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Installing software in your home directory: Difference between revisions
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Installing software in your home directory (view source)
Revision as of 13:21, 6 July 2017
, 6 years agoAdded some info about compute canada stack
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== Python, R, and Perl packages == <!--T:8--> | == Python, R, and Perl packages == <!--T:8--> | ||
[[Python]], [[R]], and [[Perl]] are languages with large libraries of extension packages, and package managers that can easily install almost any desired extension in your home directory. See the page for each language to find out if the package you're looking for is already available on our systems. If it is not, you should also find detailed guidance there on using that language's package manager to install it for yourself. | [[Python]], [[R]], and [[Perl]] are languages with large libraries of extension packages, and package managers that can easily install almost any desired extension in your home directory. See the page for each language to find out if the package you're looking for is already available on our systems. If it is not, you should also find detailed guidance there on using that language's package manager to install it for yourself. | ||
== The Compute Canada software stack == <!--T:9--> | |||
Almost all software that is used on the new clusters is distributed centrally, using the CVMFS file system. What this means in practise is that this software is not installed under <code>/usr/bin</code>, <code>/usr/include</code>, and so on, as it would be in a Linux distribution, but instead somewhere under <code>/cvmfs/soft.computecanada.ca</code>, and is identical on all new clusters. | |||
The core of this software stack is provided by the <code>nixpkgs/16.09</code> module, which is loaded by default. This software stack, internally managed using the Nix package manager, is located at <code>/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09</code>. The environment variable <code>$EBROOTNIXPKGS</code> should be used to refer to this path. | |||
Under this location you can find all of the common packages typically included with Linux distributions, for instance <code>make</code>, <code>ls</code>, <code>cat</code>, <code>grep</code>, and so on. Typically, when you compile some software, the compiler and linker will automatically look for header files and libraries in the right location (via the environment variables <code>$CPATH</code> and <code>$LIBRARY_PATH</code>, respectively). | |||
Some software, however, has been hardcoded to look under <code>/usr</code>. If that is the case, the compilation will typically fail, and needs to be explicitly told about <code>$EBROOTNIXPKGS</code>. Sometimes that means adjusting a Makefile, sometimes it needs to be specified in a certain <code>--with-</code> flag for the configure script, or a configuration file needs to be edited. If you are not sure how to do this please do not hesitate to ask for help. | |||
Similarly, if a package depends on a library that is provided by a module other than <code>nixpkgs</code>, you may need to provide the location of the header files and libraries of that module. The EBROOT convention applies to all modules, e.g. the HDF5 library is installed in <code>$EBROOTHDF5</code>, and its <code>include</code> and <code>lib</code> subdirectories once you <code>module load hdf5</code>. | |||
If a header file or library that would usually be provided by an RPM or other package manager in a typical Linux distributon is neither present via <code>nixpkgs</code> or via another module, please let us know. Most likely it can be easily added to the existing stack. | |||
Notes: | |||
* all binaries under <code>/cvmfs/soft.computecanada.ca</code> use what is called a runpath, which means that the directories for the runtime libraries that these binaries depend on are put inside the binary. That means it is generally *not* necessary to use <code>$LD_LIBRARY_PATH</code>. In fact, <code>$LD_LIBRARY_PATH</code> overrides this runpath and you should '''not''' set that environment variable to locations such as <code>/usr/lib64</code> or <code>$EBROOTNIXPKGS/lib</code>. Many binaries will no longer work if you attempt this. | |||
* if all else fails you can use <code>module --force purge</code> to remove the CVMFS environment. You are then left with a bare-bones CentOS-7 installation without modules. This may help for special situations such as compiling GCC yourself or using custom toolchains such as the [http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk MESA SDK]. Purging modules would then '''only''' be necessary when you compile such software; the modules can be reloaded when running it. | |||
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