.3.0

weblogo

3.7

wfu_pickatlas

3.0.5b

wgsim

0.3.1-r13

workspace

4.0.2

wxgtk

3.0.2

wxwidgets

3.0.3

X

xds

20170302, monash(default), mxbeamteam

xjview

9.0, 9.6, 9.7

xnat-desktop

0.96, 1.0.40

xnat-upload-assistant

1.1.3

xnat-utils

0.2.1, 0.2.5, 0.2.6, 0.4.5, 0.4.6, 0.4.9, 0.5.3

xnatpy

0.3.18

xvfb

1.19.3

Y

yade

1.20.0-cpu, 1.20.0-gpu, 2019-06-20, 2019-06-20-cpu, yade-daily-may-2019

yasm

1.2.0-4

Z

zetastitcher

0.3.3

zlib

1.2.11

zoem

11-166

zoltan

3.83

zstd

1.4.0

Requesting an install

If you require additional software please email help@massive.org.au with the following details:

  • software

  • version

  • URL for download

  • urgency

  • if there are any licensing restrictions we need to impose

Docker based work flows

Many fields are beginning to distribute fully self contained pieces of software in a container format known as docker. Unfortunately docker is unsuited as a container format for shared user systems, however it is relatively easy to convert most docker containers for scientific work flows to the Singularity format. If you wish to run software based on a Docker container, please email help@massive.org.au and let us know where we can obtain the container and we will be happy to convert it for you.

Running QIIME on M3

QIIME (Quantitative Insights Into Microbial Ecology) 2 is installed on M3. To use this software:

 # Loading module
 module load qiime2/2017.9

# Unloading module
 module unload qiime2/2017.9

If you encounter issues with this install, please contact help@massive.org.au

Running Python on M3

M3 has different versions of Python installed. To list them use the command:

# Listing python modules
module avail python

--------------------------------------------------- /usr/local/Modules/modulefiles ---------------------------------------------------
python/2.7.11-gcc           python/2.7.15-gcc5          python/3.5.2-gcc5           python/3.6.6-gcc5
python/2.7.12-gcc4(default) python/3.5.2-gcc            python/3.6.2                python/3.7.2-gcc6
python/2.7.12-gcc5          python/3.5.2-gcc4           python/3.6.2-static         python/3.7.3-system

The listed Python versions have a standard set of python modules installed using Pip. As a user, unfortunately, you are unable to update or install your own python modules into the supplied Python software on Massive.

There is an alternative, to create a Python virtual environment (venv). A Python virtual environment effectively creates your own copy of Python, allowing you to install any Python modules you require. The instructions below focus on creating a Python virtual environment using 3.6.2.

‘destinationPath’ is the location you use to install Python on Massive.

#Setup python virtualenv - need to use this path to avoid 'module load'
/usr/local/python/3.6.2-static/bin/python3 -m venv destinationPath

#Activate the virtual environment - do this for each shell session
source destinationPath/bin/activate

#Upgrade pip
pip install --upgrade pip

Note

For each new shell session created, ‘source destinationPath/bin/activate’ is required to use your Python virtual environment.

To better understand Python virtual environments please refer to https://docs.python.org/3/tutorial/venv.html

Using PyCharm with your Virtual environment

After successfully creating your own virtual environment, you can use it in your PyCharm projects.

The first step is to start PyCharm. Start a Massive desktop session and select PyCharm from the menu. Please refer to Connecting to M3 via the MASSIVE desktop

  1. Once PyCharm is up and running, select File, New Project.

2. You will be presented with the Create Project window. Click on the arrow next to ‘Project Interpreter’

PyCharm new project dialog box
  1. Select ‘Existing interpreter’ and click the ‘browse’ icon.

PyCharm new project interpreter dialog box

4. Browse to the location where you created your virtual environment, enter the ‘bin’ folder, then select the ‘python’ executable. Click OK.

PyCharm new project interpreter dialog box
  1. Click OK.

PyCharm new project interpreter dialog box

6. Back on the Create Project window, enter the new project name. Click OK. You now have a PyCharm project setup using your new virtual environment.

Running Anaconda on M3

M3 has different versions of Anaconda installed. To list them use the command module avail anaconda:

module avail anaconda

----------------------------------------------- /usr/local/Modules/modulefiles ------------------------------------------------
anaconda/2018.12-Python3.7-gcc6 anaconda/4.3.1-Python3.5-gcc5   anaconda/5.0.1-Python3.6-gcc5
anaconda/2019.03-Python3.7-gcc5 anaconda/5.0.1-Python2.7-gcc5   anaconda/5.1.0-Python3.6-gcc5
anaconda/4.3.1-Python3.5        anaconda/5.0.1-Python3.5-gcc5

The listed Anaconda versions have a standard set of modules installed. As a user, unfortunately, you are unable to update or install your own modules into the supplied Anaconda software on Massive.

There is an alternative, to create a Conda environment. A Conda environment effectively creates your own copy of Conda, allowing you to install any Conda/Python modules you require. The instructions below focus on creating an Ananconda environment using the module anaconda/2019.03-Python3.7-gcc5.

myEnv represents the environment name to use.

#Load the anaconda module
module load anaconda/2019.03-Python3.7-gcc5

#Change this to your project ID
export PROJECT=myID
export CONDA_ENVS=/projects/$PROJECT/$USER/conda_envs

#Create the conda environment - cloning the already installed packages
#change myEnv to your environment name
conda create --yes -p $CONDA_ENVS/myEnv --clone base

#OR create the conda environment with no packages installed
#change myEnv to your environment name
conda create --yes -p $CONDA_ENVS/myEnv

Conda will then create the environment and the end of the message may look like this:

Executing transaction: done
#
# To activate this environment, use:
# > conda activate myEnv
#
# To deactivate an active environment, use:
# > conda deactivate
#

On Massive, if you run conda activate for the first time, the following will be displayed:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

Note

On Massive DO NOT run conda init. Running this command will update your .bashrc file. The update prevents your Desktop session from starting.

Activating your Conda environment on Massive

Assuming you are in a new shell with no modules loaded.

#Load the anaconda module
module load anaconda/2019.03-Python3.7-gcc5

#Change this to your project ID
export PROJECT=myID
export CONDA_ENVS=/projects/$PROJECT/$USER/conda_envs

# To use the environment
source activate $CONDA_ENVS/myEnv

# Leave the enviroment
source deactivate

Installing and updating Python packages in your Conda environment

Check that your conda environment has been properly activated.

conda env list

# conda environments:
#
                      *  /projects/PROJECT_ID/USER_ID/myEnv
base                     /usr/local/anaconda/2019.03-Python3.7-gcc5
illumina-utils-2.6       /usr/local/anaconda/2019.03-Python3.7-gcc5/envs/illumina-utils-2.6
pytorch-1.0-cuda10       /usr/local/anaconda/2019.03-Python3.7-gcc5/envs/pytorch-1.0-cuda10
pytorch-1.0-cuda9        /usr/local/anaconda/2019.03-Python3.7-gcc5/envs/pytorch-1.0-cuda9

The ‘*’ indicates the active environment. Ensure the correct one is indicated. If not, refer above to correctly activate your environment.

Use the following sample commands to install or update packages.

conda install packageName
conda install pagageName=versionNumber

conda update packageName
conda update packageName=versionNumber

I ran conda init and my Desktop session no longer starts

To fix follow these instructions.

  1. ssh into Massive.

  2. Edit your .bashrc file using your favourite editor.

3. Comment out the ‘conda’ lines using a # at the start of the lines. Below is a sample .bashrc with the comments

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
      . /etc/bashrc
fi

# User specific aliases and functions
# Give bash history a decent size
export HISTFILESIZE=10000
# Helpful alias for users to quickly see their queue status
alias squ='squeue -u $USER'

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
#__conda_setup="$('/usr/local/anaconda/2019.03-Python3.7-gcc5/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
#if [ $? -eq 0 ]; then
#    eval "$__conda_setup"
#else
#    if [ -f "/usr/local/anaconda/2019.03-Python3.7-gcc5/etc/profile.d/conda.sh" ]; then
#        . "/usr/local/anaconda/2019.03-Python3.7-gcc5/etc/profile.d/conda.sh"
#    else
#        export PATH="/usr/local/anaconda/2019.03-Python3.7-gcc5/bin:$PATH"
#    fi
#fi
#unset __conda_setup
# <<< conda initialize <<<
  1. Save the file and exit your ssh session.

  2. Restart your Desktop session.

Note

If you are not comfortable updating your .bashrc file, please see Help and Support to obtain assistance.