HowTo:Migrate

Migrating from Sparc/Solaris to x86/Linux

This is an introduction to setting up your account on our systems. When first logging in, you are presented with a default set-up that enables the use of basic system commands, simple compilers, and access to the scheduler. This help file is meant to explain how to modify that default.

Access The login node for the Linux nodes is swlogin1. It may be accessed in two different ways: From the default login node sflogin0 (which stgill runs on Solaris) by secure shell: ssh -X swlogin1 . Re-issuing the password will be required. Directly from the Secure Global Desktop through the xterm (sxwlogin1) application. For people used to work on sflogin0, this iomplies an additional "node hop" to swlogin1. 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. Fortran/C/C++ Compilers Sparc/Solaris to x86/Linux Sparc/Solaris x86/Linux (gnu) x86/Linux (Intel) Name/Version Studio 12.4 Gnu gcc 4.4.7 Intel 12.1 Setup command none (default) none (default) use icsmpi MPI setup none (default) use openmpi use icsmpi Fortran / C / C++ compilers f90 / cc / CC gfortran / gcc / g++ ifort / icc / icpc MPI compoiler wrappers mpif90 / mpicc / mpiCC mpif90 / mpicc / mpicxx mpiifort / mpiicc / mpiicpc MPI runtime environment mpirun mpirun mpirun 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 Changes when migrating from Sparc/Solaris to x86/Linux Sparc/Solaris x86/Linux Version G09 Rev.D01 G09 Rev.E01 Queue name m9k.q (old default, deprecated) abaqus.q Node names m9k000* sw00**, cac0** Relative Execution Speed 1 3 GUI available no no Queue specification in submit script none #$ -q abaqus.q #$ -l qname=abaqus.q Parallel environment #$ -pe gaussian.pe #$ -pe glinux.pe Setup line . /opt/gaussian/setup.sh . /opt/gaussian/setup.sh Login node for submission sflogin0 swlogin1 Setup command use g09 use g09 Help If you have questions that you can't resolve by checking documentation, email to cac.help@queensu.ca.