Migration Q&A

• Q: Who migrates ?

A: Eventually, all of our users will migrate from the old SW (Linux) cluster to the new "Frontenac" (CAC) cluster

• Q: Can I use my old "stuff" ?

A: Much of the old data and software will be usable on the new systems. However, the data will have to be copied over as the new systems use a separate file system, and cross access is not possible.

• Q Do I have to re-compile ?

A: It is possible that you will have to re-compile some of the software you are using. We will assist you with this.

• Q: Do I copy my files over myself ?

A: No. We will do this for you in the course of the coming months.

• Q: Is this optional ?

A: Unfortunately not. We will move both user data and hardware according to a schedule.

• Q: Can I decide when to move ?

A: To a degree. We are open to "early adopters". Once they have been moved we move the bulk of users according to our schedule.

• Q: Will this disrupt my research ?

A: We will do our level best to keep disruptions to a minimum. We will give you a chance to "practise" on the new systems while you still have access to the old ones. Once you are on the new systems, access to the old ones will be cut to preserve data integrity.

What's Different ?

Shell Setup

There are several set-up files in your home directory:

• .bashrc is "sourced in" every time a bash shell is invoked.
• .bash_profile applies only to login shells, i.e. when you access the system from outside.

Most of the setup is automatic through usepackage. On login, you have a default setup that is appropriate for a Linux system. Additional packages can be set up by adding commands such as

use anaconda3

to the above setup files, if you want to use the Python 3 distribution "Anaconda" (as an example). Note that this is the same as it was on Solaris, but that the available packages may differ. For a list, use the

use -l

command.

Compiling Code

The standard Fortran/C/C++ compilers differ between the Solaris and the Linux systems. The ones on the x86/Linux platform are discussed here. Here is a comparison in table form. Since there are two compilers (gnu and Intel) on the Linux platform, they are treated separately. The default is gnu. We also list the MPI - related commands for setup, compilation, and runtime.

Note that all programs that were running on the Solaris platform have to be re-compiled on Linux. Binaries are not compatible as they are based on different instruction sets.

MPI

On both Solaris and Linux systems, the MPI distribution used is OpenMPI. On the Solaris platform this was integrated with the standard Studio compilers. On the Linux platform, two versions are in use:

• A stand-alone version of OpenMPI 1.8 is used in combination with the gcc compiler and setup through the use openmpi command.
• A second version (Intel 4.0 update 3) is used with the Intel compilers and set up together with them ("use icsmpi")

All of these versions use the mpirun command to invoke the runtime environment. Check with which mpirun to see which version you are currently using.

Binary Formats

Important: Some programs use binary format for data I/O. These files are likely not compatible between the two platforms, which means that it may be necessary to re-run the programs on the new platform or convert the data files before using them. This is due the different "Endianness" on the two platforms: Sparc/Solaris is big-Endian and x86/Linux is little-Endian. If you encounter issues with data files, please get in touch with us.

Scheduling

Both the "old" M9000 servers and the "new" SW (Linux) cluster use Sun Grid Engine as a scheduler. Please consult our Scheduler Help File for details about its usage. The following table gives an overview of the alterations that need to be made to a submission script if execution is to take place on the Linux production nodes, i.e. the "SW cluster".

#$ -pe gaussian.pe

#$ -pe glinux.pe

. /opt/gaussian/setup.sh

. /opt/gaussian/setup.sh

Note that it is strongly suggested to lower the number of processes requested when submitting to the SW cluster. This is because the nodes are substantially smaller than then the M9000 servers, but provide greatly improved per-core performance. This means that even with half the core count, a speedup of 2-3 is likely.

We have added some entries to the table describing modifications that apply only for submissions of jobs running the Computational Chemistry software Gaussian. For more details about this software, please consult our Gaussian Help File. Gaussian submissions go to a dedicated large node on the SW cluster that uses local scratch space to improve performance and avoid bandwidth issues with IO.

Help

If you have questions that you can't resolve by checking documentation, email to cac.help@queensu.ca.