Software Resources Introduction
HPC Phase II Software Resources
Operating System
| Node Category | Operating System |
|---|
|
| Management Node | Red Hat Enterprise Linux release 8.4 (Ootpa) |
| Login Node | Ubuntu 20.04 LTS |
| CPU1 | Ubuntu 20.04 LTS |
| CPU2 | Red Hat Enterprise Linux release 8.4 (Ootpa) |
| CPU3 | Ubuntu 20.04 LTS |
| GPU1 | Ubuntu 20.04 LTS |
| GPU2 | Red Hat Enterprise Linux release 8.4 (Ootpa) |
| GPU3 | Ubuntu 20.04 LTS |
| BIGMEM | Ubuntu 20.04 LTS |
### Compilation Environment
CPU1, CPU3, Large Memory Nodes
| Compilation Tool | Version | Loading Method |
|---|
| GCC | 9.4.0 (System Default) | Direct Use |
| 13.1 | module load compilers/gcc-13.1.0 |
| Python | 3.8.4 (System Default) | Direct Use |
| ICC | 2023.1.0 | module load compilers/icc-2023.1.0 |
| CMake | 3.27.0 | module load cmake/3.27.0 |
| Java | 1.8.11 | Direct Use |
CPU2 Nodes
| Compilation Tool | Version | Loading Method |
|---|
| GCC | 8.4.1 (System Default) | Direct Use |
| 13.1 | module load compilers/gcc-13.1.0 |
| Python | 3.6.8 (System Default) | Direct Use |
| ICC | 2023.1.0 | module load compilers/icc-2023.1.0 |
| CMake | 3.27.0 | module load cmake/3.27.0 |
| Java | 1.8.11 | Direct Use |
GPU1 Nodes
| Compilation Tool | Version | Loading Method |
|---|
| GCC | 9.4.0 (System Default) | Direct Use |
| GCC 13.1 | module load compilers/gcc-13.1.0 |
| Python | 3.8.4 (System Default) | Direct Use |
| ICC | 2023.1.0 | module load compilers/icc-2023.1.0 |
| CMake | 3.27.0 | module load cmake/3.27.0 |
| CUDA | 11.3 (cuDNN 8.9.3 for CUDA 11.x) | module load cuda/11.3 |
| 11.7 (cuDNN 8.9.3 for CUDA 11.x) | module load cuda/11.7 |
| 11.8 (cuDNN 8.9.3 for CUDA 11.x) | module load cuda/11.8 |
| 12.0 (cuDNN 8.9.3 for CUDA 12.x) | module load cuda/12.0 |
| 12.2 (cuDNN 8.9.3 for CUDA 12.x) | module load cuda/12.2 |
| NVIDIA SDK | 23.7 | module load nvhpc/23.7 |
Mathematical Libraries
| Software Name | Version | Loading Method |
|---|
| FFTW | 3.3.10 | |
| Intel MKL | 2023 | module load compilers/mkl-2023.1.0 |
| NVIDIA SDK | 23.7 | module load nvhpc/23.7 |
| BLAS/SCALAPACK/LAPACK | / | |
MPI Environment
| No. | Software Name | Version | Installation Path | Loading Method |
|---|
| 1 | MPICH | 4.1.2 GCC Version | /opt/mpi/mpich-4.1.2 | module load mpi/mpich-4.1.2 |
| 2 | 4.1.2 ICC Version | /opt/mpi/mpich-4.1.2_icc-2023.1.0 | module load mpi/mpich-4.1.2_icc-2023.1.0 |
| 3 | MVAPICH | 3.0b GCC Version | /opt/mpi/mvapich-3.0b | module load mpi/mvapich-3.0b |
| 4 | 3.0b ICC Version | /opt/mpi/mvapich-3.0b_icc-2023.1.0 | module load mpi/mvapich-3.0b_icc-2023.1.0 |
| 5 | MVAPICH | 2-2.3.7-1 GCC Version | /opt/mpi/mvapich2-2.3.7-1 | module load mpi/mvapich2-2.3.7-1 |
| 6 | 2-2.3.7-1 ICC Version | /opt/mpi/mvapich2-2.3.7-1_icc-2023.1.0 | module load mpi/mvapich2-2.3.7-1_icc-2023.1.0 |
| 7 | OpenMPI | 4.1.5 GCC Version | /opt/mpi/openmpi-4.1.5 | module load mpi/openmpi-4.1.5 |
| 8 | 4.1.5 ICC Version | /opt/mpi/openmpi-4.1.5_icc-2023.1.0 | module load mpi/openmpi-4.1.5_icc-2023.1.0 |
| 9 | 4.1.5 GPU Version | /hpc2ssd/softwares/cuda/openmpi-4.1.5 | module load mpi/openmpi-4.1.5_gpu |
| 10 | Intel MPI | 2021.9 | /opt/intel/oneapi/mpi/2021.9.0 | module load intelmpi-2021.9.0 |
| 11 | NVIDIA SDK | 23.7 | /hpc2ssd/softwares/nvidia/hpc_sdk/ | module load nvhpc/23.7 |
Application Software
| No. | Software Name | Version | Installation Path | Loading Method |
|---|
| 1 | GAUSS | G16 | /hpc2ssd/softwares/GAUSS | module load |
| 2 | HDF5 | 1.14.1-2 | /hpc2ssd/softwares/HDF5-1.14.1-2 | module load |
| 3 | PnetCDF | 1.12.3 | /hpc2ssd/softwares/PnetCDF-1.12.3 | module load |
| 4 | QE | 7.2 | /hpc2ssd/softwares/QE-7.2 | module load |
| 5 | R | 4.3.1 | R-4.3.1 | module load R/4.3.1 |
| 6 | RASPA2 | | /hpc2ssd/softwares/RASPA2 | module load |
| 7 | WPS | 4.2 | /hpc2ssd/softwares/WPS-4.2 | |
| 8 | WRF | 4.2.1 | /hpc2ssd/softwares/WRF-4.2.1 | |
| 9 | Abacus | 3.3.0 | /hpc2ssd/softwares/abacus | |
| 10 | Anaconda3 | 2023 | /hpc2ssd/softwares/anaconda3 | |
| 11 | CCPEM | 20221108 | /hpc2ssd/softwares/ccpem-20221108 | |
| 12 | Cistem | 1.0.0 | /hpc2ssd/softwares/cistem-1.0.0-beta | |
| 13 | CUDA | | /hpc2ssd/softwares/cuda | |
| 14 | Dushin | | /hpc2ssd/softwares/dushin | |
| 15 | Dynamo | | /hpc2ssd/softwares/dynamo | |
| 16 | Elk | 8.5.10 | /hpc2ssd/softwares/elk-8.5.10 | |
| 17 | GAMS | 44.1 | /hpc2ssd/softwares/gams44.1_linux_x64_64_sfx | |
| 18 | GROMACS | 2023.2 | /hpc2ssd/softwares/gromacs-2023.2 | module load gromacs/2023.2 |
| 19 | Jasper | 1.9 | /hpc2ssd/softwares/jasper-1.9 | |
| 20 | LAMMPS Parallel | 3-Mar-20 | /hpc2ssd/softwares/lammps_parallel | module load lammps/2022-parallel |
| 21 | LAMMPS Serial | /hpc2ssd/softwares/lammps_serial | module load lammps/2022-serial |
| 22 | NetCDF | | /hpc2ssd/softwares/netcdf | |
| 23 | Pwtk-2.0 | | /hpc2ssd/softwares/pwtk-2.0 | |
| 24 | PyCharm | 2023.1.4 | /hpc2ssd/softwares/pycharm-community-2023.1.4 | |
| 25 | PyTorch | 2.0.1 | /hpc2ssd/softwares/pytorch-2.0.1 | |
| 26 | Relion | | /hpc2ssd/softwares/relion | |
| 27 | Scipion | | /hpc2ssd/softwares/scipion | |
| 28 | TensorFlow-GPU | | /hpc2ssd/softwares/tensorflow-gpu | |
| 29 | VASP | 6.3.2 | /hpc2ssd/softwares/vasp.6.3.2 | module load vasp/6.3.2 |
| 30 | Docker | 24.0.5 | /usr/bin/docker | |
| 31 | OpenFOAM | 11 | /opt/openfoam11 | |
Bioinformatics Software
| No. | Software Name | Loading Method | Notes |
|---|
| 1 | Aspera | source /hpc2ssd/softwares/anaconda3/bin/activate biological | Key File: /hpc2ssd/softwares/anaconda3/envs/biological/etc/asperaweb_id_dsa.openssh |
| 2 | SRA Tool Kit | module load biological/sratoolkit | |
| 3 | FastP | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 4 | FastQC | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 5 | MultiQC | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 6 | Bbmap | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 7 | Megahit | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 8 | Prodigal | module load biological/prodigal | |
| 9 | HMMER3 | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 10 | CRISPRCasFinder | module load biological/crisprcasfinder | |
| 11 | MAFFT | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 12 | Blast | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 13 | MUSCLE | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 14 | Bowtie2 | source /hpc2ssd/softwares/anaconda3/bin/activate biological | |
| 15 | pSeqSid | Direct Use | |
| 16 | MMseq | module load biological/mmseqs | |
HPC EDA Software Resources
Design Compiler, FusionCompiler, Formality, ICC2, Library Compiler, PrimeTime, Starrc, VCS, IC618, INTEGRAND EMX, Genus, Innovus, JasperGold, PVS, Quantus, Spectre, OrCad, Xcelium, Calibre, Modelsim, CFD, Mechanical, Electronics Suite, Lumerical, Agilent ADS, Agilent SystemVue, Comsol, docker jobs, pycharm, vscode, Openfoam, anaconda, pytorch, tensorflow, verilator