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subversion

Versions and Availability

h4

h5
Module Names for subversion on qb2
Machine Version Module Name
qb2 1.8.13 subversion/1.8.13/gcc-4.9.0

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.

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Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

▶ Did not find the version you want to use??

If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.

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Types of request

Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:

  • The user's home directory
    • Software packages installed here will be accessible only to the user.
    • It is suitable for software packages that will be used by a single user.
    • Python, Perl and R modules should be installed here.
  • /project
    • Software packages installed in /project can be accessed by a group of users.
    • It is suitable for software packages that
      • Need to be shared by users from the same research group, or
      • are bigger than the quota on the home file syste.
    • This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.
  • /usr/local/packages
    • Software packages installed under /usr/local/packages can be accessed by all users.
    • It is suitable for software packages that will be used by users from multiple research groups.
    • This type of request must be sent by the PI of a research group.

h3

How to request

Please send an email to sys-help@loni.org with the following information:

  • Your user name
  • The name of cluster where you want to use the requested software
  • The name, version and download link of the software
  • Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
  • Why the software is needed
  • Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.

Please note that, once the software is installed, testing and validation are users' responsibility.

About the Software

Subversion is an open source version control system. It was created by CollabNet Inc. in 2000, and is now a top-level Apache project being built and used by a global community of contributors. Homepage: https://subversion.apache.org/

Usage

svn comes with the operating systems on most clusters, so one does not need to add a module or softenv key for it to work.

svn has a excellent online help system. To view the help information, simply run:

$ svn help
usage: svn  [options] [args]
Subversion command-line client, version 1.6.11.
Type 'svn help ' for help on a specific subcommand.
Type 'svn --version' to see the program version and RA modules
  or 'svn --version --quiet' to see just the version number.

Most subcommands take file and/or directory arguments, recursing
on the directories.  If no arguments are supplied to such a
command, it recurses on the current directory (inclusive) by default.

Available subcommands:
   add
   blame (praise, annotate, ann)
   cat
   changelist (cl)
   checkout (co)
   cleanup
   commit (ci)
   copy (cp)
   delete (del, remove, rm)
   diff (di)
   export
   help (?, h)
   import
   info
   list (ls)
   lock
   log
   merge
   mergeinfo
   mkdir
   move (mv, rename, ren)
   propdel (pdel, pd)
   propedit (pedit, pe)
   propget (pget, pg)
   proplist (plist, pl)
   propset (pset, ps)
   resolve
   resolved
   revert
   status (stat, st)
   switch (sw)
   unlock
   update (up)

	

For detailed help information on a specific command, run "svn help <command name>":

$ svn help up
update (up): Bring changes from the repository into the working copy.
usage: update [PATH...]

  If no revision is given, bring working copy up-to-date with HEAD rev.
  Else synchronize working copy to revision given by -r.

  For each updated item a line will start with a character reporting the
  action taken.  These characters have the following meaning:

    A  Added
    D  Deleted
    U  Updated
    C  Conflict
    G  Merged
    E  Existed

  A character in the first column signifies an update to the actual file,
  while updates to the file's properties are shown in the second column.
  A 'B' in the third column signifies that the lock for the file has
  been broken or stolen.

  If --force is used, unversioned obstructing paths in the working
  copy do not automatically cause a failure if the update attempts to
  add the same path.  If the obstructing path is the same type (file
  or directory) as the corresponding path in the repository it becomes
  versioned but its contents are left 'as-is' in the working copy.
  This means that an obstructing directory's unversioned children may
  also obstruct and become versioned.  For files, any content differences
  between the obstruction and the repository are treated like a local
  modification to the working copy.  All properties from the repository
  are applied to the obstructing path.  Obstructing paths are reported
  in the first column with code 'E'.

  Use the --set-depth option to set a new working copy depth on the
  targets of this operation.

Valid options:
  -r [--revision] ARG      : ARG (some commands also take ARG1:ARG2 range)
                             A revision argument can be one of:
                                NUMBER       revision number
                                '{' DATE '}' revision at start of the date
                                'HEAD'       latest in repository
                                'BASE'       base rev of item's working copy
                                'COMMITTED'  last commit at or before BASE
                                'PREV'       revision just before COMMITTED

...
	

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Last modified: September 10 2020 11:58:50.