Applications

7-zip

  1. Installing 7-zip on CentOS-7 and Rocky Linux 8

ANSYS

  1. Fixing can’t load screen14 issues for ANSYS 2020-R1
  2. Licensing error while opening ANSYS Fluent Meshing
  3. Software Rendering Mode for Fluent Launcher
  4. Running ANSYS Workbench with Mesa OpenGL
  5. Failover feature “HFSS SBR+Solve” is not available. Request name hfssbr_solve does not exist in the licensing pool.
  6. Updating ANSYS 2023R2 License Server Information for Linux Client using the command line
  7. Options for ANSYS Batch Mode

ANTs

  1. Compiling ANTs with GNU-6.5

ABAQUS

  1. Supported Platforms for ABAQUS
  2. Starting up and Shutting down the ABAQUS License Server
  3. Editing ABAQUS FlexLM License File to control license usage
  4. Using the ABAQUS GUI to upgrade ABAQUS script
  5. Abaqus Required TCP/IP Ports
  6. ABAQUS Command-line Parameters
  7. Topology optimization using TOSCA for ABAQUS in HPC
  8. Issues when launching ABAQUS/CAE
  9. Changing License Server on ABAQUS Clients
  10. Configuring ABAQUS Linux Client for New License Server | Step-by-Step

Clustal Omega

  1. Compiling Clustal Omega 1.24 on CentOS 7

CP2K

  1. Installing CP2K with Nvidia HPCX on Rocky Linux 8.5
  2. /usr/bin/ld: cannot find -liberty on Rocky Linux 8
  3. Errors with sirius-7.5.2 packages during installation

CPMD

  1. Compiling CPMD-3.17.1 with intel-13.0.1.117 and OpenMPI-1.8.3
  2. Compiling CPMD-3.17.1 with Intel-13.0.1.117 and iMPI-14.0.2

DCM2niix

  1. Compiling dcm2niix on CentOS 7

FastX2

  1. “The command gnome-session existed with signal 15” on CentOS 7 for FastX2

FreeSurfer

  1. Setting up FreeSurfer 7.2.0 for CentOS-7

GAMESS

  1. Compiling GAMESS-v2020.2 with Intel MPI
  2. Building the GAMESS with Intel® Compilers, Intel® MKL and OpenMPI on Linux

Gaussian

  1. “Command not found” Errors encountered in Gaussian G16
  2. G16NBO is currently configured with only 100000000 words Errors
  3. Setting up NBO-7 with Gaussian-16a
  4. Linux Binary Gaussian 09 Installation Instructions
  5. Gaussian Error – $’\r’: command not found

Gold Accounting System

  1. Starting Open-Source Gold Accounting System Services

GROMACS

  1. Gromacs Error – log: Protocol “https” not supported or disabled in libcurl
  2. Gromacs-2020.6 and Plumed-2.7.2 with Intel-2019
  3. Compiling Gromacs-2019.3 with Intel 2018 MKL and AVX-512
  4. Compiling Gromacs-2019.3 with Intel MKL and CUDA
  5. Compiling Gromacs-2019.3 with Intel 2018 and MKL
  6. Testing compatibility of Gromacs with CUDA Drivers
  7. Compiling and Installing Gromacs 4.6.2 with OpenMPI and Intel on CentOS 6
  8. Regression Test Errors during Gromacs Compilation
  9. Installing Gromacs 4.0.7 on CentOS 5
  10. Compiling Gromacs 5.0.4 on CentOS 6

g2o

  1. Compiling g2o with Eigen-3.3.9 with GNU-6.5

HDF5

  1. Compiling Parallel HDF5-1.12.0 with OpenMPI and GCC6
  2. Compiling HDF5-1.8.17 with Intel-15.0.6 and Intel-MPI-5.0.6

Julia Programming Language

  1. Running Parallel Run with Julia-1.5.3
  2. Installing Julia Programming Language on CentOS 7
  3. Compiling MPI.jl with Intel MPI
  4. Installing Julia-1.8.4 and ITensor

LAMMPS (RHEL 6/7/8)

  1. Error: Too many elements extracted from the MEAM Library on LAMMPS
  2. No MEAM parameter file in pair coefficients Errors in LAMMPS
  3. voro++.hh: No such file or directory during compilation of lammps with voronoi
  4. Compiling LAMMPS-15Jun20 with GNU 6 and OpenMPI 3
  5. Compile LATTE package for LAMMPS using Intel Compilers
  6. LAMMPS Tools and Packmol with Intel Fortran
  7. Compiling LAMMPS-14May16 with Intel-15.0.6 and Intel-MPI-5.0.3
  8. Compiling LAMMPS-7Dec2015 with OpenMPI and GNU
  9. Compiling USER-GFMD to LAMMPS-10Mar21 with OpenMPI and GNU
  10. Building LAMMPS using CMAKE with OpenMPI on Rocky Linux 8

Leptonica

  1. Compiling Leptonica-1.79 on CentOS 7

LIGGHTS

  1. Compiling LIGGGHTS with OpenMPI

MATLAB

  1. Managing MATLAB Users using MLM options for FlexLM
  2. Increasing JavaMemHeapMax for MATLAB on CentOS
  3. Testing for license checkout for MATLAB_Distrib_Comp_Engine

NWChem

  1. Compiling with NWChem-6.8 with Intel MPI 2018u3
  2. Compiling with NWChem-6.6 with Intel MPI-5.0.3
  3. Installing NWChem 6 with OpenMPI, Intel Compilers and Intel MKL on CentOS 5
  4. Installing NWChem 5 with OpenMPI, Intel Compilers and MKL and CentOS 5.x

Octopus

  1. Basic Configuration of Octopus 4.1.2 with OpenMPI on CentOS 6
  2. Basic Configuration of Octopus 5.0.0 with OpenMPI on CentOS 6

OpenFOAM

  1. Compiling OpenFOAM-9 with Third-Party-9 with Intel MPI on CentOS 7
  2. Compiling OpenFOAM-7 with Third-Party-7 with Intel MPI on CentOS 7
  3. Compiling OpenFOAM-5.0 with Intel-MPI

ORCA

  1. Installing ORCA-5.0.4 on Rocky Linux 8 with OpenMPI

Open-Source on CentOS 7

  1. Compiling STAR 2.7 with Intel Compiler 2018 on CentOS 7
  2. Compile gdal-2.4.3 on CentOS 7
  3. Compiling BoltzTraP-1.2.5 with GNU
  4. Compile StringTie on CentOS 7.6
  5. Installing SAMtools on CentOS 7
  6. Compiling tesseract-5.0 on CentOS 7
  7. Installing SPECFEM3d with GNU and OpenMPI
  8. Installing SCons-3.1.2 with Intel Python Distribution
  9. No rule to make target /usr/include/sgidefs.h, needed by `surf.o’
  10. Compiling airss-0.9.1 with GNU
  11. Compiling KALDI with OpenMPI and MKL
  12. Compiling flac-1.3.3 with GNU 6.5

Open-Source on CentOS 5/6

  1. Compiling adaptive Poisson-Boltzmann Solver (APBS) on CentOS 5
  2. Compiling AMBER 10 with Intel XE Compiler and Intel MKL 10
  3. Installing ALPS 2.0 from source on CentOS 5
  4. Compiling and Installing GAP System for Computational Discrete Algebra
  5. Compiling and Installing Meep-1.2.1 on CentOS 6 and OpenMPI
  6. Installing HTseq for python 26 for CentOS 6
  7. Compiling SQLite 3.8.1 on CentOS 5
  8. Compiling gnuplot 4.6.4 on CentOS 5
  9. Compiling Java 7 on CentOS 5 and 6
  10. Compling ANTLR 2.7.7 on CentOS 6
  11. Compiling GSL/4.1 from GIT on CentOS 5
  12. Installing and Compiling Mankai Common Lisp on CentOS 5
  13. Compiling udunits-2.1.24 on CentOS 6
  14. Installing Berkeley UPC on CentOS 6 and GNU-4.8
  15. Compiling and Installing mfix-2016.1
  16. Compiling FDS-SMV with Intel MPI-5.0.3 on CentOS 6
  17. Compiling NAMD-2.11 with Intel 2013-SP1 and iMPI 4.1.3 and FFTW-2.1.5
  18. Compiling Relion with Intel Compilers-15.0.6 and Intel MPI-5.0.3
  19. Compiling MEEP with Intel-15.0.6, Intel-MPI 5.0.3 and HDFT-1.8.17
  20. Compiling SWIG-3.0.12 on CentOS 6
  21. Installing OpenCV on CentOS 6 on yum
  22. Compiling Wannier90-2.1.0 with Intel-MPI 5.1.3

Other Applications

  1. Installing dokuwiki on CentOS 6
  2. Installing and Configuring GIT on CentOS 5

Quantum Espresso

  1. Compiling Quantum ESPRESSO-7.2 with Intel-2023.1 on Rocky Linux 8
  2. Compiling Quantum ESPRESSO-6.7.0 with BEEF and Intel MPI 2018 on CentOS 7
  3. Compiling Quantum ESPRESSO-6.5.0 with Intel MPI 2018 on CentOS 7
  4. Compiling Quantum ESPRESSO-2.4.0 with Intel Parallel Studio 2016 on CentOS 6

Paraview

  1. Paraview and OpenGL

PLUMED

  1. Compiling plumed-2.6.4 with Intel 2019

R

  1. Compiling R-3.0.2 on CentOS 5
  2. Compiling R-3.4.2 on CentOS 6 with GNU
  3. Installing rgdal_1.4-8.tar.gz with R-3.6.0 on CentOS 7
  4. Installing the Seurat Package on R-3.6.2
  5. Installing DiffBind for R-3.6.2
  6. Installing R-Studio on CentOS-7
  7. Resolving GNU MP not found on CentOS 7
  8. Resolving r.Java is not found (attached, “rJavaError”) on R-4.1.0

Rust

  1. How to Install Rustup for All Linux Users in a Cluster or Shared Environment

Scalapack

  1. Compiling Scalapack-2.0.2 on CentOS 7

VASP

  1. Compiling VASP-5.4.4 with Intel MPI-5.0.3
  2. Compiling VASP-5.2.12 with Intel MPI-5.0.3
  3. Compiling VTST Tools with VASP-5.3.5
  4. Compiling VASP 5.3.3 with OpenMPI 1.6.5 and Intel 12.1.5
  5. Compiling VASP.6.3.0 with GPGPU Capability using Nvidia HPC-SDK on Rocky Linux 8.5
  6. Interesting Issues and Resolution for VASP
  7. Compiling VASP.6.3.0 using Nvidia hpcx, gcc-12.3 and MKL on Rocky Linux 8.7
  8. Configuring VTST with VASP-6.4.2 with Intel 2023.1
  9. No rule to make target `pyamff_fortran/*.f90′, needed by `pyamff_fortran/*.o’.
  10. Installing VASP-6.4.2 with Intel-2023.1

VMD

  1. Installing VMD-1.9.3 binaries on Linux

X-Windows

  1. Installing Grace (xmgrace) on CentOS 5 and 6