Available Software Environments

This page outlines the software stacks available to the users and the module manager used to load in the desired software.

EasyBuild Stacks

The available EasyBuild stack dependancies are linked against the OS libraries and drivers using EasyBuild. A stack tree starts with a compiler environment (i.e. GCC-version). The stacks are managed with the module manager Lmod. In general it is enough to load a software module to make the software ready for use. Loading in the module correctly append the necessary binary paths and loads all dependencies.

In order to make use of a compiler environment to compile your own software several modules may have to be loaded at once. See here for compiling / development instructions.

Using Lmod

The main command for using the manager is module (or ml for short). A list of options is available by typing:

[..]$ module --help

To see a list of avalable modules type:

[..]$ module avail

For a complete list, which includes dependencies of all of the software, type:

[..]$ module --show-hidden avail

This command can also be used to list specific software and all available versions, for example:

[..]$ module avail Anaconda3
   Anaconda3/2021.11 (D)	Anaconda3/2022.05

Loading Modules

To load a module type:

[..]$ module load Anaconda3

In this particular case it will load the (D)efault module. To list the currently loaded modules type:

[..]$ module list
Currently Loaded Modules:
  1) Anaconda3/2021.11

You can load in as many modules at any time as you please. Note that some modules may conflict with each other.

If you wish to switch from one particular version to another type:

[..]$ module switch Anaconda3/2021.11 Anaconda3/2022.05

To unload a module type:

[..]$ module unload Anaconda3

If you wish to clear your whole list of currently loaded modules type:

[..]$ module purge

Storing Module Environments

When you have loaded in a set of modules which you frequently use for your work it can be a good idea to store the set, for example:

[..]$ module save env1                                                   

where env1 is just an example name. In a later session you can reload the desired set of modules by typing:

[..]$ module restore env1

To see a list of stored module sets type:

[..]$ module savelist
Named collection list :
  1) default  2) env1

Pre-built environments

Some package environments are loaded in by default, others need to be loaded in manually. See the list of pre-built package environments described below.

libsci-gcc

The libsci-gcc tree provides a compilation of free and open source software providing commonly used numerical libraries for scientific software and applications. It starts with GCC-11.2.0, and is located in /hpcapps/libsci-gcc/.

Precompiled software

GCC/OpenMPI

Modules	Version	Toolchain
ASE	3.2.2	system
ASE	3.23.0b1	dev
Autotools	20210726	GCCcore-11.2.0
Brotli	1.0.9	GCCcore-11.2.0
DBus	1.13.18	GCCcore-11.2.0
EasyBuild	4.5.4
Eigen	3.4.0	GCCcore-11.2.0
FFTW	3.3.10	gompi-2021b
FLTK	1.3.7	GCCcore-11.2.0
GCC	11.2.0
GCCcore	11.2.0
GPAW	22.8.0	foss-2021b
Go	1.20.2	system
Gurobi	10.0.0
OpenBLAS	0.3.18	GCC-11.2.0
OpenMPI	4.1.1	GCC-11.2.0
PISM	2.0.6	System
Python	3.9.6	GCCcore-11.2.0
SQLite	3.36	GCCcore-11.2.0
ScaLAPACK	2.1.0	gompi-2021-fb
VASP	6.3.2	foss-2021b
VASP	6.3.2	nvhpc
VaspBeef	6.3.2	foss-2021b
Xauth	1.0.9
foss	2021b
gompi	2021b
intltool	0.51.0	GCCcore-11.2.0
libbeef	6.3.2	system
libxc	5.1.6	GCC-11.2.0
nodejs	14.17.6	GCCcore-11.2.0
petsc	3.18	system
pkgconf	1.8.0	GCCcore-11.2.0
udunits	2.2.28	system
util-linux	2.37	GCCcore-11.2.0
xprop	1.2.5	GCCcore-11.2.0
zstd	1.5.0	GCCcore-11.2.0

Python includes Numpy and Scipy linked to OpenBLAS and FFTW.

libbio-gpu

This libbio-gpu tree provides a compilation of free and open source software providing commonly used numerical libraries for scientific software and applications it starts with GCC-11.3.0 and is located in /hpcapps/libbio-gpu.

To load in the package environment type

[..]$ module use /hpcapps/libbio-gpu/modules/all

The modules are now available and can be viewed by typing

[..]$ module avail

Precompiled software

GCC/OpenMPI

Modules	Version	Toolchain
AlphaFold	2.3.0	system
aria2	1.36.0	system
BLIS	0.9.0	GCC-11.3.0
Bazel	5.1.1	GCCcore-11.3.0
Biopython	1.80	foss-2022a
BLIS	0.9.0	GCC-11.3.0
CMake	3.23.1	GCCcore-11.3.0
CUDA	11.7.0
Doxygen	1.9.1	GCCcore-11.3.0
EasyBuild	4.6.2
FFTW.MPI	3.3.10	gompi-2022a
FFTW	3.3.10	GCCcore-11.3.0
FFmpeg	4.4.2	GCCcore-11.3.0
FLEXIBLAS	3.2.0	GCCcore-11.3.0
FriBidi	1.0.12	GCCcore-11.3.0
GCC	11.3.0
GCCcore	11.3.0
Kalign	3.3.2	GCCcore-11.3.0
NCCL	2.12.12	GCCcore-11.3.0-CUDA-11.7.0
NVHPC	22.5
ORCA	5.0.3
OpenBLAS	0.3.20	GCC-11.3.0
OpenMM	7.7.0	CUDA-11.7
OpenMPI	4.1.4	GCC-11.3.0
PyTorch	1.12.0	foss-2022a-CUDA-11.7.0
Python	3.10.4	GCCcore-11.3.0
QuantumEspresso	7.1	foss-2022a
SWIG	4.0.2	GCCcore-11.3.0
ScaLAPACK	2.2.0	gompi-2022a-fb
TensorRT	8.4.3.1	CUDA-11.7
Tkinter	3.10.4	GCCcore-11.3.0
X11	20220504	GCCcore-11.3.0
aria2	1.36.0
crest	2.12	foss-2022a
cuDNN	8.4.1.50	CUDA-11.7.0
foss	2022a
gettext	0.21	GCCcore-11.3.0
gompi	2022a
hh-suite	3.3.0	GCCcore-11.3.0
hmmer	3.3.2	GCCcore-11.3.0
libiconv	1.17	GCCcore-11.3.0
libtool	2.4.7	GCCcore-11.3.0
ncurses	6.3	GCCcore-11.3.0
protobuf	3.22	dev
rpmrebuild	2.11
xtb	6.5.1	foss-2022a

lib-mimir

The libsci-mimir tree provides a compilation of free and open source software providing commonly used numerical libraries for scientific software and applications. It starts with GCC-11.2.0, and is located in /hpcapps/lib-mimir/.

Precompiled software

Modules	Version	Toolchain
Anaconda3	2021.11
Anaconda3	2022.05
BCFtools	1.14	GCC-11.2.0
BEDTools	2.30.0	GCC-11.2.0
BamTools	2.5.2	GCC-11.2.0
Biopython	1.79	foss-2021b
Bowtie2	2.4.4	GCC-11.2.0
CMake	3.22.1	GCCcore-11.2.0
CellRanger	7.0.0
Dorado	0.1.1
EasyBuild	4.6.0
FastQC	0.11.9	Java-11
GNU-parallel	20221022
HISAT2	2.2.1	gompi-2021b
HTSlib	1.14	GCC-11.2.0
Java	11.0.2
Java	15.0.1
MACS2	2.2.7.1	foss-2021b
MIB	glnx64
Perl	5.34.0	GCCcore-11.2.0
R	4.1.2	foss-2021b
SAMtools	1.15	GCC-11.2.0
SEACR	1.3
SRA-Toolkit	3.0.0
TrimGalore	0.6.7
VCFtools	0.1.16	GCC-11.2.0
bcl-convert	3.6.3
bcl2fastq2	2.20.0	GCC-11.2.0
bzip2	1.0.8	GCCcore-11.2.0
cutadapt	4.1
deepTools	3.5.1	foss-2021b
file	5.41	GCCcore-11.2.0
kallisto	0.48.0
matplotlib	3.4.3	foss-2021b
megalodon	2.3.0
minimap2	2.24	GCCcore-11.2.0
modbam2bed	0.6.2
nanopolish	0.14.0
ont-guppy	6.2.1
picard	2.26.10	Java-15
remora	1.1.1
stacks	2.62
subread-featureCounts	2.0.3
wigToBigWig	4

libsci-intel

The libsci-intel tree provides a compilation of free and open source software providing commonly used numerical libraries for scientific software and applications. It starts with GCC-11.2.0, and is located in /hpcapps/libsci-intel/.

To load in the package environment type

[..]$ module use /hpcapps/libsci-intel/modules/all

The modules are now available and can be viewed by typing

[..]$ module avail

Precompiled software

Modules	Version	Toolchain
Automake	1.16.5	GCCcore-12.2.0
Autotools	20220317	GCCcore-12.2.0
EasyBuild	4.7.0
GCCcore	12.2.0
Perl	5.36.0	GCCcore-12.2.0
expat	2.4.9	GCCcore-12.2.0
groff	1.22.4	GCCcore-12.2.0
iimpi	2022b
imkl	2022.2.1
impi	2021.7.1	intel-compilers-2022.2.1
intel-compilers	2022.2.1
libreadline	8.2	GCCcore-12.2.0
libtool	2.4.7	GCCcore-12.2.0
ncurses	6.3	GCCcore-12.2.0
numactl	2.0.16	GCCcore-12.2.0
pkgconf	1.9.3	GCCcore-12.2.0
zlib	1.2.12	GCCcore-12.2.0

libsci-amd

The libsci-amd tree provides a compilation of free and open source software providing commonly used numerical libraries for scientific software and applications. It starts with GCC-11.2.0, and is located in /hpcapps/libsci-amd/.

Precompiled software

Modules	Version	Toolchain
EasyBuild	4.6.2

libsci-nvhpc

The libsci-nvhpc tree provides a compilation of free and open source software providing commonly used numerical libraries for scientific software and applications. It starts with GCC-11.2.0, and is located in /hpcapps/libsci-nvhpc/.

Precompiled software

Modules	Version	Toolchain
VASP	6.3.2	nvhpc