.. _installed_applications: ====================== Installed Applications ====================== .. contents:: In this section: :local: :depth: 2 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: .. code-block:: bash module avail The list can be extensive. Use ``grep`` to filter: .. code-block:: bash module avail | grep -i conda module avail | grep -i gromacs Or simply: .. code-block:: bash module avail conda module avail gromacs Module System ============= GridUnesp uses **Lmod** for module management. Basic commands: .. list-table:: Module commands :header-rows: 1 :widths: 30 70 * - 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 ---------------------------------- .. list-table:: Libraries, compilers and languages :header-rows: 1 :widths: 40 60 * - 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 -------------- .. list-table:: Bioinformatics applications :header-rows: 1 :widths: 40 60 * - 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 ------------------------------------- .. list-table:: Chemistry and Materials applications :header-rows: 1 :widths: 40 60 * - 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 ----------------------- .. list-table:: Physics and Engineering applications :header-rows: 1 :widths: 40 60 * - 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 ----------- .. list-table:: Geosciences applications :header-rows: 1 :widths: 40 60 * - Software - Installed Versions * - GAMIT - 10.61, 10.70 * - GMT - 5.4.3 * - RNXCMP - 4.0.7 Environments and Tools ---------------------- .. list-table:: Environments and tools :header-rows: 1 :widths: 40 60 * - 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 ------------------ .. list-table:: Other applications :header-rows: 1 :widths: 40 60 * - 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) --------------------------------------- .. code-block:: bash :caption: 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 --------------------------- .. code-block:: bash :caption: 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 ------------------------------------------ .. code-block:: bash :caption: 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 ------------------------------------- .. code-block:: bash :caption: 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 ----------------- .. code-block:: bash :caption: 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 --------------- .. code-block:: bash :caption: 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 .. Creating Your Own Modules ========================= For applications installed locally (in your ``/home/``), you can create your own modules: 1. **Create the directory for personal modules:** .. code-block:: bash mkdir -p ~/modules 2. **Create a module file:** .. code-block:: text :caption: ~/modules/meu_app/1.0.lua help([[ Meu aplicativo pessoal versão 1.0 ]]) whatis("Meu aplicativo pessoal") local app_dir = "/home/$USER/local/meu_app/1.0" prepend_path("PATH", pathJoin(app_dir, "bin")) prepend_path("LD_LIBRARY_PATH", pathJoin(app_dir, "lib")) prepend_path("MANPATH", pathJoin(app_dir, "share/man")) 3. **Add to your ``.bashrc``:** .. code-block:: bash export MODULEPATH=$HOME/modules:$MODULEPATH 4. **Use your module:** .. code-block:: bash module load meu_app/1.0 Requesting New Applications =========================== If the application you need is not available: 1. **Check** whether you can install it locally (:ref:`installing_applications`) 2. 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`` .. _all_applications: Installed Scientific Applications and More Complete Examples ============================================================ This section lists all available applications and provides links to the specific documentation for each one. .. toctree:: :maxdepth: 2 aplicacoes/amber aplicacoes/anaconda aplicacoes/ansys aplicacoes/beast aplicacoes/bowtie2 aplicacoes/busco aplicacoes/ccdc aplicacoes/charmm aplicacoes/clustalw aplicacoes/cp2k aplicacoes/crystal aplicacoes/cuda aplicacoes/dftb aplicacoes/dirac aplicacoes/espresso aplicacoes/exabayes aplicacoes/exciting aplicacoes/fastStructure aplicacoes/foam-extend aplicacoes/g_mmpbsa aplicacoes/gamess aplicacoes/gamit aplicacoes/gaussian aplicacoes/gcc aplicacoes/gromacs aplicacoes/hmmer aplicacoes/intel aplicacoes/kraken2 aplicacoes/lammps aplicacoes/mathematica aplicacoes/matlab aplicacoes/mfannot aplicacoes/miniconda aplicacoes/mopac aplicacoes/namd aplicacoes/netcdf aplicacoes/openfoam aplicacoes/openmpi aplicacoes/orca aplicacoes/partitionfinder aplicacoes/pfinderuce-swsc-en aplicacoes/phyluce aplicacoes/plumed aplicacoes/quantum-espresso aplicacoes/quest-qmc aplicacoes/r aplicacoes/raxml aplicacoes/raxml-ng aplicacoes/rnxcmp aplicacoes/root aplicacoes/rsem aplicacoes/salmon aplicacoes/siesta aplicacoes/spades aplicacoes/stacks aplicacoes/structure aplicacoes/su2 aplicacoes/swan aplicacoes/tesseract aplicacoes/trimgalore aplicacoes/trinity aplicacoes/vasp aplicacoes/vcftools aplicacoes/weka aplicacoes/xtb .. seealso:: - :ref:`installing_applications` - Local installation - :ref:`containers` - Using containers for custom environments - :ref:`running_simulations` - How to submit jobs - :ref:`system_administrator_installation` - Requesting an installation