Module Changes

The table below lists old Oscar modules and their corresponding LMOD modules.

If a cell

• is blank, that module will be installed later

• says "(system RPM)", that software is installed on the nodes. Users don't need to load this module.

• says "N/A", that module will NOT be installed

• lists one or more modules , users can load a listed module using the command module load <name>

Old Oscar Module	LMOD Module
abaqus	abaqus/2021.1
abinit	abinit-mpi/9.8.3
admixture	admixture/1.3.0
afni	afni/23.3.07s
ambertools
anaconda	miniconda3/22.11.1
angsd	angsd/0.935
ants	ants/2.4.3
apache-ant	ant/1.10.13
argweaver	N/A - Users install in their python/conda environments
aria2	aria2/1.36.0
ase	N/A - Users install in their python/conda environments
aspera
assura
atlas	openblas/0.3.23
atom	atom/1.19.3
awscli	awscli/1.27.84
bamtools	bamtools/2.5.2
basilisk	basilisk/2023.11.11s
bazel	bazel/6.1.1
bbmap	bbmap/39.01
bbtools	bbmap/39.01
bcftools	bcftools/1.16
bcl2fastq	bcl2fastq2/2.20.0.422
beagle	beagle/5.4
bedGraphToBigWig
bedops	bedops/2.4.40
bedtools	bedtools2/2.31.0
binutils	(system RPM)
biopython	N/A - User install in their python/conda environments
bismark	bismark/0.23.0
blas	netlib-lapack/3.11.0
blast	blast-plus/2.2.30
blat	blat/37
blender	blender/4.0.0
boost	boost/1.80.0 boost-mpi/1.82.0
bowtie	bowtie/1.3.1
bowtie2	bowtie2/2.4.2
brotli	brotli/1.0.9
busco	N/A - Users install in their python/conda environments
bwa	bwa/0.7.17
bxh_xcede_tools
bzip2	(system RPM)
cadence	cadence/IC06.18.090
caffe
cantera	N/A - deprecated
cartopy	N/A - Users install in their python/conda environments
casa	casa/6.6.0-20-py3.8.el7
cave-utils	N/A
cdhit	cdhit/4.8.1
cdo	cdo-mpi/2.1.1
cellranger	cellranger/arc-2.0.1 cellranger/atac-2.0.0 cellranger/6.0.0
cesm	N/A
cfitsio	cfitsio/4.2.0
cgal	cgal/5.4.1
CharMM
chrome	chrome/119.0.6045.159s
circlator	N/A - User install in their python/conda environments
clang	llvm/16.0.2
CloudCompare
clustal_omega	clustal-omega/1.2.4
cmake	cmake/3.26.3
colordiff	olordiff/1.0.21
comsol	comsol/5.2 comsol/5.6
conn	conn/22a
connectome_workbench	connectome-workbench/1.5.0
cp2k
cppunit	cppunit@1.14.0
crossrate
cuda	cuda/12.1.1
cudnn	cudnn/8.7.0.84-11.8
cufflinks	cufflinks/2.2.1
curl	(system RPM)
cutadapt	N/A - User install in their python/conda environments
dada2	N/A - User install in their python/conda environments
datamash	datamash/1.8
dcm2bids	N/A - User install in their python/conda environments
dcm2niix	dcm2niix/1.0.20220720
dedalus
deeparg	N/A - User install in their python/conda environments
deeplabcut	N/A - User install in their python/conda environments
deeptools	N/A - User install in their python/conda environments
deeptoolsintervals	N/A - User install in their python/conda environments
diamond	diamond/2.0.15
dicombrowser	dicombrowser/20181217
dlib	dlib/19.22
dmtcp	dmtcp/3.0.0
dos2unix	dos2unix/7.4.2
dotnet	dotnet/8.0.100
dropest	dropest/0.8.6
ds9	ds/9.8.5s
dsi	dsi-studio/chen-2023-sif
dtitk	dtitk/2.3.1s
eigen	eigen/3.4.0
eigensoft	eigensoft/7.2.1
elbencho	N/A
emacs	(system RPM)
emboss
engineering
fastme	fastme/2.1.5.1
fastq_screen
fastqc	fastqc/0.11.9
fasttree	fasttree/2.1.11
fastx-toolkit	fastx-toolkit/0.0.14
ferret	ferret/7.6.0
ffmpeg	ffmpeg/6.0
fftw	fftw/3.3.10
fiji	fiji/20231107-1617
fileZilla	filezilla/3.49.1
firefox	firefox-102.9.0
flashpca	flashpca/2.0
freebayes	freebayes/1.3.6
freeglut	freeglut/3.2.2
freesurfer	freesurfer/7.3.2
freetype	freetype/2.11.1
fsl	fsl/6.0.7.7s
fv	fv/5.5.2
gatk	gatk/4.3.0.0
gaussian	gaussian/09_v1
gaussview	gaussview/v05
gcc	(system RPM)
gdal	gdal/3.7.0
gdb	(system RPM)
geos	geos/3.11.2
ghostscript	ghostscript/10.0.0
gimp	gimp/2.10.32
git	(system RPM)
gitlfs	git-lfs/3.3.0
glew	glew/2.2.0
glm	glm/0.9.9.8
glmnet	N/A - User install in their python/conda environments
global_arrays	globalarrays-mpi/5.8.
globus	N/A - User install in their python/conda environments
gmp	gmp/6.2.1
gnuplot	gnuplot/5.4.3
golang	go/1.20.3
gpaw
grace	grace/5.1.25
graphviz	graphviz/8.0.1
gromacs	gromacs-mpi/2022.3 gromacs-mpi/2021.5
gsl	gsl/2.7.1
gsutil	google-cloud-cli/456.0.0
guppy	guppy/6.0.1 guppy/6.1.2
gurobi	gurobi/10.0.1
h5py	N/A - User install in their python/conda environments
haplostrips
hdf5	hdf5/1.14.1-2
hdfview	hdf5-mpi/1.12.2 hdf5/1.14.1-2
hisat2	hisat2/2.2.1
hmmer	hmmer-mpi/3.3.2
homer	homer/4.11.1
htop	htop/3.2.2
htseq	N/A - User install in their python/conda environments
htslib	htslib/1.17
idba	idba/1.1.3
idemp	idemp/201706
idl	idl/8.8.2
idl_DEEPS	N/A
igraph	igraph/0.7.1
imagej	imagej/154-linux64-java8
imagemagick	imagemagick/7.1.1-3
incisive
inkscape	inkscape/1.3s
intel	intel-oneapi-compilers/2023.1.0
intltool	intltool/0.51.0
ior	ior-mpi/3.3.0
iq-tree	iq-tree/2.1.3
iraf	iraf/2.17.1s
isis	N/A - User install in their python/conda environments
JAGS	jags/4.3.1
java	openjdk/11.0.17_8
jellyfish	jellyfish/2.2.7
jo	jo/1.9
json_cpp	jsoncpp/1.9.5
json_fortran	json-fortran@8.3.0
julia	julia/1.9.0
keras	N/A - User install in their python/conda environments
kneaddata	N/A - User install in their python/conda environments
kraken	kraken/1.1.1
lammps	lammps-mpi/20220623.3
lapack	netlib-lapack/3.11.0
leveldb	leveldb/1.23
lftp	lftp/4.9.2
libarchive	libarchive/3.6.2
libbeef	libbeef/Nov2020
libcutensor	cutensor/1.5.0.3
libgd	libgd/2.3.3
libgeotiff	libgeotiff/1.6.0
libgit	libgit2/1.6.4
libjpeg	libjpeg/9e
libjpeg-turbo	libjpeg-turbo/2.1.5
libpng12	libpng/1.6.39
libreoffice	libreoffice/7.2.2.sif
libtiff	libtiff/4.5.0
libvdwxc	libvdwxc-mpi/0.4.0
libwnck	libwnck/3.24.1
libxc	libxc/5.2.3
libzip	libzip/1.3.2
llvm	llvm/16.0.2
macs	N/A - User install in their python/conda environments
mafft	mafft/7.505
magma-gpu	magma/2.7.1
maple	maple/22
mark	mark/2018.07.08
materialstudio	materialstudio/2020s
mathematica	mathematica/13.2.0
matlab	matlab/R2023a
matplotlib	N/A - User install in their python/conda environments
maven	maven/3.8.4
mayavi	N/A - User install in their python/conda environments
meme	meme-mpi/5.3.0
mentor-calibre
mercurial	mercurial/5.8
meshlab
metaphlan	N/A - User install in their python/conda environments
metis	metis/5.1.0
miniconda	miniconda3/23.11.0
minimap2	minimap2/2.14
minvr
mne	N/A - User install in their python/conda environments
molden	molden/6.7
Molpro
mpfr	mpfr/4.2.0
mpi	hpcx-mpi/4.1.5rc2s openmpi/4.1.2
mpi4py	N/A - User install in their python/conda environments
mrcc
mriconvert	mriconvert/2.1.0
mricrogl	mricrogl/2022.07.20
mricron	mricron/201909
msmc	msmc2/2.1.4
msprime	N/A - User install in their python/conda environments
mujoco-py	N/A - User install in their python/conda environments
MultiQC	N/A - User install in their python/conda environments
multiwfn	multiwfn/3.8_1208
mummer	mummer4/4.0.0rc1
muscle	muscle/3.8.1551
mysql	mysql/8.0.29
n2p2	n2p2-mpi/2.2.0
nbo	nbo/7.0
nccl	nccl/2.16.2-1
ncdu	ncdu/1.18.1
ncl	ncl-mpi/6.6.2
nco	nco/5.1.5
ncview	ncview/2.1.8
neovim	neovim/0.9.4
netcdf	netcdf-c/4.7.4
netpbm	netpbm/10.73.43
neuron	N/A - User install in their python/conda environments
ninja	ninja/1.11.1
nipype	N/A - User install in their python/conda environments
nlopt	nlopt/2.7.1
node.js	node-js/18.12.1
numpy	N/A - User install in their python/conda environments
numpydoc	N/A - User install in their python/conda environments
nvhpc-sdk	nvhpc/23.3
nvtop	nvtop/3.0.1
nwchem	nwchem-mpi/7.2.0
obitools	N/A - User install in their python/conda environments
octopus	octopus-lunter/0.7.4
openbabel	openbabel/3.1.1
openblas	openblas/0.3.23
opencv	opencv/4.6.0s
opencv-python	N/A - User install in their python/conda environments
openexr	openexr/3.1.5
openfoam
opengl	mesa/22.1.6
openjpeg	openjpeg/2.5.0
openmolcas
openscenegraph	N/A
openslide	openslide/3.4.1
openslide-python	N/A - User install in their python/conda environments
openssl	openssl/3.0.7s openssl/1.1.1t
orca	orca-mpi/5.0.7
osgearth	N/A
ovito	ovito/3.6.0
p7zip	p7zip/17.05
pandas	N/A - User install in their python/conda environments
pandoc	pandoc/2.19.2
paraview
patchelf	patchelf/0.17.2
paup	paup/4.0a168
pcre2	pcre2/10.42
pdftk	pdftk/2.02
pdsh	pdsh-chaos/22.12
perl	perl/5.36.0
petsc
photoscan
picard-tools	picard/2.26.2
pigz	pigz/2.7
planetaryviewer	N/A - User install in their python/conda environments
plink	plink/2.00
plotly	N/A - User install in their python/conda environments
plumed
pnetcdf	parallel-netcdf-mpi/1.12.3
popoolation2	popoolation2/1.205s
prodigal	prodigal/2.6.3
proj	proj/9.2.0
protobuf	protobuf/3.22.2
py2bit	N/A - User install in their python/conda environments
pybigwig	N/A - User install in their python/conda environments
pycharm	pycharm-community/2021.3.3
pymol	N/A - User install in their python/conda environments
pypy	pypy/7.3.13
pysam	N/A - User install in their python/conda environments
pyscf	N/A - User install in their python/conda environments
python	(system RPM - python/3.9.16)
pytorch	N/A - User install in their python/conda environments
qchem
qgis	qgis/3.22
qiime	N/A - User install in their python/conda environments
qit	qit/2023-04-04
qmcpack	qmcpack-mpi/3.16.0s
qt	qt/5.15.9
qualimap	qualimap/2.2.1
quantumespresso	quantum-espresso/7.1
quast	N/A - User install in their python/conda environments
R	r/4.2.2
RAiSD	raisd/2.9
raxml
raxml-ng	raxml-ng-mpi/1.1.0
rclone	rclone/1.62.2
repeatmasker	repeatmasker-mpi/4.1.2-p1
root	root/6.28.04
rsem	rsem/1.3.3
rstudio	rstudio/2023.09.1
rsync	(system RPM)
ruby	ruby/3.1.0
rust	rust/1.74.0s
sage	sage/9.5
salmon	salmon/1.9.0
samtools	samtools/1.16.1
SAS
scalable	N/A
scalapack	netlib-scalapack
schrodinger	schrodinger/2023-4
scikit-image	N/A - Users install in their python/conda environments
scikit-learn	N/A - Users install in their python/conda environments
scons	scons/4.5.2
scotch	scotch-mpi/7.0.3
seaborn	N/A - Users install in their python/conda environments
selscan	selscan/2.0.0
seqkit	seqkit/0.10.1
seqtk	seqtk/1.3
sextractor	sextractor/2.25.0
sga	N/A
sharc	sharc-mpi/3.0.1
singularity2	(system RPM)
six	N/A - Users install in their python/conda environments
skewer	skewer/0.2.2
slicer	slicer/5.4.0
slim	slim/4.0.1
snakemake	N/A - Users install in their python/conda environments
SNAP	N/A
spectre
splash	splash/2.1.4
spm	spm/12_r7606
spyder	N/A - Users install in their python/conda environments
sqlite	(system RPM)
sratoolkit	sratoolkit/3.0.0
stacks	stacks/2.65
star	star/2.7.10b
stata	stata/mp17
statsmodels	N/A - Users install in their python/conda environments
stringtie	stringtie/2.2.1
sublime	sublime-text/4.4143
subread	subread/2.0.2
svn	subversion/1.14.1
swarp	swarp/2.41.5
sympy	N/A - Users install in their python/conda environments
synopsys
sysstat	sysstat/12.5.4
tabix	tabix/2013-12-16
tecplot	tecplot/2022r1
tensorflow	N/A - Users install in their python/conda environments
tesseract	tesseract/4.1.1
texlive	texlive/20220321
texstudio	texstudio/3.0.1
tmux	tmux/3.3a
tn93	tn93/1.0.12-
tophat
tortoise	N/A
tree	tree/2.1.0-7
trimal	trimal/1.4.1
trimgalore	trimgalore/0.6.6
trimmomatic	trimmomatic/0.39
trinity
udunits	udunits/2.2.28
usearch	usearch/11.0.667
v8	v8/3.14.5
vasp	vasp-mpi/5.4.4-mdh3hpy vasp-mpi/6.3.2_avandewa-chn3w3j vasp-mpi/6.4.2_cfgoldsm-7krhcss vasp-mpi/6.4.2_cfgoldsm_vtst-cff5qmk
vcftools	vcftools/0.1.14
vep
vim	(system RPM)
virtualgl	virtualgl/3.1
visit	N/A
vmd	vmd/1.9.3
vrg3d	N/A
vrpn	N/A
vscode	vscode/1.84.2
vtk	vtk-mpi/9.2.6
wcstools	wcstools/3.9.7
weblogo	N/A - Users install in their python/conda environments
workshop	N/A
xcrysden	xcrysden/1.5.60
xeyes	xeyes/1.2.0
xfce
xgboost	xgboost/1.6.2
Xvfb	(system RPM)
yaml-cpp	yaml-cpp/0.7.0
zlib	zlib/1.2.13
zsh	(system RPM)