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Handling of data sets with access restrictions
Handling of data sets with access restrictions
Revision as of 12:23, 7 November 2017
Software and Data Installation Guide
= Version history
Version Date Note 0.1 2017-04-26 Initial draft by trz 0.2 2017-05-20 Added information on modules and accessing shared storage space, cleaned up doc (moving future topics to section at the end) 0.3 2017-05-31 Small fixes; 1st version to be used as guidelines
Guidelines to install software and data at resources provided within the Nordic Language Processing Laboratory.
Taito is a cluster operated at CSC (Finland). User documentation is available at https://research.csc.fi/taito-user-guide. Each user has access to different areas for storing files: `$HOME` with a quota of 50 GB, `$USERAPPL` with a quota of 50 GB, and a project area under `/proj/nlpl/` (access via storage project NLPL managed by Stephan Oepen, email@example.com).
Abel is a cluster operated at UiO (Norway). User documentation is available at http://www.uio.no/english/services/it/research/hpc/abel/help/user-guide/. Each user has access to different areas for storing files: `$HOME` with a quota of 500 GB, and a project area under `/projects/nlpl/` (access via UNIX group hpc-nlpl managed by Stephan Oepen, firstname.lastname@example.org).
The software environment of the laboratory shall be as identical as possible from a user point perspective. The software environment is made of libraries and applications installed system wide or in a space specific for the laboratory. System wide libraries and applications are not considered at the current stage (see section Future topics).
Laboratory specific software is stored under $NLPL_SOFTWARE which points to /proj/nlpl/software and /projects/nlpl/software for Taito and Abel respectively.
Under $NLPL_SOFTWARE applications and libraries are stored with the following directory layout
where __APPNAME__ contains only lower case symbols (with some exceptions such as R) and __APPVERSION__ contains the version of the software (as provided by its "vendor").
For each installation, there should be a page on the wiki documenting the exact versions used (and how to obtain them) and steps used to build the software.
Optionally, for each software that is installed the sources and build scripts (if adjusted to the lab environment) can be stored under $NLPL_SOFTWARE/sources. This directory should be ‘cleaned up’ after the installation, possibly compressed Possibly keep log files?
A user's environment is configured using the module system which abstracts actual installation paths and sets certain environment variables in a standardised form. The necessary module files are stored under $NLPL_SOFTWARE/modulefiles/__APPNAME__/__APPVERSION__
See section Modules below for further details on defining module files.
At start only limited documentation will be available through the module system. A subsequent version of this guide will recommend best practices for documentation.
The data sets provided by NLPL shall be presented as uniformly as possible from a user point perspective. The data set environment is predominantly comprised of freely available data. Restricted data sets are not considered at the current stage (see section Future guide topics).
Data sets shall be installed under $NLPL_DATA which points to /proj/nlpl/data and /projects/nlpl/data for Taito and Abel, respectively. The top-level data directory is sub-divided by NLPL activities, with sub-directories translation, parsing, corpora, vectors, and opus. In principle, each activity is free to decide on the directory layout within their sub-directory, where it may or may not be most practicaly to organize according to languages. Where language identifiers are part of directory or file names, they should follow the three-letter ISO codes. Here as elsewhere in the NLPL directory space, upper-case letters shall be avoided in file and directory names (except maybe for de-facto standard names like Makefile or README).
The Modules System
At start only limited documentation will be available through the module system. A subsequent version of this guide will recommend best practices for documentation. Modules Modules (command line tool module) allow for a simple and common way of configuring a user's environment to get access to executables, libraries, development files, data sets, etc.
The most essential commands are
module avail Shows which modules are available. module list Shows which modules have been loaded. module load name/version Loads module with name name and version version. module rm name/version Unloads module with name name and version version. module purge Unloads all modules. module show name/version Shows the definition of the module. module whatis name/version Shows a brief information on what this module provides (for Abel). module help name/version Shows a brief information on what this module provides (for Taito). module use -a PATH Append PATH to the search path for module definition files.
Modules are defined with (short) text files using Tcl and Lua on Abel and Taito, respectively. For modules specific to the laboratory, these files shall be stored under the above mentioned directory layout (see sections on Software and Data sets). Integrating modules in the system requires the directory containing these files be included in the search path of the module system (see module use -a above). For example, include the command
module use -a $NLPL_SOFTWARE/modulefiles
in your .bashrc on Abel and Taito which requires that $NLPL_SOFTWARE is set (see section Software above).
Where and how to provide documentation (likely on www.nlpl.eu) How to test/validate a software that it actually works (e.g., by someone else than the one who has installed it ... based on the provided documentation) How to test software to ensure functional identity across systems How to sync data sets across systems Handling of data sets with access restrictions
|0.2||2017-05-20||trz||added information on modules and accessing shared storage space, cleaned up doc|
|0.3||2017-05-31||trz||small fixes; first version to be used as guidelines|
|0.4||2017-11-06||oe||updates from the infrastructure task force|