Package Programs List
Last update: Sep 9, 2024.

Compilers and Libraries
Most packages are installed under /apl.
nameGCC

AOCC

versionnote

8.5.0*(system default package)

9.2.1

module: gcc-toolset/9 (gcc-toolset-9)10.3.1

module: gcc-toolset/10 (gcc-toolset-10)

11.2.1

module: gcc-toolset/11 (gcc-toolset-11)

12.2.1

module: gcc-toolset/12 (gcc-toolset-12)

13.1.1

module: gcc-toolset/13 (gcc-toolset-13)

4.2.0

module: aocc/4.2.0

4.1.0

module: aocc/4.1.0

4.0.0*

module: aocc/4.0.0

3.2.0

module: aocc/3.2.0

4.2.0

module: aocl/4.2.0-aocc4.2 (built with AOCC),
aocl/4.2.0-gcc13.1 (built with GCC)

4.1.0

module: aocl/4.1.0-aocc4.1 (built with AOCC),
aocl/4.1.0-gcc13.1 (built with GCC)

4.0

module: aocl/4.0-aocc4.0 (built with AOCC),
aocl/4.0-gcc11.2 (built with GCC)

3.2.0

module: aocl/3.2.0-aocc3.2 (built with AOCC),
aocl/3.2.0-gcc11.2 (built with GCC)

AOCL

3.9.18

Python [1]3.6.8*(/usr/bin/python3)

2.7.18*(/usr/bin/python2)

3.10.13 (base)
3.12.2 (gpuenv)

miniforge3 env (/apl/conda/20240305; source
conda_init.sh or conda_init.csh to load env)

3.10.9miniforge3 env (/apl/conda/20230214; source
conda_init.sh or conda_init.csh to load env)

24.3

module: nvhpc/24.3, nvhpc/24.3-byo,
nvhpc/24.3-nompi

23.9

module: nvhpc/23.9, nvhpc/23.9-byo,
nvhpc/23.9-nompi

23.5

module: nvhpc/23.5, nvhpc/23.5-byo,
nvhpc/23.5-nompi

22.11

module: nvhpc/22.11, nvhpc/22.11-byo,
nvhpc/22.11-nompi

2024.2.1, 2024.2, 2024.1.0, 2024.0.2, 2024.0,
2023.2.0, 2023.1.0, 2023.0.0, 2022.2.1, 2022.0.2

module: compiler-rt/(version)

2024.2

module: mkl/2024.2

2024.1

module: mkl/2024.1

2024.0module: mkl/2024.0

2023.2.0

module: mkl/2023.2.0

2023.1.0

module: mkl/2023.1.0

2023.0.0

module: mkl/2023.0.0

2022.2.1

module: mkl/2022.2.1

2022.0.2

module: mkl/2022.0.2

NVIDIA HPC SDKIntel oneAPI
Compiler Runtime[2]Intel MKL

nameIntel MPI

CUDA

Open MPI

HPC-X

versionnote

2021.13

module: intelmpi/2021.13

2021.12

module: intelmpi/2021.12

2021.11

module: intelmpi/2021.11

2021.10.0

module: intelmpi/2021.10.0

2021.9module: intelmpi/2021.9

2021.8module: intelmpi/2021.8

2021.7.1

module: intelmpi/2021.7.1

2021.5.1

module: intelmpi/2021.5.1

12.4 Update 1

module: cuda/12.4u1

12.2 Update 2

module: cuda/12.2u2

12.1 Update 1

module: cuda/12.1u1

12.0*

module: cuda/12.0

11.6

module: cuda/11.6

11.2

module: cuda/11.2

5.0.5

module: openmpi/5.0.5 (modules for eachcompiler available)

5.0.1

module: openmpi/5.0.1 (modules for eachcompiler available)

4.1.6

module: openmpi/4.1.6 (modules for eachcompiler available)

4.1.5

module: openmpi/4.1.5 (modules for eachcompiler available)

3.1.6

module: openmpi/3.1.6 (modules for eachcompiler available)

2.16 (Open MPI 4.1.5)

module: openmpi/4.1.5-hpcx2.16 (modules foreach compiler available)

2.13.1 (Open MPI 4.1.5)

module: openmpi/4.1.5-hpcx (modules for eachcompiler available)

2.11 (Open MPI 4.1.4)

module: openmpi/4.1.4-hpcx (modules for eachcompiler available)

3.0

module: mvapich/3.0 (modules for GCC andAOCC available)

2.3.7

module: mvapich/2.3.7 (modules for eachcompiler available)

1.10.0module: julia/1.10.0

1.8.5

module: julia/1.8.5

1.6.7 (LTS)

module: julia/1.6.7

MVAPICH

Julia

Apptainer/Singularity 1.3.1(singularity is an alias of apptainer)*: default version[1]: you can install packages to your home directory by using "pip install (package name) --user" command. Installing
miniforge might be another good choice. However, the initialization of conda environment might take long time (only upon
first time; this is due to the fundamental mechanism of lustre filesystem). If you need only a few packages, you should
install them to your home directory via "pip".
[2]: Compilers (such as ifort, ifx) are not installed in /apl. In case you need Intel compilers, please install Intel oneAPI Base
Toolkit or HPC Toolkit into your directory.

Application Software
The list of installed software is shown below. (Blacked out package names indicate that they have not yet been installed
but will be installed.) For the manual/documentations, please visit the official website. Packages are installed under /apl
directory which are accessible from both of frontend and computation nodes. See this page for detailed information aboutinstallation.

namedescription

ABINIT-MP

A software for fast Fragment-Molecular-Orbital (FMO) calculations.

AlphaFoldAI program for predictions of protein structure.

AMBER

Package of molecular simulation programs.

CENSO
CP2K

Program for evaluating structure ensembles at DFT level.
A quantum chemistry and solid state physics software package.

CREST

A program for the automated exploration of the low-energy molecular chemical space.

CRYSTAL

General-purpose programs for the study of crystalline solids.

DFTB+

Fast and efficient versatile quantum mechanical simulation software package

DIRAC(*22)

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, andtheir 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.

MolproComplete system of ab initio programs.

NAMD

Scalable molecular dynamics program.

NBO

Discovery tool for chemical insights from complex wavefunctions.

NTChem(*17)

Comprehensive new software of ab initio quantum chemistry made in Riken-RCCS from scratch.

NWChemComputational 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 andsolids

TURBOMOLE

One of the fastest programs for standard quantum chemical applications.

GaussView

Viewer for Gaussian 09 / 16.

MoldenVisualization program of molecular and structure.

VMD

Molecular graphics viewer

nameversion

install date

ABCluster

3.0○ (2023-Nov-28)

v2r4○ (2023-Feb-21)

v1r22○ (2023-Feb-21)

ABINIT-MP(not available)

ADF(*9)2.3.2

AlphaFold△ (2024-Feb-8)☆

2.3.1△ (2023-Feb-6)☆

2.2.0△ (2022-Mar-14)☆

2.1.1△ (2021-Nov-8)☆

notenameversion

install date

2.1.0

△ (X-X-X)☆

2.0.0 (2021/8/19)△ (2021-Aug-23)☆

2.0.0 (2021/7/20)△ (2021-Jul-26)☆

24-update1○ (2024-Jun-11)☆

note(AmberTools24-update2)

22-update4○ (2023-Aug-25)☆

(Ambertools23-update4)

22-update1○ (2023-Jan-X)☆

(AmberTools22-update4)

20-update13○ (2023-Jan-X)☆

(built with configure)

AutoDock

4.2.6○ (2023-Nov-24)

AutoDock-GPU

1.5.3○ (2023-Nov-24)☆

AutoDock Vina

1.2.5

○ (2023-Nov-24)

AmberCENSO

1.2.0○ (2024-May-22)

ColabFold

1.5.5○ (2023-Apr-6)

CP2K

2024.2○ (2024-Aug-22)

2023.1○ (2023-Apr-6)

9.1○ (2023-Jan-X)

CREST
CRYSTAL

DFTB+

DIRAC

GAMESS

Gaussian

3.0.1○ (2024-May-21)

23-1.0.1○ (2024-Jul-19)(precomipled binary)anmr and nmrplot.py from ENSO 2.0.2
are added manually.

(*21)

17-1.0.2○ (2023-Jan-X)

23.1○ (2023-Jul-19)☆
MPI / OpenMP

23.0○ (2023-May-8)

19.0○ (2023-Jan-27)

2023-R2(Sep30)○ (2023-Dec-7)(NBO 7.0.7 enabled)

2022-R2(Sep30)○ (2023-Jan-X)(NBO 7.0.7 enabled)

2021-R1(Jun30)○ (2023-Jan-X)(NBO 7.0.7 enabled)

16.C.02○ (2022-Mar-14)(NBO 7.0.10 enabled)

16.C.01○ (2019-Aug-2)(NBO 7.0.10 enabled)

16.B.01○ (2018-Mar-12)

09.E.01○ (2015-Dec-24)

2.1.2○ (2024-Jan-16)☆
CPU / GPU

2.0.3

○ (2023-Jan-X)☆
CPU / GPU

GENESIS2024.2○ (2024-May-16)☆
CPU / GPU

2023.5○ (2024-May-7)☆
CPU / GPU

2023.4○ (2024-Jan-26)☆
CPU / GPU

2023.2○ (2023-Aug-9)☆
CPU / GPU

2022.6○ (2023-Jul-12)☆
CPU / GPU

2022.4○ (2023-Jan-X)☆
CPU / GPUGROMACS

MPI and OpenMP versions available

nameversion

install date

2021.7○ (2023-Apr-14)☆
CPU / GPU

2021.6○ (2023-Jan-X)☆
CPU / GPU

2021.4○ (2023-Jan-X)☆
CPU / GPU23

〇 (2024-Jan-11)

note

Application is required for use.
(multinode parallel available)

GRRM
17(*5)○ (2021-Jan-27)

14○ (2015-Jul-29)
29Aug2024

Intel MPI

○ (2023-Jan-X)☆
CPU / GPU

(netcdf off)

○ (2023-Apr-18)☆
CPU / GPUIntel MPI

29Sep21 Update 3○ (2023-Apr-18)☆
CPU / GPUIntel MPI29Sep21○ (2023-Jan-X) ☆
CPU / GPU

(netcdf off)

23Jun22 Update 2

LigandMPNN

Molpro(*2)

NTChem2024.2.0△ (2024-Sep-9)2024.1.0△ (2024-Mar-11)

2023.2.0△ (2023-Oct-11)

2023.1.0△ (2023-Sep-19)

2022.3.0△ (2023-Jan-X)(HPC-X)△ (2023-May-18)(MVAPICH)

2022.2.2△ (2023-Jan-X)

2021.3.1△ (2023-May-10)

2015.1-44△ (2023-Jan-X)

3.0○ (2024-Jul-5)☆
MPI / SMP / SMP+CUDA

3.0b7○ (2024-May-23)☆
MPI / SMP / SMP+CUDA

3.0b6○ (2024-Mar-6)☆
MPI / SMP / SMP+CUDA

3.0b2○ (2023-Apr-10)☆

2.14○ (2023-Jan-X)☆
CPU / GPU

7.0.10△ (2023-Feb-14)

7.0.7△ (2023-Jan-X)

2013.13.0.0○ (2023-Apr-28)

7.2.2
NWChemlatest code on Mar 27, 2024

△ (2024-Mar-27)☆

NAMD

NBO

○ (2024-Sep-6)☆
CPU(GCC,Intel) / GPU○ (2023-Oct-16)☆
CPU(GCC,Intel) / GPU

2Aug23

LAMMPS(multinode parallel available)

7.0.2○ (2024-Mar-5)☆
CPU / GPU○ (2023-Mar-6)(GPU version only)nameversion

install datenote

6.8○ (2023-Mar-6)

for ReactionPlusOmegaFold

1.1.0

OpenMM

OpenMolcas

ORCA○ (2024-Jun-12)☆

8.1.0○ (2023-Dec-5)

23.06○ (2023-Jul-25)

22.10○ (2023-Mar-6)

21.10○ (2023-Mar-6)

5.0.4○ (2023-Mar-20)

5.0.3○ (2022-Feb-22)

4.2.1○ (2020-Jan-8)(registration required)

Parallel CONFLEX (*9)
ProteinMPNN△ (2023-Oct-26)☆
1.9.1

PSI4

○ (2023-Jan-30)

7.3○ (2024-Feb-6)☆
CPU / GPU
7.2

ReactionPlus○ (2024-Mar-5)

1.7

Quantum ESPRESSO○ (2023-Apr-11)☆
CPU / GPU

6.8

○ (2023-Jan-26)☆
CPU / GPU1.0○ (2018-Jan-22)

RFdiffusion△ (2023-Oct-26)☆

RFDiffusion AA

SIESTA

TURBOMOLE(*3)

latest code on Oct 25, 2023

latest code on Oct 25, 2023

△ (2024-Mar-27)☆

latest code on Mar 27, 2024

5.0.1

○ (2024-Jul-29)
OpenMPI / IntelMPI

Open MPI and Intel MPI versions avail

5.0.0○ (2024-May-29)
OpenMPI / IntelMPI

Open MPI and Intel MPI versions avail

4.1.5○ (2023-Jan-X)
MPI / OpenMP

7.8○ (2023-Dec-18)

7.7○ (2023-Jul-18)

7.6○ (2021-Dec-23)

MPI and OpenMP versions available(not available)

VASP(*4)
xTB

6.7.0

○ (2024/5/7)

6.5.1○ (2024/5/22)

Following GUI applications are available (X11 forwarding necessary). On Windows, you can use X11 forwarding easily withMobaXterm (WSLg, Xming, VcXsrv may also work). On mac, install and start XQuartz, and then connect via ssh with "-XY"
option.
name

GaussView

iMolproLuscus
MoldenVMD

versioncommand name / pathinstall date

6.1.1

gview6△ (2019-Oct-29)

6.0.16/apl/gaussian/16b01/gv/gview.sh△ (2017-Feb-2)

5.0.9

gview5△ (2013-Mar-13)

1.0.1
0.8.6
7.2.1

/apl/imolpro/1.0.1/bin/imolpro-*/apl/luscus/0.8.6/bin/luscus/apl/molden/7.2.1/bin/molden

1.9.4 alpha/apl/vmd/1.9.4a57/bin/vmd(2022/4/27)○ (2024-Mar-8)○ (2023-Oct-4)○ (2023-Feb-6)○ (2023-Jan-X)

nameversion

command name / pathinstall dateexec "module load xcrysden/1.6.2" and then
XCrySDen

1.6.2○ (2024-Aug-23)
xcrysden○: module available△: module not available/not necessary☆: GPU version available

Note(*2) molpro license will be expired on Sep 15, 2024. The license will be renewed every year.
(*3) Only non-commercial users in Japan can use this. The license will be expired in Jan, 2024. The license will be renewed
every year.
(*4) We cannot install. (Licensed users can install into their directories.)(*5) English guide for GRRM17 is available at https://afir.sci.hokudai.ac.jp/documents/manual/54. Japanese guide for thiscenter (for GRRM14) is also available.
(*9) We cannot install ADF and Parallel CONFLEX due to their very high license fee.
(*17) You have to cite some papers when you publish papers with NTChem results. Please readofficial page anddocumentation(japanese) of NTChem.
(*21) To use CRYSTAL, license agreement is required for each user and version. CRYSTAL17 users also need to sign a newlicense agreement to use CRYSTAL23. Once the agreement is arrived at RCCS, you will be able to use CRYSTAL23 or/andCRYSTAL17. (CRYSTAL23 license agreement) (CRYSTAL17 license agreement)(*22) References listed in this page must be cited when you publish results obtained with DIRAC.
Attachment

Size

CRYSTAL17 license agreement 255.58 KB
CRYSTAL23 license agreement 314 KB