HPC has a very small team of computational scientists that are responsible for everything related to helping users run their applications on the Henry2 cluster. Henry2 has hundreds of users in very different fields of expertise, each using different types of software. Additionally, there are a huge number of permutations of possible ways to install that software (versions, dependencies, options, etc.). This is why the core set of software that is officially supported by staff must remain small. HPC staff will help all users with any problems in installing user maintained software, but users are asked to first look at the documentation and make efforts to do installs themselves as much as feasible. Providing as much detail as possible when requesting support for software installs will result in much speedier resolution times for all.

Please help us grow this FAQ by emailing Support with additional questions or with suggestions on additions and clarifications.

Install FAQ

Clicking on the topic will expand the text with further details.

Will my software run on Henry2?

  • Henry2 has a Linux Operating System.
    • The application must run on Linux. Specifically, Henry2 runs Linux CentOS 7 (use cat /etc/centos-release to check current release), which also is usually compatible with RHEL. If an application says "Windows only", or is only supported on a different flavor of Linux (e.g. Ubuntu), it cannot be installed on Henry2. Check out the VCL or contact VCL support for using applications that require a different operating system.

      To find out the OS requirements for an application, look on the website under Download, "Buy it", Specs, or Install/Compiling documentation.

      When Singularity is fully deployed on the cluster, users may be able to run applications that require root to install, or that only run on Ubuntu, etc.
      IT staff from different departments:, please contact HPC if you are willing to assist with creating Singularity containers for your users.

  • Installations may not be done as root, or with sudo.
    • There are generally three resolutions to this issue: 1) The program may be installed by specifying the proper installation directory, 2) The program may be installed 'from source' rather than via package manager, or 3) The program actually needs to be installed as root and therefore cannot be installed.

      1) Generally, the basic install instructions for an application automatically try to install to a directory that only has root write access, such as /usr/bin. The solution is to specify a different install path, which should generally be in a space for user maintained software in /usr/local/usrapps/$GROUP/$USER/[packagename]. It is most commonly done in a configure step by adding --prefix=[path to installation location].

      2)Many applications recommend installing an application and/or all the necessary dependencies via a package manager, e.g. sudo yum install, etc. For these, look for instructions on How to install from source. Package managers greatly simplify installations, but they are rarely necessary.

      3)There are some applications that need to be installed system wide as root to function properly. These may not be installed on the cluster. Check out the VCL or contact VCL support to install these applications. Henry2 also has basic support for running containers. Users may run working Singularity images, or Docker images that may convert to a Singularity image, in the sif queue. There are not enough resources (i.e. HPC staff) to install or debug containers at this time.

  • Check the License, and test software before buying licences.
    • Before buying a software licence with the intention of running the application on the cluster, check whether or not it can be successfully installed and properly run on the cluster, but also check the licensing requirements. Some licences are system wide, but others require a license for every node that might run it - in the case of Henry2, that can be over 900 licences needed. Contact HPC Staff or NCSU Software Licensing Management for more information.

  • The HPC is not usually ideal for GUI based applications.
    • Before spending a lot of time doing a complicated software install, and before buying software licenses, check the requirements for running especially if the application requires a GUI. While GUI applications may be run on the HPC, rendering performance is often poor unless it is run directly from the HPC-VCL. HPC-VCL images are not as powerful as the compute nodes on the cluster, and by default they have 16GB of RAM and a limited number of cores. Contact VCL for information about the possibility of requesting a more powerful image.

    What should I do first?

  • Check that it isn't already installed.
    • While on Henry2, type module avail to see the officially supported software packages. See the Software page as well, which contains additional available sponsored software that is not officially maintained by staff, but sponsored by an individual willing to install and maintain the software for others. To use sponsored software, send a request to be added to the appropriate group.
  • Verify that it will run on Henry2.
    • See the above section: Will my software run on Henry2.
  • Request a space for user maintained executables.
    • Since the home directory is small and scratch is not permanent, HPC provides a space for installing user maintained software:

      Space for user maintained executables

      Acceptable use
        The directory /usr/local/usrapps provides space for user installed and maintained applications.
        A project may request a directory in which all group members may install software.
        All new /usrapps directories will be named for the project group unless otherwise requested.
        Directories in /usr/local/usrapps may not be used for data or as a working space from which to execute jobs. A compute node cannot write to /usr/local/usrapps. Globus and HPC-VCL cannot write to this space either.
        Applications must be maintained/patched to minimize potential security vulnerabilities.
        Access should be managed via Linux group permissions to comply with license restrictions.
        Applications that require root access to install are not permitted.
      Procedure to request space under /usr/local/usrapps
        The Project PI, or a group member with the Project PI cc'ed, should submit a request via email to HPC Support including the following information:
        • Name of HPC project that will be responsible for the application
        • The following statement: "The HPC group [mygroup] certifies that we will only install appropriately licensed applications on the HPC Linux cluster - e.g., applications where the license is fully open source with no applicable restrictions, applications for which NCSU has approved a clickwrap, or applications with licences purchased by our group. For licenses purchased by our group, we will maintain proper file and directory permissions to comply with the licence. The group will maintain software by installing security patches or upgrades when necessary."
        A directory will be created with group read/write access for the requesting project. The project group will be responsible for installing and maintaining the application. Please contact HPC staff with any questions about licensing when installing software.

      Where to install?

      A space in /usrapps is by default writable by everyone in the project, so all members have permissions to write directly to the /usrapps/$GROUP space. This leads to confusion and potential permissions problems. Users should create their own space within the group directory. Each user should make their own directory to install software and adjust permissions as necessary.

      mkdir /usr/local/usrapps/$GROUP/$USER

      How to install?

      Please see the general guidance for installing software.
  • Learn about basic Linux and environment variables.
  • A note on how to get the software, where to install, and where to install from.
    • To get the software, download from trusted websites to Henry2.

      • Use wget. Instead of clicking to download a tar file, then scp-ing to Henry2, right click on the link and Copy Link Location, e.g. https:some-domain/mysoftware/latest.tar.gz. Then on Henry2, do
        wget https:some-domain/mysoftware/latest.tar.gz
        tar zxvf latest.tar.gz
      • Use git. Go to the GitHub repo for the code, click the Clone or download button, and copy the URL. Then, on Henry2, do
        git clone https:github-path/mysoftware/latest.git
        That will download the source to a directory called latest.

      Where to install? For software to be used regularly by a research group, install to the group's space in /usr/local/usrapps. Software that is used temporarily for testing purposes only might more appropriately be installed in the scratch directory at the discretion of the user.

      Where to install from? Usually, installations should be done from a login node. Note that compute nodes cannot download source code and packages from the internet, and neither compute nodes nor VCL nodes may write to /usr/local/usrapps. When compiling a software using compiler options to optimize for architecture, the compilation might be done on a node with the targeted architecture, with the understanding that it consequently may not run on any nodes not having the instruction set(ISA) specified. See Advanced Compiler Options for more details on creating binaries optimized for multiple ISAs.

    How to install?
    Sometimes there are multiple ways to install a software package. Here are some methods, in order of increasing difficulty.

  • Download and untar prepackaged binaries
    • Some applications are available as binary executables, and they need not be compiled. Download the software, unpack, and use the applications immediately. Confirm the binaries will run on CentOS Linux, and after installation, create a script that sets the environment. Some applications depend on other applications or libraries, and in that case, the dependencies must also be installed and the environment set before using. If the application has multiple dependencies, using a Conda environment may be preferable.
  • Install with Conda
    • Conda is a package manager that downloads binaries of the applications specified and all of their proper dependencies. Please see the Conda documentation for detailed instructions.
  • Configure, cmake, or ccmake, then make
    • For these applications, download and unpack the source code, then read the instructions (usually contained in a file called README or INSTALL). Then the general procedures are
        The configuring is done with a script, usually called configure or configure.sh.
        cd [path to source directory]
        ./configure --prefix=[path to installation location]
        make check  #or 'make test'
        make install
        The configure script checks the environment and creates a makefile accordingly; therefore, the environment must be set so that the necessary dependencies are found when running configure. For example, if the application requires the Intel compiler and Intel MPI, do
        module load PrgEnv-intel
        ./configure --prefix=[path to installation location]
        make check  #or 'make test'
        make install
        The configuring is done by CMake.
        mkdir build
        cd build
        module load cmake
        cmake [path to source directory]
        make check #or 'make test'
        make install
        The program ccmake is similar to cmake, except instead of specifying any options through the command line (e.g. --prefix), they are set in a GUI. The GUI is text on the screen, not a pop-up window. Using ccmake is often very useful when a package has many dependencies, because the paths to the include files (header files) may not be set automatically by loading modules, in which case they will need to be specified explicitly.
        mkdir build
        cd build
        module load cmake
        ccmake [path to source directory]
        [Use the GUI to set the install prefix and other environment variables.  Choose the options listed at the bottom, typically configure, then generate, then exit.]
        make check #or 'make test'
        make install

    Common problems

  • Installation instructions are for using sudo and a package manager.
    • Search for phrases like "install from source" or "git repo". Then follow the install instructions, which are likely to be configure/make.
  • The default shell is tcsh, but instructions are in bash.
    • Type bash before following the instructions. Type exit to return to the default shell.
  • Permission denied when executing a file or running a script.
    • This usually means there are no execute permissions on the script. In this case, do
      chmod u+x script.csh
  • Permission denied when using the 'touch' command.
    • Users do not have access to the touch command by default. Open a help ticket requesting access to the touch command, and copy/paste the compile error that indicates the requirement of the touch command.
  • [Something] not found - additional troubleshooting for the compute environment.
    • See the documentation on setting the compute environment. For "Command not found", set PATH. For "error while loading share libraries", set LD_LIBRARY_PATH. For errors regarding location of header files, or .h files, set the INCLUDE paths. Variables containing include paths vary by makefile, but often include CFLAGS, CPPFLAGS, or FFLAGS.
  • Disk quota exceeded.
    • This error usually means the install has filled the home directory, either with the source and executables themselves, or with hidden files. Some programs create a "dot" directory, e.g. Conda creates .conda if an alternate path is not given in the .condarc. Check the documentation for how to specify an alternative path for temporary files.
  • Cannot find a common library
    • If it appears that the compiler cannot find a common library, e.g. -lm, check the makefile for static. The static versions of libraries for system compilers are not installed. Usually the -static compiler flag may be omitted without consequence.

    How can I get help?

  • When you get stuck, open a help ticket containing the following...
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