- calcoloscientifico:userguide

Abaqus

Anonymous (anonymous@undisclosed.example.com) — 2025-03-17T12:31:38+00:00

Abaqus Before you run your batch script, you may execute newgrp G_ABAQUS Now your current working directory is /hpc/group/G_ABAQUS. Create and use your own sub-directory. Load Abaqus module module load abaqus and submit from this new shell.

Alphafold

Anonymous (anonymous@undisclosed.example.com) — 2025-02-06T18:46:02+00:00

Alphafold Alphafold Alphafold3 Alphafold3 Alphafold3 Apptainer File Image Alphafold3 Apptainer File Image: /hpc/share/containers/apptainer/alphafold/3.0.1/alphafold-3.0.1.sif Alphafold3 GPU demo mkdir -p demo/af_input cp -p /hpc/share/containers/apptainer/alphafold/3/af_input/fold_input.json demo/af_input cp -p /hpc/share/containers/apptainer/alphafold/3.0.1/slurm-alphafold-gpu-a100_40g.sh demo cd demo sbatch slurm-alphafold-gpu-a100_40g.sh

Amber

Anonymous (anonymous@undisclosed.example.com) — 2023-03-20T17:50:02+00:00

Amber Amber 20 sander Script slurm-amber-20-cpu.sh to run sander.MPI on 2 nodes (16 tasks per node): #!/bin/bash --login #SBATCH --job-name=amber20cpu #SBATCH --output=%x.o%j #SBATCH --error=%x.e%j #SBATCH --nodes=2 #SBATCH --ntasks-per-node=16 #SBATCH --time=0-01:00:00 #SBATCH --mem=16G #SBATCH --partition=cpu #SBATCH --constraint='broadwell|skylake' #SBATCH --account= shopt -q login_shell || exit 1 module load gnu8 openmpi4 module load apptainer/1.0 container='/hpc/share/appli…

Apptainer

Anonymous (anonymous@undisclosed.example.com) — 2025-01-14T12:00:39+00:00

Apptainer * Apptainer * Apptainer on GitHub Apptainer is already available on the HPC cluster. Users are encouraged to use it on their system. Install a binary package These instructions are intended for users who wish to install Apptainer on their Linux system. On a

Blender

Anonymous (anonymous@undisclosed.example.com) — 2025-04-16T15:35:18+00:00

Blender Blender Blender is a free and open-source 3D computer graphics software tool set. Interactive Job Blender Connect to the Graphical User Interface using Remote Desktop Protocol (RDP). Right click on the desktop and select "Open Terminal". Alternatively, open an X11 connection to the login machine:

Boltz2

Anonymous (anonymous@undisclosed.example.com) — 2025-12-17T20:02:17+00:00

Boltz2 * Boltz2 * Introducing Boltz-2 Boltz2 Apptainer File Image Boltz2 Apptainer File Image: /hpc/share/containers/apptainer/boltz2/1.4.0/boltz2-1.4.0.sif Boltz2 python script Download the Boltz2 script file boltz2.py and save it: import requests import json from typing import Dict, Any import os port = os.getenv('NIM_HTTP_API_PORT', '8000') print(port) SEQUENCE = "MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVID" def query_boltz2_nim( input_data: Dict[str, Any], base_u…

CAVER

Anonymous (anonymous@undisclosed.example.com) — 2024-06-06T21:25:44+00:00

CAVER CAVER CAVER is a software tool for analysis and visualization of tunnels and channels in protein structures. Tunnels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Unlike tunnels, channels lead through the protein structure and their both endings are opened to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology.

Crystal

Anonymous (anonymous@undisclosed.example.com) — 2024-04-08T16:11:28+00:00

Crystal Crystal14 Crystal14 Crystal23 Crystal23

Dalton

Anonymous (anonymous@undisclosed.example.com) — 2023-09-03T08:41:39+00:00

Dalton The kernel of the Dalton suite is the two powerful molecular electronic structure programs, Dalton and LSDalton: Dalton and LSDalton Dalton examples Dalton 2020.1 tddft_tda Job Dalton CPU Dalton 2020.1 #!/bin/bash --login #SBATCH --job-name=dalton_cpu #SBATCH --output=%x.o%j #SBATCH --error=%x.e%j #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --time=0-00:30:00 #SBATCH --mem=8G #SBATCH --partition=vrt #SBATCH --qos=vrt #SBATCH --account= shopt -q login_shell || e…

deal.II

Anonymous (anonymous@undisclosed.example.com) — 2023-12-04T08:05:30+00:00

deal.II deal.II - Open source finite element library. deal.II library deal.II library - Class and function documentation. deal.II tutorial deal.II tutorial - Tutorial programs on the use of the library. deal.II code gallery deal.II Code Gallery - Code Gallery. deal.II available versions Run the following command to view all available versions of the library:

dfnWorks

Anonymous (anonymous@undisclosed.example.com) — 2026-01-28T13:35:23+00:00

dfnWorks dfnWorks dfnWorks is a parallelized computational suite to generate three-dimensional discrete fracture networks (DFN) and simulate flow and transport. Developed at Los Alamos National Laboratory, it has been used to study flow and transport in fractured media at scales ranging from millimeters to kilometers.

FSL

Anonymous (anonymous@undisclosed.example.com) — 2026-01-28T15:14:23+00:00

FSL FSL FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. Most of the tools can be run both from the command line and as GUIs (point-and-click graphical user interfaces). Job FSL 6.0.7.19 (single node, multitasks) for CPU

Gaussian

Anonymous (anonymous@undisclosed.example.com) — 2022-06-30T10:52:57+00:00

Gaussian Gaussian Job Gaussian MPI Example script slurm-gaussian16-mpi.sh to run Gaussian 16 on 1 node using 28 cores and at most 80 GB of memory: #!/bin/bash #SBATCH --job-name=gaussian16_mpi #SBATCH --output=%x.%j.out #SBATCH --error=%x.%j.err #SBATCH --nodes=1 #SBATCH --ntasks-per-node=28 #SBATCH --mem=80G #SBATCH --time=1-00:00:00 #SBATCH --partition=cpu # # Edit next line #SBATCH --account= test -n "$SLURM_NODELIST" || exit test $SLURM_NNODES -eq 1 || exit module load gaussi…

Go

Anonymous (anonymous@undisclosed.example.com) — 2023-09-19T10:51:37+00:00

Go * Home page: The Go Programming Language * Licenza: BSD Available versions: Go 1.13.7 1.13.8 1.13.10 1.14.2 1.17.3 1.17.8 1.18.9 1.19.4 1.19.6 1.20.4 Environment modules: Go Prerequisites Module 1.13.7

Gromacs

Anonymous (anonymous@undisclosed.example.com) — 2025-08-20T16:00:12+00:00

Gromacs Several versions of Gromacs are available, check below: Gromacs 4.5.7 5.1.4 5.1.5 2016.4 2016.6 2018.6 2018.8 2019.4 2019.6 2020.7 2021.4 2021.7 2022.6 Compilation details: Gromacs Plumed Compiler MPI

Graphical User Interface

Anonymous (anonymous@undisclosed.example.com) — 2025-04-15T14:22:15+00:00

Graphical User Interface This page shows how to connect to the gui.hpc.unipr.it server using Remote Desktop Protocol (RDP). Microsoft Windows (client) Install the FortiClient VPN. Activate the VPN connection: VPN connection activated: Connect to the gui.hpc.unipr.it server:

IQmol

Anonymous (anonymous@undisclosed.example.com) — 2023-05-24T16:28:46+00:00

IQmol IQmol Qmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways). Interactive Job IQmol

Julia

Anonymous (anonymous@undisclosed.example.com) — 2025-03-18T12:07:12+00:00

Julia * Home page: The Julia Language * Licenza: MIT Available versions: Julia 1.4.0 1.10.9 Environment modules: Julia Prerequisites Module 1.4.0 julia/1.4.0 1.4.0 julia/1.4 1.10.9

Mathematica

Anonymous (anonymous@undisclosed.example.com) — 2022-11-03T10:33:16+00:00

Mathematica Mathematica serial job Execution of a Mathematica serial program Script math-vrt.m: Print[Integrate[1/(x^4 - a^4), x]]; (*Prints all Mersenne PRime numbers less than 10000*) Print[Select[Range[10000],PrimeQ[2^#-1]&]]; A = Sum[i, {i,1,100}]; B = Mean[{25, 36, 22, 16, 8, 42}]; Print[A + B]; Quit[];

MATLAB

Anonymous (anonymous@undisclosed.example.com) — 2022-06-30T10:53:00+00:00

MATLAB MATLAB programs can be submitted in a serial or parallel way in the sense you can use instructions like parfor or parfeval to obtain parallel code execution. Depending on the kind of interactivity you wish to have, you should choose what is best parallel paradigm that suits your needs.

NAMD

Anonymous (anonymous@undisclosed.example.com) — 2022-06-30T10:52:57+00:00

NAMD NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD Job NAMD on BDW Job NAMD multicore (single BDW node) Example script slurm-namd-bdw.sh to run NAMD multicore on 1 node using 16 cores and at most 32

Nextflow

Anonymous (anonymous@undisclosed.example.com) — 2025-05-30T17:53:59+00:00

Nextflow Nextflow Available versions of Nextflow: Nextflow 23.10.0 24.04.4 25.04.2 Job Nextflow Example script slurm-nextflow-chipseq.sh to run nf-core/chipseq on 1 node of the cpu partition using 4 cores and at most 8 GB of memory: #!/bin/bash --login #SBATCH --job-name=nextflow_chipseq #SBATCH --output=%x.%j.out #SBATCH --error=%x.%j.err #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --cpus-per-task=4 #SBATCH --mem=8G #SBATCH --partition=cpu #SBATCH --qos=cpu #SBATCH --…

Python

Anonymous (anonymous@undisclosed.example.com) — 2025-08-27T16:13:24+00:00

Python Versions of Python available via modules: * python/2.7.14 * python/3.6.3 * python/3.7.2 * python/3.7.12 * python/3.8.12 * python/3.9.10 * python/3.11.5 Python virtualenv Virtualenv is a tool to create isolated Python environments. Python 2.7.14 virtualenv

Q-Chem

Anonymous (anonymous@undisclosed.example.com) — 2023-08-02T21:38:12+00:00

Q-Chem Q-Chem Q-Chem is a comprehensive ab initio quantum chemistry software for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra. Job Q-Chem (single node) Example script slurm-qchem-script.sh to run Q-CHEM on 1 node of the

Quantum-Espresso

Anonymous (anonymous@undisclosed.example.com) — 2024-06-14T07:02:42+00:00

Quantum-Espresso Quantum-Espresso Quantum-Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. Job Quantum-Espresso (single node)

R

Anonymous (anonymous@undisclosed.example.com) — 2023-07-05T07:50:03+00:00

R * Home page: The R Project for Statistical Computing * Licenza: GPL Several versions of R are available: R 3.4.4 3.5.2 3.5.3 3.6.3 4.0.5 4.1.2 Compilation details: R Compiler BLAS 3.4.4 GNU 5.4.0 OpenBLAS 0.2.20 3.5.2 GNU 5.4.0 OpenBLAS 0.2.20

Rust

Anonymous (anonymous@undisclosed.example.com) — 2022-06-30T10:53:43+00:00

Rust * Home page: Rust Programming Language * Licenza: MIT/Apache 2 Available versions: Rust 1.42.0 Environment modules: Rust Prerequisites Module 1.42.0 rust/1.42.0 1.42.0 rust/1.42 1.42.0

Scala

Anonymous (anonymous@undisclosed.example.com) — 2022-06-30T10:53:43+00:00

Scala * Home page: Scala Programming Language * Licenza: BSD Available versions: scala 2.13.3 Environment modules: scala Prerequisites Module 2.13.3 scala/2.13.3 2.13.3 scala/2.13 2.13.3

Schrodinger

Anonymous (anonymous@undisclosed.example.com) — 2024-09-02T16:41:19+00:00

Schrodinger SCHRODINGER_TMPDIRschrodinger Job Desmond GPU Example script desmond-md-gpu.sh to launch Desmond multisim on 1 node, 1 core, 1 GPU: #!/bin/bash --login #SBATCH --job-name=desmond_md_gpu #SBATCH --output=%x.o%j #SBATCH --error=%x.e%j #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --gres=gpu:1 #SBATCH --time=0-24:00:00 #SBATCH --mem=10G #SBATCH --partition=gpu #SBATCH --qos=gpu # # Charge resources to account #SBATCH --account= shopt -q login_shell || exit 1 test -…

Singularity

Anonymous (anonymous@undisclosed.example.com) — 2023-02-20T17:37:49+00:00

Singularity Singularity has been replaced by Apptainer. outdated CityChrone CityChrone Project CityChrone from Rocky 8.5 docker Singularity Definition File: BootStrap: docker From: rockylinux:8.5 %environment export PATH=/miniconda3/bin:$PATH %runscript exec vcontact "$@" %post dnf -y update dnf -y install scl-utils dnf -y install gcc-toolset-9 scl enable gcc-toolset-9 bash dnf -y install git cmake3 zlib-devel wget # Install miniconda wget https://repo.continuum.io/miniconda/Miniconda…

SRA Toolkit

Anonymous (anonymous@undisclosed.example.com) — 2023-11-05T17:19:00+00:00

SRA Toolkit SRA Toolkit Job SRA Toolkit Example script slurm-sratoolkit.sh to run fastq-dump on 1 node of the cpu partition using 2 cores and at most 4 GB of memory: #!/bin/bash --login #SBATCH --job-name=sratoolkit #SBATCH --output=%x.o%j #SBATCH --error=%x.e%j #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --cpus-per-task=2 #SBATCH --mem=4G #SBATCH --partition=cpu #SBATCH --qos=cpu #SBATCH --time=0-01:00:00 ##SBATCH --account= shopt -q login_shell || exit 1 module load s…

SSHFS

Anonymous (anonymous@undisclosed.example.com) — 2023-10-06T15:28:12+00:00

SSHFS SSHFS (SSH Filesystem) is a filesystem client to mount and interact with directories and files located on a remote server or workstation over a normal ssh connection. The client interacts with the remote file system via the SSH File Transfer Protocol (SFTP), a network protocol providing file access, file transfer, and file management functionality over any reliable data stream that was designed as an extension of the Secure Shell protocol (SSH) version 2.0.

Accesso

Anonymous (anonymous@undisclosed.example.com) — 2017-05-10T05:01:55+00:00

Accesso Per poter accedere alle risorse occorre essere inseriti nel DataBase LDAP del servizio HPC. Le richieste di accesso o in generale di assistenza vanno inviate a es_calcolo@unipr.it Una volta abilitati l'accesso avviene via SSH sull'host di login (login.hpc.unipr.it oppure login.pr.infn.it) utilizzando come username .

XCrySDen

Anonymous (anonymous@undisclosed.example.com) — 2025-04-15T21:08:54+00:00

XCrySDen XCrySDen XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It runs on GNU/Linux. Interactive Job XCrySDen