Module File Naming Convention
TSUBAME4 manages applications using the "Environment Modules(module command)".
The naming convention for module files specified to the module command is as follows:
<module name>/<version>
/<version>is optional. If omitted, the default version (bolded) is specified.- This page introduces only the default version and latest versions. To view all available versions, use the command “module avail <module name>”.
- The default version is updated during the regular maintenance performed at the end of each fiscal year.
- Some applications provide multiple binaries for a single version. In such cases, an identifying keyword is appended after the version number.
- Keywords like
gcc,intel,nvhpc, orcudain names such asopenmpi/5.0.2-gccindicate the development environment used for building. - For application-specific keywords like
_cpuingaussian/16C2_cpu, you can use the “module whatis <module name>/<version>” command to view a brief description.
- Keywords like
Commercial Applications
There are restrictions on the applications that can be used by non-University users.
Also, some applications have restrictions on execution due to the number of licenses.
For details, please refer to About license restriction of commercial applications.
For usage instructions, please also refer to the “TSUBAME4.0 User's Guide” and the User's Guide provided for each application (Japanese only).
| Application name | module name | Overview | GPU compatible | Main versions available | Remarks |
|---|---|---|---|---|---|
| Development Environment, Library | |||||
| Intel oneAPI | intel | Development environment for CPU | 2025.0.0 | ||
| NVIDIA HPC SDK | nvhpc | Development environment for CPU/GPU | ○ | 25.1_cuda12.6 | |
| AMD AOCC | aocc | Development environment for CPU | 4.1.0 | ||
| Commercial Applications | |||||
| ANSYS | ansys | Analysis software | R25.1 R25.2 | Academic Product Reference Guide | |
| ABAQUS/ CAE | abaqus | Analysis software | ○ | 2025 | |
| Gaussian | gaussian | Quantum chemical calculation program | 16C2_cpu | GPU version is waiting for H100 support | |
| GaussView | gaussview | Quantum chemical calculation pre-post tool | 6.1 | ||
| AMBER | amber | Molecular dynamics calculation program | ○ | 24up03_ambertools24up10 pmemd24.01_ambertools25.02 | Starting with Ambertools25, the version naming convention has changed. For details, please refer here. |
| Materials Studio | Chemical simulation software | Materials Studio is intended for use with application distribution (Windows). On TSUBAME4, only the “AGE batch execution feature(Japanese only)” is available. The module command is not used. | |||
| Discovery Studio | Chemical simulation software | Discovery Studio is available only for Distribution of Commercial Applications on Campus (Windows). | |||
| Mathematica | mathematica | Mathematical processing software | 14.2 14.3 | ||
| COMSOL Multiphysics | comsol | Analysis software | 63 64_u1 | ||
| Schrödinger Small-Molecule Drug Discovery Suite | schrodinger | chemical simulation software | 2025-1 2026-1 | ||
| MATLAB | matlab | Numerical calculation software | ○ | R2024b R2025b | |
| VASP | VASP6 | Quantum molecular dynamics calculation program | ○ | 6.4.3/5.0.2-nvhpc | License holders can apply for access to compiled binaries here. Effective 2025/04/04, the module file name has been changed from VASP to VASP6. |
| VASP6.5 | VASP6.5 | Quantum molecular dynamics calculation program | ○ | 6.5.0/5.0.2-nvhpc | License holders can apply for access to compiled binaries here. |
Free software
| Application name | module name | Overview | GPU compatible | Main versions available | Remarks |
|---|---|---|---|---|---|
| Solver , Simulator | |||||
| GAMESS | gamess | solver , simulator | Jun302023R1 | ||
| Tinker | tinker | solver , simulator | 〇 | 8.10.5 | |
| GROMACS | gromacs | solver , simulator | 〇 | 2025.1 | |
| LAMMPS | lammps | solver , simulator | 〇 | 2aug2023_u3 | |
| NAMD | namd | solver , simulator | 〇 | 3.0.1 3.0.2_verbs-smp-CUDA | For version information, please refer here. |
| QUANTUM ESPRESSO | quantumespresso | solver , simulator | 〇 | 7.3.1 | |
| CP2K | cp2k | solver , simulator | 〇 | 2024.1 | |
| OpenFOAM | openfoam | solver , simulator , visualization | 11.0 | ||
| OpenFOAM (ESI) | openfoam-esi | solver , simulator , visualization | v2312 | ||
| GPU , Machine learning , Visualization | |||||
| CUDA | cuda | GPU library | 〇 | 12.8.0 | |
| CuDNN | cudnn | GPU library | 〇 | 9.8.0 | |
| NCCL | nccl | GPU library | 〇 | 2.26.2 | |
| TensorFlow | DeepLearning framework | 〇 | Install in user environment | ||
| DeePMD-kit | deepmd-kit | MD用DeepLearning framework | 〇 | 2.2.9 | |
| PyTorch | Machine learning | Install in user environment | |||
| R | R | Interpreter (compatible with Rmpi, rpud) | 4.4.0 | ||
| Hadoop | hadoop | Distributed data processing tools | 3.3.6 | ||
| POV-Ray | pov-ray | Visualization | 3.7.0.9 | ||
| ParaView | paraview | Visualization | 〇 | 5.12.0 | |
| VisIt | visit | Visualization | 3.1.4 | ||
| vmd | vmd | Visualization | 1.9.4 | ||
| VESTA | VESTA | Visualization | 3.5.8 | ||
| turbovnc | turbovnc | Remote GUI (X11) display | 3.1.1 3.2 | ||
| VirtualGL | turbovnc | Remote GUI | 〇 | 3.1.1 3.2 | Included in turbovnc module |
| Open OnDemand | Web portal for HPC | 3.0.3 | |||
| gnuplot | Data visualization | 5.4.3 | |||
| NVIDIA Nsight Systems | nsys | Profiler | 〇 | 2025.1.1_cuda12.8 | |
| Others | |||||
| GIMP | Image display/edit | 2.99.8 | |||
| Tgif | tgif | Image display/edit | 4.2.5 | ||
| ImageMagick | Image display/edit | 7.1.1-29 | |||
| TeX Live | TeX distribution | 2020 | |||
| OpenJDK | openjdk | Development environment | 1.8.0 11.0.2 23.0.2 | Default is 11.0.2 | |
| python | Development environment | 3.9.18 | How to install other versions | ||
| ruby | Development environment | 3.0.4p208 | |||
| perl | Development environment | 5.32.1 | |||
| PHP | Development environment | 8.0.30 | |||
| golang | Development environment | 1.20.10 | |||
| Emacs | Editor | 27.2 | |||
| vim | Editor | 8.2 | |||
| PETSc | petsc | Linear system solver, library | 3.20.4-real | ||
| FFTW | fftw | Fast Fourier Transform Library | 3.3.10-nvhpc | ||
| Apptainer | Container management | 1.2.5-1.el9 | |||
| Spack | spack | Software package management | 0.21.2 | ||
| miniconda | miniconda | Software package management | 24.1.2 | ||
| PyPl | Software package management | 3.9 | |||
| Rbenv | Software package management | 1.2.0 | |||
| Alphafold | alphafold | bio | 〇 | 2.3.2 | |
| tmux | tmux | Terminal multiple connection | 3.3 | ||
| NetCDF | netcdf-parallel | Multidimensional data format | 4.9.2/nvhpc24.1 | ||
| HDF5 | hdf5-parallel | Hierarchical data format | 1.14.3/nvhpc24.1 | ||
| ffmpeg | ffmpeg | Video/audio processing | 〇 | 7.1.1 | |
| Automake | automake | Compiling | ( 1.16.2 ) 1.17 | If the module command is not used, version 1.16.2 will be used. | |
| Autoconf | autoconf | Environment building | ( 2.69 ) 2.72 | If the module command is not used, version 2.69 will be used. | |
| ninja | ninja | Build system | 1.12.2 | ||
| MMseqs2 | mmseqs2 | Search | 〇 | 17-b804f | |
| Ambertools | ambertools | Molecular dynamics calculation program | 〇 | 25_singlenode 25.02 | For those for whom an Amber licence is not available. Multiple node execution not possible |
Databases for software
We have prepared databases on TSUBAME for use with some software.
Because of the large size of these database files, please avoid downloading them individually if possible.
The database is scheduled to be updated about once a month, and the latest database is loaded by default.
If you wish to fix the database, specify the version at module load.
The database is scheduled for updates approximately once a month, and the default version is always the latest version on TSUBAME.
If you wish to use a specific database version, please specify the version.( Example: alphafold2_database/202602 )
| Supported Software | module name | Remarks |
|---|---|---|
| Bio | ||
| Alphafold2 | alphafold2_database | |
| Alphafold3 | alphafold3_database | |
| LocalColabfold | colabfold_database | |