Okazaki Research Facilities
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Package Programs List
Compilers and Libraries
(Status on Apr. 1, 2019.)
|
Name |
Version | misc info |
|---|---|---|
| Intel Parallel Studio XE | 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* | |
| 7.3.1 | Devtoolset-7 Software Collections | |
| 6.3.1 | Devtoolset-6 Software Collections | |
| 5.3.1 | Devtoolset-4 Software Collections | |
| 4.9.2 | Devtoolset-3 Software Collections | |
| PGI Compilers and Tools | 18.1-1* | |
| 17.5-0 | ||
| 16.5-0 | ||
| CUDA | 9.1.85* | |
| 8.0.61 | ||
| Python1 | 3.4.5 | (default version for python3) |
| 2.7.5* | ||
| Open MPI | 4.0.0 | (cxx support enabled) |
| 3.1.0 | ||
| 2.1.3 |
*: default version
1: installation of Anaconda (to the homedir) is also recommended
Application Software
(May 14, 2019) 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. |
| Molcas | 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(*B) | 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 |
| 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. |
| Molden | Visualization program of molecular and structure. |
| VMD | Molecular graphics viewer |
| name | version | revision | status (install date) |
|---|---|---|---|
| ABINIT | 8.8.3 | ◎ (2018/7/10) | |
| 7.8.2 | － | ||
| ADF(*9) | 2014 | ▼ | |
| Amber | 18 | bugfix 12 | ◎ (2019/2/14)☆ |
| 18 | bugfix 11-volta | ○ (2019/2/14)☆ | |
| 18 | bugfix 1 | ○ (2018/6/4)☆ | |
| 16 | bugfix 15 | ○ (2018/7/25)☆ | |
| 16 | bugfix 10 | ○ (2017/10/01)☆ | |
| 14 | bugfix 11 | ○ (2015/7/21) | |
| 12 | bugfix 21 | ○ (2013/12/10) | |
| AutoDock | 4.2.6 | － | |
| CP2K | 6.1.0 | ○ (2018/11/22)☆‖ | |
| CRYSTAL(*C) | 14 | 1.0.4 | ◎ (2016/5/11) |
| DIRAC(*D) | 18.0 | ○ (2019/5/14) | |
| GAMESS | 2018 | Sep30 | ◎ (2018/11/9) |
| 2018 | Feb14 | ○ (2018/3/19)★ | |
| 2017 | Nov11 | ○ (2017/12/15) | |
| 2017(*11) | Apr20 | ○ (2017/10/1) | |
| Gaussian | 16 | B.01 | ◎ (2018/3/12)☆★ |
| 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 | 1.3.0 | ○ (2018/9/4)☆ | |
| 1.1.6 | ○ (2017/12/13)☆ | ||
| 1.1.5 | ○ (2017/8/4) | ||
| GROMACS | 2019.2 | ○ (2019/4/18)☆‖ | |
| 2018.6 | ◎ (2019/3/27)☆‖ | ||
| 2018.3 | ○ (2018/9/4)☆‖ | ||
| 2018.1(*14) | ○ (2018/4/17)‖ | ||
| 2016.6 | ○ (2019/2/22)☆‖ | ||
| 2016.5 | ○ (2018/4/17)☆‖ | ||
| 2016.4 | ○ (2017/10/01)☆ | ||
| 2016.3(*10) | ○ (2017/3/16)☆ | ||
| 2016.1(*10) | ○ (2017/2/2)☆ | ||
| 5.1.5(*12) | ○ (2018/4/17)☆‖ | ||
| 5.1.4 | ○ (2018/1/19)☆ | ||
| 4.5.5 | ○ (2012/6/12)☆ | ||
| GRRM(*5) | 14 | ◎ (2015/7/29) | |
| 11 | ○ (2012/9/26) | ||
| LAMMPS | 22Aug18 | ◎ (2018/11/6)☆ | |
| 16Mar18(*15) | ○ (2018/5/10)☆‖ (2018/7/4 update) |
||
| Molcas(*1) | 8.2 | ◎ (2017/10/1) | |
| Molpro(*2) | 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)☆ | |
| 2.11 | ○ (2017/10/1)☆ | ||
| NBO | 7.0 | 2 | ◎ (2019/1/23) |
| 6.0 | 18 | ◎ (2018/3/16) | |
| 6.0 | 15 | ○ (2018/2/6) | |
| NTChem(*B) | 2013.5.0 | ◎ (2015/4/20) | |
| NWChem | 6.8 | ◎ (2018/1/22) | |
| PSI4 | 1.1 | ◎ (2018/1/12) | |
| Quantum ESPRESSO | 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(*A) | ○ (2012/8/16) | ||
| SMASH | 2.2.0 | ○ (2017/5/16) | |
| TURBOMOLE(*3) | 7.3 | ◎ (2018/7/23) | |
| 7.2.1 | ○ (2017/12/12) | ||
| 7.2 | ○ (2017/8/4) | ||
| VASP(*4) | ▼ |
| name | version | revision | command name / path | install date |
|---|---|---|---|---|
| GaussView | 6.0.16 | gview6 | ◎ (2017/2/2) | |
| 5.0.9 | gview5 | ◎ (2013/3/13) | ||
| Molden | 5.7 | 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.
△: couldn't compile successfully. Investigating now.
×: impossible to install.
※: installing now.
￥: will soon be installed.
－: no plan to install (at least for now)
◆: closed
▼: unavailable
☆: GPU version available
★: compatible with NBO 6.0
‖: GCC and Intel versions available
Notices
(*1) molcas license will be expired on Jan 29, 2020. The license will be renewed every year.
(*2) molpro license will be expired on Sep 15, 2019. The license will be renewed every year.
(*3) Only non-commercial users in Japan can use this. The license will be expired in Jan, 2020. 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) Cannot install ADF due to its very expensive 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)).
(*A) 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).
(*B) 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.
(*C) To use CRYSTAL, license agreement is required for each user. Once the agreement is arrivied at RCCS, you will be able to use CRYSTAL.
(*D) References listed in this page must be cited when you publish results obtained with DIRAC.
| Attachment | Size |
|---|---|
 CRYSTAL14 license agreement | 281.59 KB |