FranklinQuad Core Upgrade
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Franklin User EnvironmentOperating SystemFranklin's service nodes (login, network, I/O, and system nodes) run a full-featured standard SuSE Linux.Franklin's compute nodes run a light weight Linux-based OS, Compute Node Linux (CNL), which is optimized for application performance. CNL interacts with with an application process in a limited way, including managing virtual memory addressing, providing memory protection and performing basic scheduling. CNL reduces system overhead, ensures reproducible run-times for MPP jobs, and high performance, low latency MPI and SHMEM communications, which are critical for the system to scale to thousands of processors. User EnvironmentThird-party and public domain software installed and managed by NERSC's User Services Group (USG) is accessible through the module system. Most third-party software is not in the default command search path; the corresponding module must be loaded to use the software.
Shell Initialization FilesEnvironment initialization files ("dot-files") in home directories have been configured for maximum flexibility and ease of maintenance, both for the user and for NERSC staff. A long listing of a newly-created home directory (for user aaa) should look similar to this:
% ls -al total 156 drwx------ 4 aaa aaa 4096 Feb 2 13:39 . drwxr-xr-x 3 bin bin 4096 Feb 2 13:39 .. lrwxrwxrwx 1 aaa aaa 38 Feb 2 13:39 .bash_profile -> /usr/common/usg/etc/skel/.bash_profile -rw------- 1 aaa aaa 157 Feb 2 13:39 .bash_profile.ext lrwxrwxrwx 1 aaa aaa 32 Feb 2 13:39 .bashrc -> /usr/common/usg/etc/skel/.bashrc -rw------- 1 aaa aaa 141 Feb 2 13:39 .bashrc.ext lrwxrwxrwx 1 aaa aaa 31 Feb 2 13:39 .cshrc -> /usr/common/usg/etc/skel/.cshrc -rw------- 1 aaa aaa 160 Feb 2 13:39 .cshrc.ext lrwxrwxrwx 1 aaa aaa 31 Feb 2 13:39 .kshrc -> /usr/common/usg/etc/skel/.kshrc -rw------- 1 aaa aaa 138 Feb 2 13:39 .kshrc.ext lrwxrwxrwx 1 aaa aaa 31 Feb 2 13:39 .login -> /usr/common/usg/etc/skel/.login -rw------- 1 aaa aaa 159 Feb 2 13:39 .login.ext lrwxrwxrwx 1 aaa aaa 33 Feb 2 13:39 .profile -> /usr/common/usg/etc/skel/.profile -rw------- 1 aaa aaa 144 Feb 2 13:39 .profile.ext lrwxrwxrwx 1 aaa aaa 32 Feb 2 13:39 .tcshrc -> /usr/common/usg/etc/skel/.tcshrc -rw------- 1 aaa aaa 162 Feb 2 13:39 .tcshrc.ext The files .bash_profile, .bashrc, .cshrc, .kshenv, .login, .profile, and .tcshrc are links to read-only files, and should not be deleted. All individual customizations (aliases, environment variables, etc.) should be made in the files named .bashrc.ext, .cshrc.ext, .kshenv.ext, .login.ext, .profile.ext, and .tcshrc.ext. These .ext files are sourced by the corresponding dot-files. If these links and .ext files are missing, please run the fixdots, as shown below, to re-create them; then log out and log in again. All current dot files will be saved in a directory named $HOME/KeepDots.$Current_Time.
% /usr/common/usg/bin/fixdots After running the fixdots tool, modify the appropriate .ext files to customize the login shell, using the settings saved in the KeepDots directory. ShellsThe default login shell for all new accounts on Franklin is C-shell (csh). Other available login shells are bash, csh, ksh, and sh. Users may not change their login shell directly on Franklin; NIM is used to accomplish this function. See Change Default Login Shell. Default Programming Environment
Upon login, the example list of the default modules being loaded are:
% module list Currently Loaded Modulefiles: 1) modules/3.1.6 7) pgi/7.0.7 13) xt-libc/2.0.24b 2) moab/5.1.0 8) xt-libsci/10.2.0 14) xt-os/2.0.24b 3) torque/2.2.0 9) xt-mpt/2.0.24d 15) xt-catamount/2.0.24b 4) MySQL/4.0.27 10) xt-pe/2.0.24b 16) xt-boot/2.0.24b 5) xtpe-target-cnl 11) PrgEnv-pgi/2.0.24d 17) xt-lustre-ss/2.0.24b 6) acml/3.6.1 12) xt-service/2.0.24b 18) Base-opts/2.0.24b The default programming environment is PGI (via module PrgEnv-pgi). The default PGI compiler version (in this example, pgi/7.0.7) is also loaded. Other loaded modules include Torque/Moab for batch system management (via modules torque and moab), Message Passing Tool Kit (via module xt-mpt) for MPI, Shmem, and OpenMP libraries, ACML and Cray LibSci math and scientific libraries (via modules acml and libsci), CNL glibc functions (via module xt-libc), and Lustre support (via module xt-lustre-ss). Process LimitsFor processes running on Franklin service nodes (launched from login nodes or from batch scripts) there is a CPU limit of 60 min being enforced and the memory limit being set to 2,097,152 kbytes (2 GB soft limit and hard limit). |
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