Okazaki Research Facilities
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Package Programs List
Compilers and Libraries
(Status on Dec 8, 2020.) Most packages are installed under /local/apl/lx.
|
Name |
Version | misc info |
|---|---|---|
| Intel Parallel Studio XE | 2020 update 2 | icc 19.1.2 |
| icpc 19.1.2 | ||
| ifort 19.1.2 | ||
| impi 2019.0.8 (2019.8.254) | ||
| 2019 update 5 | icc 19.0.5 | |
| icpc 19.0.5 | ||
| ifort 19.0.5 | ||
| impi 2019.0.5 (2019.5.281) | ||
| 2019 update 1 | icc 19.0.1 | |
| icpc 19.0.1 | ||
| ifort 19.0.1 | ||
| impi 2019 Update 1 (2019.1.144) | ||
| 2018 update 4* | icc 18.0.5 | |
| icpc 18.0.5 | ||
| ifort 18.0.5 | ||
| impi 2018.0.4 | ||
| 2018 update 2 | icc 18.0.2 | |
| icpc 18.0.2 | ||
| ifort 18.0.2 | ||
| impi 2018.0.2 | ||
| 2017 update 8 | icc 17.0.8 | |
| icpc 17.0.8 | ||
| ifort 17.0.8 | ||
| impi 2017.0.4 | ||
| 2017 update 4 | icc 17.0.4 | |
| icpc 17.0.4 | ||
| ifort 17.0.4 | ||
| impi 2017.0.3 | ||
| 2015 update 1 | icc 15.0.1 | |
| icpc 15.0.1 | ||
| ifort 15.0.1 | ||
| impi 5.0 Update 2 | ||
| GCC | 4.8.5* | |
| 9.3.1 | Devtoolset-9 Software Collections[2] | |
| 8.3.1 | Devtoolset-8 Software Collections[2] | |
| 7.3.1 | Devtoolset-7 Software Collections[2] | |
| 6.3.1 | Devtoolset-6 Software Collections[2] | |
| 5.3.1 | Devtoolset-4 Software Collections[2] | |
| 4.9.2 | Devtoolset-3 Software Collections[2] | |
| PGI Compilers and Tools | 20.4-0 | |
| 18.1-1* | ||
| 17.5-0 | ||
| 16.5-0 | ||
| CUDA | 11.1.105 | |
| 10.1.243 | ||
| 9.1.85* | ||
| 8.0.61 | ||
| Python1 | 3.4.5 | (default version for python3) |
| 2.7.5* | ||
| 3.7.7 (Anaconda3-2020.02) | ||
| 3.7.3 (Anaconda3-2019.03) | ||
| 2.7.16 (Anaconda2-2019.03) | ||
| Julia | 1.3.1 | /local/apl/lx/julia-1.3.1/bin/julia |
| Open MPI | 4.0.2 | (mpi1 and cxx support enabled) |
| 4.0.0 | (cxx support enabled) | |
| 3.1.0 | ||
| 2.1.3 | ||
| Singularity | 3.6.4 |
*: default version
[1]: you can install packages in your home directory by using "pip install (package name) --user" command. Installation of Anaconda (to the homedir) is also recommended. Miniconda might be better if you want to avoid long wait time upon loading anaconda env (current RCCS file system is not good at handling many small files).
[2]: installed under /opt/rh/devtoolset-(version-number). For example, you can load gcc-6.3.1 environment conveniently by "module load scl/devtoolset-6".
Application Software
(Jan 5, 2021) The following packages are installed in the system. Please see the official documents/manuals for the detailed usage. These packages are installed under /local/apl/lx directory of the frotend hosts and calculation nodes. See this page for detailed information about installation.
| name | description |
|---|---|
| ABINIT | Package for material science within density functional theory, using a plane wave basis set and pseudopotentials. |
| AMBER | Package of molecular simulation programs. |
| AutoDock | Suite of automated docking tools. |
| CP2K | A quantum chemistry and solid state physics software package. |
| CRYSTAL | General-purpose programs for the study of crystalline solids. |
| DIRAC | Computes molecular properties using relativistic quantum chemical methods (named after P. A. M. Dirac). |
| GAMESS | General atomic and molecular electronic structure system. |
| Gaussian | Ab initio molecular orbital calculations. |
| GENESIS | Molecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes. |
| GROMACS | Fast, Free and Flexible MD |
| GRRM | Automated Exploration of Reaction Pathways. |
| LAMMPS | Large-scale Atomic/Molecular Massively Parallel Simulator. |
| OpenMolcas | Quantum chemistry software. |
| Molpro | Complete system of ab initio programs. |
| NAMD | Scalable molecular dynamics program. |
| NBO/NBOView | Discovery tool for chemical insights from complex wavefunctions. |
| NTChem(*17) | Comprehensive new software of ab initio quantum chemistry made in AICS from scratch. |
| NWChem | Computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems |
| ORCA | An ab initio quantum chemistry program package |
| PSI4 | Open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. |
| Quantum ESPRESSO | Integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. |
| Reaction Plus | Program to obtain the transition state and reaction path along the user’s expected reaction mechanism. |
| SIESTA | Efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids |
| SMASH | Scalable Molecular Analysis Solver for High performance computing systems |
| TURBOMOLE | One of the fastest programs for standard quantum chemical applications. |
| GaussView | Viewer for Gaussin 03 / 09. |
| Luscus | A portable GUI for MOLCAS and other quantum chemical software. |
| Molden | Visualization program of molecular and structure. |
| VMD | Molecular graphics viewer |
| name | version | revision | status (install date) | notes |
|---|---|---|---|---|
| ABINIT | 8.8.3 | ◎ (2018/7/10) | ||
| 7.8.2 | － | |||
| ADF(*9) | (unavailable) | |||
| Amber | 20 | update 0 | ○ (2020/6/9)☆ | P100, V100 supported |
| 18 | bugfix 16 | ◎ (2019/9/10)☆ | P100, V100 supported | |
| 18 | bugfix 12 | ○ (2019/2/14)☆ | P100, V100 supported | |
| 18 | bugfix 11-volta | ○ (2019/2/14)☆ | V100 supported | |
| 18 | bugfix 1 | ○ (2018/6/4)☆ | P100, V100 supported | |
| 16 | bugfix 15 | ○ (2018/7/25)☆ | P100 supported | |
| 16 | bugfix 10 | ○ (2017/10/01)☆ | P100 supported | |
| 14 | bugfix 11 | ○ (2015/7/21) | ||
| 12 | bugfix 21 | ○ (2013/12/10) | ||
| AutoDock | 4.2.6 | － | ||
| CP2K | 7.1.0 | ◎ (2020/2/27)‖ | ||
| 6.1.0 | ○ (2018/11/22)☆‖ | P100, V100 supported | ||
| CRYSTAL | 17(*21) | 1.0.2 | ○ (2020/1/27) | |
| 14(*18) | 1.0.4 | ○ (2016/5/11) | ||
| DIRAC(*19) | 18.0 | ○ (2019/5/14) | ||
| GAMESS | 2020 | Jun30 (R1) | ○ (2020/8/19)△ | |
| 2019 | Sep30 (R2) | ◎ (2019/12/13)△ | ||
| 2018 | Sep30 | ○ (2018/11/9)▲ | ||
| 2018 | Feb14 | ○ (2018/3/19)▲ | ||
| 2017 | Nov11 | ○ (2017/12/15) | ||
| 2017(*11) | Apr20 | ○ (2017/10/1) | ||
| Gaussian | 16 | C.01 | ◎ (2019/8/2)☆▲△ | P100, V100 supported |
| 16 | B.01 | ○ (2018/3/12)☆▲ | P100 supported | |
| 16 | A.03 | ○ (2017/2/13)▲ | ||
| 09 | E.01 | ◎ (2015/12/24) | ||
| 09 | D.01 | ○ (2013/7/25)▲ | ||
| 09 | C.01 | ○ (2012/2/1) | ||
| 09 | B.01 | ○ (2012/2/7) | ||
| GENESIS | 1.6.0 | ○ (2020/12/28)☆ | P100, V100★ supported | |
| 1.4.0 | ○ (2019/11/21)☆ | P100, V100★ supported | ||
| 1.3.0 | ○ (2018/9/4)☆ | P100, V100★ supported | ||
| 1.1.6 | ○ (2017/12/13)☆ | P100, V100★ supported | ||
| 1.1.5 | ○ (2017/8/4) | |||
| GROMACS | 2020.4 | ○ (2020/10/12)☆‖ | P100, V100 supported | |
| 2020.2 | ○ (2020/5/13)☆‖ | P100, V100 supported | ||
| 2019.6 | ◎ (2020/3/5)☆‖ | P100, V100 supported | ||
| 2019.4 | ○ (2019/10/8)☆‖ | P100, V100 supported | ||
| 2019.2 | ○ (2019/4/18)☆‖ | P100, V100 supported | ||
| 2018.8 | ○ (2019/10/8)☆‖ | P100, V100 supported | ||
| 2018.7 | ○ (2019/7/19)☆‖ | P100, V100 supported | ||
| 2018.6 | ○ (2019/3/27)☆‖ | P100, V100 supported | ||
| 2018.3 | ○ (2018/9/4)☆‖ | P100, V100 supported | ||
| 2018.1(*14) | ○ (2018/4/17)‖ | |||
| 2016.6 | ○ (2019/2/22)☆‖ | P100, V100 supported | ||
| 2016.5 | ○ (2018/4/17)☆‖ | P100, V100★ supported | ||
| 2016.4 | ○ (2017/10/01)☆ | P100, V100★ supported | ||
| 2016.3(*10) | ○ (2017/3/16)☆ | P100, V100★ supported | ||
| 2016.1(*10) | ○ (2017/2/2)☆ | P100, V100★ supported | ||
| 5.1.5(*12) | ○ (2018/4/17)☆‖ | P100, V100★ supported | ||
| 5.1.4 | ○ (2018/1/19)☆ | P100, V100★ supported | ||
| 4.5.5 | ○ (2012/6/12)☆ | |||
| GRRM(*5) | 14 | ◎ (2015/7/29) | ||
| 11 | ○ (2012/9/26) | |||
| LAMMPS | 7Aug19 | ◎ (2019/11/14)☆ | P100, V100 supported | |
| 22Aug18 | ○ (2018/11/6)☆ | P100 supported (lmp_rccs_gpu) V100 supported (lmp_rccs_volta) |
||
| 16Mar18(*15) | ○ (2018/5/10)☆‖ (2018/7/4 update) |
P100 supported | ||
| Molcas | 8.2 | (2020/1/30 license expired) | ||
| Molpro(*2) | 2020.1.2(*8) | ○ (2020/10/20)‖ | (Manual in pdf format (converted via wkhtmltopdf@Nov 12, 2020)) |
|
| 2019.2.3(*8) | ◎ (2019/12/10) | |||
| 2019.1.2(*8) | ○ (2019/4/16) | |||
| 2018.2(*8) | ○ (2018/12/20) | |||
| 2015.1(*8) | 33 | ○ (2018/6/12) | ||
| 2015.1(*8) | 27 | ○ (2017/12/14) | ||
| 2015.1(*8) | 19 | ○ (2017/10/1) | ||
| 2012.1(*8) | 37 | ○ (2016/4/19) | ||
| NAMD | 2.13 | ◎ (2018/12/7)☆ | P100, V100 supported | |
| 2.11 | ○ (2017/10/1)☆ | P100, V100★ supported | ||
| NBO | 7.0 | 7 | ◎ (2020/1/6) | |
| 7.0 | 2 | ○ (2019/1/23) | ||
| 6.0 | 18 | ◎ (2018/3/16) | ||
| 6.0 | 15 | ○ (2018/2/6) | ||
| NTChem(*17) | 2013.5.0 | ◎ (2015/4/20) | ||
| NWChem | 6.8 | ◎ (2018/1/22) | ||
| OpenMolcas | 20.10 | ○ (2020/12/7) | ||
| ◎ (2019/6/7) | master branch on June 4, 2019 | |||
| ORCA(*20) | 4.2.1 | ○ (2020/1/8) | ||
| Parallel CONFLEX(*9) | ||||
| PSI4 | 1.1 | ◎ (2018/1/12) | ||
| Quantum ESPRESSO | 6.7 | ○ (2021/1/5)☆ | P100, V100 supported | |
| 6.5 | ○ (2020/7/9) | |||
| 6.3 | ◎ (2018/12/17) | |||
| 6.1 | ○ (2017/9/14) | |||
| 5.4 | ○ (2018/12/17) | |||
| 5.1.2 | ○ (2015/4/8) | |||
| ReactionPlus | 1.0 | ◎ (2018/1/22) | ||
| SIESTA | 4.0.2 | ◎ (2019/3/14) | ||
| 3.1(*16) | ○ (2012/8/16) | |||
| SMASH | 2.2.0 | ○ (2017/5/16) | ||
| TURBOMOLE(*3) | 7.5 | ○ (2020/7/30) | ||
| 7.4.1 | ◎ (2020/3/2) | |||
| 7.4 | ○ (2019/8/20) | |||
| 7.3 | ○ (2018/7/23) | |||
| 7.2.1 | ○ (2017/12/12) | |||
| 7.2 | ○ (2017/8/4) | |||
| VASP(*4) | (unavailable) |
| name | version | revision | command name / path | install date |
|---|---|---|---|---|
| GaussView | 6.1.1 | /local/apl/lx/g16c01/gv/gview.sh | ○ (2019/10/29) | |
| 6.0.16 | gview6 | ◎ (2017/2/2) | ||
| 5.0.9 | gview5 | ◎ (2013/3/13) | ||
| Luscus | 0.8.6 | /local/apl/lx/luscus086/bin/luscus | ◎ (2019/6/10) | |
| Molden | 5.7 | /local/apl/lx/molden/bin/molden | ◎ (2016/11/22) | |
| NBOView2 | 2 | /local/apl/lx/nboview2/nboview2 | ◎ (2018/2/6) | |
| VMD | 1.9.3 | /local/apl/lx/vmd193/bin/vmd | ◎ (2018/2/19) |
◎: installed. Simplified alias (such as g16) is also available.
○: installed. Version number (such as g16a03) has to be specified explicitly.
▲: compatible with NBO 6.0
△: compatible with NBO 7.0
☆: GPU version available
★: Not a native build for this architecture. Performance might be limited due to its nature.
‖: GCC and Intel versions available
Notices
(*2) molpro license will be expired on Sep 15, 2021. The license will be renewed every year.
(*3) Only non-commercial users in Japan can use this. The license will be expired in Jan, 2022. The license will be renewed every year.
(*4) VASP considers a small research group as a unit of licensee. We cannot install it in this center due to the policy. Users should get the license by yourselves.
(*5) (English guide is not available...) User guide by the developers (for GRRM14/for GRRM11) and a guide for this center (for GRRM14/for GRRM11) are available. But both of them are written in Japanese.
(*8) SMILES (a package for molecular integrals with Slater functions) is enabled.
(*9) We cannot install ADF and Parallel CONFLEX due to their very high license fee.
(*10) double precision version is not installed becuase of failures on some regression tests.
(*11) Parallel executioin of exam13.inp results in a fail. This is due to the bug in the parallel computation of higher order electrostatic moments. (already reported to the official)
(*12) SelectionCollectionDataTest.HandlesCharge unittest failed on intel, single precision version due to a tricky numerical error
(*14) GPU versions (intel and gcc) are not installed, since they fail on some tests. (tip4p for intel15-cuda8, lj-pme for gcc5-cuda8)
(*15) Package list and result of tests for each version can be found in (CPU(intel) / GPU(intel) / CPU(gcc) / GPU(gcc)).
(*16) The following papers must be cited when you publish papers involving SIESTA 3.x calculations.
1. “Self-consistent order-N density-functional calculations for
very large systems”, P. Ordejón, E. Artacho and J. M. Soler,
Phys. Rev. B (Rapid Comm.) 53, R10441-10443 (1996).
2. “The SIESTA method for ab initio order-N materials simulation”
J. M. Soler, E. Artacho,J. D. Gale, A. García, J. Junquera,
P. Ordejón, and D. Sánchez-Portal, J. Phys.: Condens. Matt. 14,
2745-2779 (2002).
(*17) You have to cite some papers when you publish papers with NTChem results. Please read documentations of NTChem. They are available in /local/apl/pg/ntchem/doc at the frontend nodes.
(*18) To use CRYSTAL14, license agreement is required for each user. Once the agreement is arrivied at RCCS, you will be able to use CRYSTAL14.
(*19) References listed in this page must be cited when you publish results obtained with DIRAC.
(*20) User registration is required for ORCA. Please read this page for further details.
(*21) To use CRYSTAL17, license agreement is required for each user. Once the agreement is arrivied at RCCS, you will be able to use CRYSTAL17.
| Attachment | Size |
|---|---|
 CRYSTAL14 license agreement | 281.59 KB |
| CRYSTAL17 license agreement | 255.88 KB |