subversion
Table of Content
Versions and Availability
▶ Display Module Names for subversion on all clusters.
| Machine | Version | Module |
|---|---|---|
| None Available | N/A | N/A |
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
h4
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):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.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.
h3
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
...
Resources
Last modified: September 10 2020 11:58:50.