Installed Applications

In this section:

Module System
List of Applications by Category
Quick Usage Examples
Requesting New Applications
Installed Scientific Applications and More Complete Examples

GridUnesp has dozens of scientific applications pre-installed and available through the module system. This section lists the main applications and provides usage examples.

Note

To see the complete and up-to-date list of available modules:

module avail

The list can be extensive. Use grep to filter:

module avail | grep -i conda
module avail | grep -i gromacs

Or simply:

module avail conda
module avail gromacs

Module System 

GridUnesp uses Lmod for module management. Basic commands:

Module commands
Command	Description
`module avail`	List all available modules
`module load name/version`	Load a specific module
`module list`	View currently loaded modules
`module unload name`	Unload a module
`module purge`	Unload all modules
`module show name`	View module details (paths, dependencies)

List of Applications by Category 

Libraries, Compilers and Languages 

Libraries, compilers and languages
Software	Installed Versions
Boost	1.64.0, 1.70.0
CMake	3.9.0, 3.20.0-rc3, 4.0.3
GCC	5.3.0, 7.2.0, 9.3.0, 10.2.0, 11.5.0, 13.2.0, 14.3.0, 15.1.0
GSL	2.6
Intel Compilers	2017, oneapi/2025.2
Intel MPI	2017
Java	1.8
MKL	2022.2.0
NetCDF	c/4.6.3, fortran/4.4.5
OpenMPI	2.1.1, 3.1.4, 4.0.1, 4.1.1, 4.1.5, 4.1.6, 4.1.8
Python	Via Conda (2.7, 3.6, 3.8, 3.9, 3.10, 3.11)
R	4.0.2
UDUNITS	2.2.26

Bioinformatics 

Bioinformatics applications
Software	Installed Versions
BEAST	1.8.4, 1.10.4, 2.4.7
Bowtie2	2.3.5.1
BUSCO	5.5.0
ClustalW	2.1, clustalw-mpi/0.13
fastStructure	1.0
HMMER	3.1b2
Kraken2	2.1.3
MFannot	1.37
PFinderUCE-SWSC-EN	1.0.0
Phyluce	1.5.0
RAxML	8.2.11
RAxML-NG	1.0.3
RSEM	1.2.25
Salmon	0.14.0
SPAdes	3.15.5
Stacks	2.4
Structure	2.3.4
TrimGalore	2.2.0
Trinity	2.8.5, 2.15.1
VCFtools	0.1.16

Computational Chemistry and Materials 

Chemistry and Materials applications
Software	Installed Versions
Amber	20, 24
CHARMM	c26b2, c26b2-serial, c37b2, c37b2-serial
CP2K	2023.1
CRYSTAL	17_v1.0.2, 17_v1.0.2_v2
CUDA	12.4, 12.9
DFTB+	20.2.1
DIRAC	12.3-mpi, 12.3-serial, 12.3-smp
Exciting	carbon, neon-21
GAMESS	2018, 2020
Gaussian	09, 09.lsm
GROMACS	4.5.4, 4.5.4-sbm1.0, 5.1.4, 2016.3, 2018.2, 2025.2
LAMMPS	20170331, 20180316, 20200303, 20230802
MOPAC	17.162
NAMD	2.12, 2.12-tcp, 2.13-smp, 2.13-tcp
ORCA	4.0.1, 4.2.1, 5.0.3, 5.0.4, 6.0.0, 6.0.1, 6.1.0
PLUMED	2.7.1
Quantum ESPRESSO	6.1, 6.6, 7.2, 7.5/mpi, 7.5/serial
Siesta	4.0.2, 4.1-b3, 4.1.5.mpi, 4.1.5.serial, 5.2.0.mpi, 5.2.0.serial
VASP	6.4.3
xtb	6.6.1

Physics and Engineering 

Physics and Engineering applications
Software	Installed Versions
ANSYS	2025R2/fluids, 2025R2/structures
ESPResSo	3.3.1
foam-extend	4.0, 4.1
OpenFOAM	4.1, 5.x, 7, 8, 1912, 2012, 2112
QUEST-QMC	1.4.9
ROOT	6.10.02
SU2	6.0.0, 6.2.0
SWAN	41.31-mpi, 41.31-omp, 41.31-serial

Geosciences 

Geosciences applications
Software	Installed Versions
GAMIT	10.61, 10.70
GMT	5.4.3
RNXCMP	4.0.7

Environments and Tools 

Environments and tools
Software	Installed Versions
Anaconda	2/5.1.0, 3/4.4.0
Miniconda	3, 3-2023-09, 24.4.0-libmamba, 25.x
Backmap	0.5
g_mmpbsa	gromacs-5.1
Grace	5.1.25
Tesseract	4.00.00alpha
Weka	3.8.2

Other Applications 

Other applications
Software	Installed Versions
allpathslg	44837
beagle	2.1.2, 4.0.0
blobtoolkit	4.4.5
cln	1.3.4
eems	0.0.0
evigene	23jul15
fcs-gx	0.5.5
fhi	071914
gdal	2.4.1
ginac	1.7.2
glibc	2.29
gridunesp	1
migrate-n	5.0.6
platanus	1.2.4
sga	0.10.15

Quick Usage Examples 

Each application has its own particularities. Below are basic examples for some common applications.

Example 1: GROMACS (Molecular Dynamics)

gromacs_example.sh

#!/bin/bash
#SBATCH -J gromacs_job
#SBATCH -N 2
#SBATCH --ntasks-per-node=28
#SBATCH -t 24:00:00

export INPUT="topol.tpr"
export OUTPUT="resultado_gromacs/"

# Load modules
module load gromacs/2025.2

# Run MD
job-nanny mpirun -n 56 gmx_mpi mdrun -deffnm resultado -v

Example 2: Quantum ESPRESSO 

qe_example.sh

#!/bin/bash
#SBATCH -J qe_job
#SBATCH -N 2
#SBATCH --ntasks-per-node=28
#SBATCH -t 48:00:00

export INPUT="si.scf.in"
export OUTPUT="si.scf.out"

module load quantum-espresso/7.2

job-nanny mpirun -n 56 pw.x -inp si.scf.in > si.scf.out

Example 3: Python with scientific packages 

python_example.sh

#!/bin/bash
#SBATCH -J python_job
#SBATCH -n 1
#SBATCH -t 02:00:00
#SBATCH --mem=8G

export INPUT="script.py dados.csv"
export OUTPUT="resultados/"

# Use a custom Conda environment
module load miniconda/24.4.0-libmamba
source activate meu_ambiente_python

job-nanny python script.py

Example 4: R for statistical analysis 

r_example.sh

#!/bin/bash
#SBATCH -J r_job
#SBATCH -n 1
#SBATCH -t 01:00:00
#SBATCH --mem=4G

export INPUT="analise.R dados.csv"
export OUTPUT="resultados_R/"

module load R/4.0.2

job-nanny Rscript analise.R

Example 5: MATLAB 

matlab_example.sh

#!/bin/bash
#SBATCH -J matlab_job
#SBATCH -n 1
#SBATCH -t 02:00:00
#SBATCH --mem=8G

export INPUT="script.m dados.mat"
export OUTPUT="resultados_matlab/"

module load matlab/R2019b

job-nanny matlab -batch "script"

Example 6: VASP 

vasp_example.sh

#!/bin/bash
#SBATCH -J vasp_job
#SBATCH -N 4
#SBATCH --ntasks-per-node=28
#SBATCH -t 72:00:00

export INPUT="INCAR POSCAR POTCAR KPOINTS"
export OUTPUT="OUTCAR OSZICAR"

module load vasp/6.4.3

job-nanny mpirun -n 112 vasp_std

Requesting New Applications 

If the application you need is not available:

Check whether you can install it locally (Installing Applications)
Otherwise, request it from the GridUnesp team

Required information:
- Application name
- Desired version
- Link to the official documentation
- Justification for a global installation
- Whether specific libraries are needed
Support contact e-mail: support.ncc@unesp.br

Installed Scientific Applications and More Complete Examples 

This section lists all available applications and provides links to the specific documentation for each one.