https://docs.hpc.udel.edu/ Tue, 14 Apr 2026 20:26:09 +0000 FeedCreator 1.8 https://docs.hpc.udel.edu/_media/wiki/dokuwiki.svg https://docs.hpc.udel.edu/ https://docs.hpc.udel.edu/technical/recipes/cryosparc Guide to using CryoSPARC on DARWIN CryoSPARC is an advanced software platform designed for cryo-electron microscopy (cryo-EM), playing a crucial role in research and drug discovery processes. This document provides the user manual for CryoSPARC v4.3.1, which has been installed on DARWIN. anonymous@undisclosed.example.com (Anonymous) Fri, 08 Nov 2024 18:49:41 +0000 https://docs.hpc.udel.edu/technical/recipes/deepmd DeepMD Python Virtual Environment This page documents the creation of a Python virtual environment (virtualenv) containing the DeepMD software on the Caviness HPC system. It assumes that the user is adding the software to the workgroup storage. Prepare Workgroup Directory anonymous@undisclosed.example.com (Anonymous) Sun, 18 Aug 2024 15:30:10 +0000 https://docs.hpc.udel.edu/technical/recipes/emcee-in-virtualenv Python Virtualenv: emcee and pyKLIP Some portions of this recipe are specific to the IT-RCI HPC clusters (VALET-based environment setup) but otherwise should work on any system. Preparations Choose a directory in which to install the one (or more) virtual environments (virtualenvs). The string anonymous@undisclosed.example.com (Anonymous) Thu, 25 Feb 2021 04:45:42 +0000 https://docs.hpc.udel.edu/technical/recipes/gcc-openacc Building GCC 12.2 with OpenACC Offload The GNU compiler suite includes an implementation of the OpenACC standard. Offload is supported to AMD and NVIDIA GPU devices (as well as single-thread host CPU fallback). The GNU OpenACC implementation is currently still a work in progress and is very likely not the most efficient OpenACC runtime for your code. The NVIDIA HPC SDK (known as Portland Group compilers before they were purchased by NVIDIA) seems to generally be considered the most feature-c… anonymous@undisclosed.example.com (Anonymous) Wed, 23 Oct 2024 20:18:19 +0000 https://docs.hpc.udel.edu/technical/recipes/git-cmake-valet-package Managing multiple versions of revision-controlled repositories Revision-controlled source code retains a historical record of the changes that a project has gone through. Milestones along this path typically represent distinct releases of the software (a.k.a. versions). Git has become an extremely popular revision-control system, partly because its embedding of all history in the local copy of the repository produces less round-trip access with the canonical repository: once a local reposit… anonymous@undisclosed.example.com (Anonymous) Thu, 18 Nov 2021 22:58:36 +0000 https://docs.hpc.udel.edu/technical/recipes/gnnunlock Installing GNNUnlock on Caviness The GNNUnlock Python code (available on GitHub) makes use of the GraphSaint Python code (available on GitHub) which makes use of TensorFlow and its underlying dependencies (like numpy, scipy). GNNUnlock is pure Python code (with two Perl helpers) but GraphSAINT includes compiled components. The recipe is thus: anonymous@undisclosed.example.com (Anonymous) Fri, 05 Jul 2024 15:15:17 +0000 https://docs.hpc.udel.edu/technical/recipes/gromacs-plumed Building Gromacs-Plumed on Caviness/DARWIN The build procedure outlined herein uses Open MPI on top of the Intel compiler suite. Directory Preparation To begin, choose a directory in which the Gromacs_Plumed version(s) will be built and installed. To build in your home directory, for example: anonymous@undisclosed.example.com (Anonymous) Sun, 12 May 2024 19:03:18 +0000 https://docs.hpc.udel.edu/technical/recipes/jupyter-notebook Jupyter Notebook Python Virtual Environment The following steps will walk you through setting up an Anaconda virtual environment with Python 3 and Jupyter Notebook. It will also cover the steps of requesting a compute note to run a Jupyter Notebook session on Caviness. Lastly, it will explain how to set up SSH connections to be able to connect to the Jupyter Notebook session running on a compute node. This setup will be done in the anonymous@undisclosed.example.com (Anonymous) Tue, 04 Feb 2025 14:48:14 +0000 https://docs.hpc.udel.edu/technical/recipes/keras-in-virtualenv Keras Python Virtual Environment This page documents the creation of a Python virtual environment (virtualenv) containing the Keras deep-learning suite on the Caviness HPC system. It assumes that the user is adding the software to the workgroup storage. anonymous@undisclosed.example.com (Anonymous) Fri, 06 Aug 2021 17:00:30 +0000 https://docs.hpc.udel.edu/technical/recipes/lammps Installing and managing LAMMPS on Caviness/DARWIN IT-RCI does its best to maintain a variety of software packages for all cluster users. Most of these packages tend to be software libraries and tools that can be extended by users. Software having optional features or targeted optimizations would be impossible for IT-RCI to maintain to meet the specifications of every user over the lifetime of a cluster. anonymous@undisclosed.example.com (Anonymous) Tue, 04 Nov 2025 16:49:29 +0000 https://docs.hpc.udel.edu/technical/recipes/ls-dyna LS-DYNA: Installation and Usage on Caviness/DARWIN LS-DYNA is an explicit dynamics solver that simulates the extreme materials deformation response of structures to periods of severe loading. It is a commercial product, so prior to using it on an IT RCI cluster a license must be purchased. A floating (network-based) license is required for use of LS-DYNA on clusters; the user must coordinate with his/her IT support staff to have a license server present on the anonymous@undisclosed.example.com (Anonymous) Fri, 07 Jun 2024 16:51:58 +0000 https://docs.hpc.udel.edu/technical/recipes/mcfost Building MCFOST on Caviness Two distinct use cases are described in this document. The first represents a build of the MCFOST program alone. The result of this scheme is the mcfost executable for stand-alone usage. The second integrates the MCFOST program into a Python virtual environment (virtualenv). In this scheme, the anonymous@undisclosed.example.com (Anonymous) Sat, 25 Mar 2023 03:03:47 +0000 https://docs.hpc.udel.edu/technical/recipes/mpi4py-in-virtualenv Python Virtual Environments with mpi4py Most conda channels include copies of the mpi4py module to satisfy dependencies of MPI-parallelized packages. But the mpi4py Python code must be built on top of a native MPI library (like MPICH, Open MPI, Intel anonymous@undisclosed.example.com (Anonymous) Fri, 31 Jan 2025 20:29:52 +0000 https://docs.hpc.udel.edu/technical/recipes/openmm OpenMM Python Virtual Environment This page documents the creation of a Python virtual environment (virtualenv) containing the OpenMM software on the Caviness HPC system. It assumes that the user is adding the software to the workgroup storage. Prepare Workgroup Directory anonymous@undisclosed.example.com (Anonymous) Mon, 29 Jul 2024 18:50:24 +0000 https://docs.hpc.udel.edu/technical/recipes/pyqt5-in-virtualenv Building PyQt5 in a Python Virtual Environment By its construction, the PyQt5 library contains very little native Python code and consists primarily of compiled shared libraries that expose C++ Qt5 APIs via Python interfaces. Any pre-built binary copy of PyQt5 (e.g. a wheel) thus has quite a few dependencies that PyPI cannot track: what Qt5, libc, libxml, et al. libraries were used to build that wheel. Users of our clusters (built on CentOS/RedHat that tend to use older releases at the anonymous@undisclosed.example.com (Anonymous) Mon, 06 Jan 2020 15:52:23 +0000 https://docs.hpc.udel.edu/technical/recipes/quantum-espresso Building Quantum Espresso on Caviness/DARWIN The build procedure outlined herein uses Open MPI on top of the Intel compiler suite. Directory Preparation To begin, choose a directory in which the Quantum Espresso version(s) will be built and installed. To build in your home directory, for example: anonymous@undisclosed.example.com (Anonymous) Sun, 12 May 2024 15:05:58 +0000 https://docs.hpc.udel.edu/technical/recipes/r-in-rlibs Adding your own library of R modules (packages) in R_LIBS The following instructions were adapted from installing personal/program specific R libraries and extensions on Caviness. List of packages requested to be installed * rlang - needed to install an updated version for other requested packages * Rcpp - needed to install an updated version for other requested packages anonymous@undisclosed.example.com (Anonymous) Sat, 05 Sep 2020 16:51:23 +0000 https://docs.hpc.udel.edu/technical/recipes/software-managment Software Management This document offers an introduction to the mechanisms — organizational and procedural — used by IT RCI staff to build and manage the software made available to users on the HPC systems: Organizational It is most often the case that you do not use a single version of a piece of software. Bug fixes and feature additions drive change in software over time, leading to anonymous@undisclosed.example.com (Anonymous) Thu, 04 Jan 2024 21:48:39 +0000 https://docs.hpc.udel.edu/technical/recipes/telemac Building and using TELEMAC-MASCARET with VALET integration TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having been used in the context of many studies throughout the world, it has become one of the major standards in its field. anonymous@undisclosed.example.com (Anonymous) Sun, 11 Apr 2021 14:29:27 +0000 https://docs.hpc.udel.edu/technical/recipes/tensorflow-in-virtualenv TensorFlow Python Virtual Environment This page documents the creation of a Python virtual environment (virtualenv) containing the TensorFlow software for machine learning on the Caviness HPC system. It assumes that the user is adding the software to the workgroup storage. anonymous@undisclosed.example.com (Anonymous) Thu, 06 Nov 2025 20:30:10 +0000 https://docs.hpc.udel.edu/technical/recipes/tensorflow-rocm TensorFlow using AMD GPUs Complementing the NVIDIA T4 and V100 GPU nodes in the DARWIN cluster are nodes with an AMD Mi50 and an AMD Mi100 GPU coprocessor, respectively. The AMD GPU device and software stack are far newer than NVIDIA's CUDA stack: support for them is evolving. anonymous@undisclosed.example.com (Anonymous) Thu, 07 Jul 2022 16:58:14 +0000 https://docs.hpc.udel.edu/technical/recipes/vasp-6-darwin Building VASP 6 on Caviness/DARWIN Over the years the VASP build system has changed significantly. In version 6, the use of the makefile.include to encapsulate machine-specific options has improved the portability and reproducibility of the build procedures. anonymous@undisclosed.example.com (Anonymous) Tue, 16 Feb 2021 15:00:20 +0000 https://docs.hpc.udel.edu/technical/recipes/vasp-wannier Building VASP with Wannier90 Support The VASP electronic structure code can be extended with the Wannier90 library. This document outlines a procedure for building VASP 6.3.2 + Wannier90 3.1.0 and integrating the product with the VALET package management system. anonymous@undisclosed.example.com (Anonymous) Tue, 14 Mar 2023 19:17:36 +0000 https://docs.hpc.udel.edu/technical/recipes/visit-remote-host Using Caviness or DARWIN as a Remote VisIt 3.2.x Host The VisIt data visualization software can be used to post-process and interact with myriad kinds of data. One useful feature is the software's ability to run a local graphical user interface on the user's laptop or desktop which connects to data-access and computational engines running on another host. When that other host is a cluster anonymous@undisclosed.example.com (Anonymous) Fri, 28 Jan 2022 17:03:16 +0000 https://docs.hpc.udel.edu/technical/recipes/vnc-usage Using VNC for X11 Applications The X11 graphics standard has been around for a long time. Originally, an X11 program would be started with $DISPLAY pointing directly to an X11 display on another computer on the network: the X11 traffic traversed the network unencrypted and unfiltered. Eventually this insecure method was augmented by SSH tunneling of the X11 traffic: with a local X11 server, the anonymous@undisclosed.example.com (Anonymous) Wed, 13 Apr 2022 21:30:44 +0000