Common CentOS7 Upgrade Questions

April 16, 2018
Halstead, Rice, Snyder

The Halstead, Rice, and Snyder clusters will be upgraded to newer CentOS7 operating system in May 2018 (detailed announcements in: Rice Upgrade to CentOS7, Halstead Upgrade to CentOS7, Snyder Upgrade to CentOS7). Along with operating system upgrade, the available software modules on these systems will also change. The objective of this guide is to answer some common questions related to the supported softwares and libraries on the Halstead, Rice, and Snyder clusters post-upgrade.

  • The software package I use isn't available, will you recreate the module?

The software offerings on ITaP Community Clusters are periodically evaluated to ensure our efforts are spent on softwares beneficial to the greater community. Packages that are not frequently used are periodically removed. If you feel that the missing software may be useful for a large group of people, please send us a request at rcac-help@purdue.edu and we shall work with you to install it at a suitable location.

  • The specific version of a module I use isn't available, will you recreate the old version?

Many of the old software versions currently installed on Halstead, Rice, and Snyder clusters will be replaced by newer versions. This is to make sure that we are bringing you the latest enhancements (performance, features, and bug-fixes) in these softwares. Old software versions removed from the clusters will NOT be reinstalled centrally. Please recompile your code using the new module. If your continued research relies on an older version, please contact us and we will work with you to install it at a suitable location.

  • The command I use isn't available, will you install the system library?

One of the objectives of the cluster upgrades is to keep the system images clean. This generally leads to fewer library conflicts and reduces system overhead. If you need a specific tool/command to be installed on the system (that used to be available outside of a module), please send us a request at rcac-help@purdue.edu. We will evaluate the requested tool to see if it follows our guidelines and does not conflict with any existing application.

  • I cannot find a module for nco, cdo, or ncview, will you rebuild these applications?

The executables and libraries for nco, cdo, and ncview are now integrated into the netcdf installation. Please load the netcdf module to use any of these applications. An example is given below:

     module spider netcdf
     module load netcdf

Please read the following article for details: NetCDF and Related Module Changes

  • I cannot compile my application with BLAS or LAPACK. Where can I find these packages?

If you notice that your compilation fails with warnings about missing blas or lapack libraries ("-lblas -llapack"), please consider loading the openblas module with the command "module load openblas". This modules provides the necessary libraries.

If you prefer using the Intel MKL libraries, you won't need to load the openblas module. You can determine the compiler flags for linking against MKL using this online tool: Intel MKL Link Line Advisor

  • I cannot find a module for Python. What should I do?

We use the Anaconda distribution to manage Python installations on ITaP Community Clusters. Please load one of the anaconda modules to use your preferred version of Python. An example is given below:

     module spider anaconda
     module load anaconda/5.0.0-py36

  • I cannot find package XYZ in Anaconda. What should I do?

Unlike previous Anaconda installations, newer Anaconda installers come with few popular packages. Since different users prefer different compilers and prerequisites (versions), we shall NOT install additional python packages in the central Anaconda installation. The preferred way to install the package you need is to use the 'pip' installer as shown in the example below:

     pip install --user XYZ

Please see our Python user guide for more details.

  • The software I use only runs on the current operating system (RHEL6). What should I do?

This is a very rare situation. We have not yet encountered any application that does not run on the newer CentOS7 system. However, if you cannot figure out how to run your application on the upgraded clusters OR if its user guide suggests that it is NOT compatible with CentOS7, please send us an email at rcac-help@purdue.edu

Originally posted: April 16, 2018  6:53pm

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