Package Programs List

Last update: Sep 9, 2024.

Compilers and Libraries

Most packages are installed under /apl.

nameversionnote
GCC8.5.0*(system default package)
9.2.1module: gcc-toolset/9 (gcc-toolset-9)
10.3.1module: gcc-toolset/10 (gcc-toolset-10)
11.2.1module: gcc-toolset/11 (gcc-toolset-11)
12.2.1module: gcc-toolset/12 (gcc-toolset-12)
13.1.1module: gcc-toolset/13 (gcc-toolset-13)
AOCC4.2.0module: aocc/4.2.0
4.1.0module: aocc/4.1.0
4.0.0*module: aocc/4.0.0
3.2.0module: aocc/3.2.0
AOCL4.2.0module: aocl/4.2.0-aocc4.2 (built with AOCC), aocl/4.2.0-gcc13.1 (built with GCC)
4.1.0module: aocl/4.1.0-aocc4.1 (built with AOCC), aocl/4.1.0-gcc13.1 (built with GCC)
4.0module: aocl/4.0-aocc4.0 (built with AOCC), aocl/4.0-gcc11.2 (built with GCC)
3.2.0module: aocl/3.2.0-aocc3.2 (built with AOCC), aocl/3.2.0-gcc11.2 (built with GCC)
Python [1]3.9.18 
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)
NVIDIA HPC SDK24.3module: nvhpc/24.3, nvhpc/24.3-byo, nvhpc/24.3-nompi
23.9module: nvhpc/23.9, nvhpc/23.9-byo, nvhpc/23.9-nompi
23.5module: nvhpc/23.5, nvhpc/23.5-byo, nvhpc/23.5-nompi
22.11module: nvhpc/22.11, nvhpc/22.11-byo, nvhpc/22.11-nompi
Intel oneAPI Compiler Runtime [2]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, 2022.0.2module: compiler-rt/(version)
Intel MKL2024.2module: mkl/2024.2
2024.1module: mkl/2024.1
2024.0module: mkl/2024.0
2023.2.0module: mkl/2023.2.0
2023.1.0module: mkl/2023.1.0
2023.0.0module: mkl/2023.0.0
2022.2.1module: mkl/2022.2.1
2022.0.2module: mkl/2022.0.2
Intel MPI2021.13module: intelmpi/2021.13
2021.12module: intelmpi/2021.12
2021.11module: intelmpi/2021.11
2021.10.0module: intelmpi/2021.10.0
2021.9module: intelmpi/2021.9
2021.8module: intelmpi/2021.8
2021.7.1module: intelmpi/2021.7.1
2021.5.1module: intelmpi/2021.5.1
CUDA12.4 Update 1module: cuda/12.4u1
12.2 Update 2module: cuda/12.2u2
12.1 Update 1module: cuda/12.1u1
12.0*module: cuda/12.0
11.6module: cuda/11.6
11.2module: cuda/11.2
Open MPI5.0.5module: openmpi/5.0.5 (modules for each compiler available)
5.0.1module: openmpi/5.0.1 (modules for each compiler available)
4.1.6module: openmpi/4.1.6 (modules for each compiler available)
4.1.5module: openmpi/4.1.5 (modules for each compiler available)
3.1.6module: openmpi/3.1.6 (modules for each compiler available)
HPC-X2.16 (Open MPI 4.1.5)module: openmpi/4.1.5-hpcx2.16 (modules for each compiler available)
2.13.1 (Open MPI 4.1.5)module: openmpi/4.1.5-hpcx (modules for each compiler available)
2.11 (Open MPI 4.1.4)module: openmpi/4.1.4-hpcx (modules for each compiler available)
MVAPICH3.0module: mvapich/3.0 (modules for GCC and AOCC available)
2.3.7module: mvapich/2.3.7 (modules for each compiler available)
Julia1.10.0module: julia/1.10.0
1.8.5module: julia/1.8.5
1.6.7 (LTS)module: julia/1.6.7
Apptainer/Singularity1.3.1(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 about installation.

namedescription
ABINIT-MPA software for fast Fragment-Molecular-Orbital (FMO) calculations.
AlphaFoldAI program for predictions of protein structure.
AMBERPackage of molecular simulation programs.
CENSOProgram for evaluating structure ensembles at DFT level. 
CP2KA quantum chemistry and solid state physics software package.
CRESTA program for the automated exploration of the low-energy molecular chemical space.
CRYSTALGeneral-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).
GAMESSGeneral atomic and molecular electronic structure system.
GaussianAb initio molecular orbital calculations.
GENESISMolecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes.
GROMACSFast, Free and Flexible MD
GRRMAutomated Exploration of Reaction Pathways.
LAMMPSLarge-scale Atomic/Molecular Massively Parallel Simulator.
OpenMolcasQuantum chemistry software.
MolproComplete system of ab initio programs.
NAMDScalable molecular dynamics program.
NBODiscovery 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
ORCAAn ab initio quantum chemistry program package
PSI4Open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.
Quantum ESPRESSOIntegrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
Reaction PlusProgram to obtain the transition state and reaction path along the user’s expected reaction mechanism.
SIESTAEfficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
TURBOMOLEOne of the fastest programs for standard quantum chemical applications.
 
GaussViewViewer for Gaussian 09 / 16.
MoldenVisualization program of molecular and structure.
VMDMolecular graphics viewer

 

nameversioninstall datenote
ABCluster3.0○ (2023-Nov-28) 
ABINIT-MPv2r4○ (2023-Feb-21) 
v1r22○ (2023-Feb-21) 
ADF(*9) (not available) 
AlphaFold2.3.2△ (2024-Feb-8) 
2.3.1△ (2023-Feb-6) 
2.2.0△ (2022-Mar-14) 
2.1.1△ (2021-Nov-8) 
2.1.0△ (X-X-X) 
2.0.0 (2021/8/19)△ (2021-Aug-23) 
2.0.0 (2021/7/20)△ (2021-Jul-26) 
Amber24-update1○ (2024-Jun-11)(AmberTools24-update2)
22-update4○ (2023-Aug-25)(Ambertools23-update4)
22-update1○ (2023-Jan-X)(AmberTools22-update4)
20-update13○ (2023-Jan-X)(built with configure)
AutoDock4.2.6○ (2023-Nov-24) 
AutoDock-GPU1.5.3○ (2023-Nov-24) 
AutoDock Vina1.2.5○ (2023-Nov-24) 
CENSO1.2.0○ (2024-May-22)(precomipled binary)
anmr and nmrplot.py from ENSO 2.0.2
are added manually.
ColabFold1.5.5○ (2023-Apr-6) 

CP2K

2024.2

○ (2024-Aug-22)

 
2023.1

○ (2023-Apr-6)

 
9.1

○ (2023-Jan-X)

 
CREST3.0.1○ (2024-May-21) 
CRYSTAL23-1.0.1○ (2024-Jul-19)(*21)
17-1.0.2○ (2023-Jan-X)
DFTB+23.1○ (2023-Jul-19)
MPI / OpenMP
MPI and OpenMP versions available
DIRAC23.0○ (2023-May-8) 
19.0○ (2023-Jan-27) 
GAMESS2023-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)
Gaussian16.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) 
GENESIS2.1.2○ (2024-Jan-16)
CPU / GPU
 
2.0.3○  (2023-Jan-X)
CPU / GPU
 
GROMACS2024.2○ (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 / GPU
 
2021.7○ (2023-Apr-14)
CPU / GPU
 
2021.6○ (2023-Jan-X)
CPU / GPU
 
2021.4○ (2023-Jan-X)
CPU / GPU
 
GRRM23〇 (2024-Jan-11)

Application is required for use.

(multinode parallel available)

17(*5)(2021-Jan-27)(multinode parallel available)
14○ (2015-Jul-29) 
LAMMPS29Aug2024○ (2024-Sep-6)
CPU(GCC,Intel) / GPU
 
2Aug23○ (2023-Oct-16)
CPU(GCC,Intel) / GPU
Intel MPI
23Jun22 Update 2○ (2023-Jan-X)
CPU / GPU
(netcdf off)
○ (2023-Apr-18)
CPU / GPU
Intel MPI
29Sep21 Update 3○ (2023-Apr-18)
CPU / GPU
Intel MPI
29Sep21○ (2023-Jan-X)
CPU / GPU
(netcdf off)
LigandMPNN △ (2024-Mar-27)latest code on Mar 27, 2024
Molpro(*2)2024.2.0△ (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) 
NAMD3.0○ (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)(GPU version only)
2.14○ (2023-Jan-X)
CPU / GPU
 
NBO7.0.10△ (2023-Feb-14) 
7.0.7△ (2023-Jan-X) 
NTChem2013.13.0.0○ (2023-Apr-28) 
NWChem7.2.2○ (2024-Mar-5)
CPU / GPU
 
7.0.2○ (2023-Mar-6) 
6.8○ (2023-Mar-6)for ReactionPlus
OmegaFold1.1.0○ (2024-Jun-12) 
OpenMM8.1.0○ (2023-Dec-5) 
OpenMolcas23.06○ (2023-Jul-25) 
22.10○ (2023-Mar-6) 
21.10○ (2023-Mar-6) 
ORCA5.0.4○ (2023-Mar-20)(registration required)
5.0.3○ (2022-Feb-22)
4.2.1○ (2020-Jan-8)
Parallel CONFLEX(*9)   
ProteinMPNN △ (2023-Oct-26)latest code on Oct 25, 2023
PSI41.9.1○ (2024-Mar-5) 
1.7○ (2023-Jan-30) 
Quantum ESPRESSO7.3○ (2024-Feb-6)
CPU / GPU
 
7.2○ (2023-Apr-11)
CPU / GPU
 
6.8○ (2023-Jan-26)
CPU / GPU
 
ReactionPlus1.0○ (2018-Jan-22) 
RFdiffusion △ (2023-Oct-26)latest code on Oct 25, 2023
RFDiffusion AA △ (2024-Mar-27)latest code on Mar 27, 2024
SIESTA5.0.1○ (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
MPI and OpenMP versions available
TURBOMOLE(*3)7.8○ (2023-Dec-18) 
7.7○ (2023-Jul-18) 
7.6○ (2021-Dec-23) 
VASP(*4) (not available) 
xTB6.7.0○ (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 with MobaXterm (WSLg, Xming, VcXsrv may also work). On mac, install and start XQuartz, and then connect via ssh with "-XY" option.

nameversioncommand name / pathinstall date
GaussView6.1.1gview6△ (2019-Oct-29)
6.0.16/apl/gaussian/16b01/gv/gview.sh△ (2017-Feb-2)
5.0.9gview5△ (2013-Mar-13)
iMolpro1.0.1/apl/imolpro/1.0.1/bin/imolpro-*○ (2024-Mar-8)
Luscus0.8.6/apl/luscus/0.8.6/bin/luscus○ (2023-Oct-4)
Molden7.2.1/apl/molden/7.2.1/bin/molden○ (2023-Feb-6)
VMD1.9.4 alpha
(2022/4/27)
/apl/vmd/1.9.4a57/bin/vmd○ (2023-Jan-X)
XCrySDen1.6.2

exec "module load xcrysden/1.6.2" and then

xcrysden

○ (2024-Aug-23)

○: 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 this center (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 read official page and documentation(japanese) of NTChem.
(*21) To use CRYSTAL, license agreement is required for each user and version. CRYSTAL17 users also need to sign a new license agreement to use CRYSTAL23. Once the agreement is arrived at RCCS, you will be able to use CRYSTAL23 or/and CRYSTAL17. (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