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mxtools/prun/prun.md

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NAME SYNOPSIS DESCRIPTION EXAMPLES FILES BUGS AUTHORS SEE ALSO
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% PRUN(1) Version n/a | Mariux Tools Documentation

NAME

prun - Run Mariux packages (reads 'Package RUN').

SYNOPSIS

| prun package command [COMMANDOPTION]...

DESCRIPTION

Runs applications, scripting languages, compilers, etc., from a dedicated directory.

The main usage is to run software in a specific version, or to provide a given environment. See EXAMPLES below.

There are some advantages over so called 'virtual environments' and the like. Packages are immutable, once installed they never change, thereby increasing the chances that an old program/script will also run in a few years. The packages also use a standardized call procedure, independent of personal (un-)settings, thus an existing pipeline may be shared between different users.

The whole 'magic' behind prun is, that it transparently sets the PATH variable and possibly LD_LIBRARY_PATH for the actual call without spoiling the default environment.

EXAMPLES

Run R-Studio with a brand new R version

: prun R-4.1.0-0 rstudio

Use an ancient python to run an unmaintained script

: prun python-2.7.13-2 /project/cruft/bin/old_script.py

Run nvidia nvcc from cuda-11.3 and list supported architectures

: prun cuda-11.3 nvcc --list-gpu-code

Start a plain shell with gcc-10.2 in the PATH

: prun gcc-10.2.0-0 bash --norc

Or just show the manual page for gcc-10.2

: prun gcc-10.2.0-0 man gcc

Create an own alias for a scripting language

: alias myperl='prun perl-5.18.2-0 perl'

Use prun in a script shebang

: #! /usr/bin/prun perl-5.18.2-0 perl

Alternatively using source

: An alternative way to set a distinct environment is to source the profile from /pkg/FooBar-12.3. But beware, such a source command should never make it into the ~/.bashrc - in the worst case it may inhibit your login! (N.b. the alias method mentioned above is safe)

\ : source /pkg/gcc-10.2.0-0/profile

FILES

/package/FOO or /pkg/BAR

: Mountpoint (top directory) for selected package.

/package/FOO/profile or /pkg/BAR/profile

: Contains settings for PATH, libraries, and possibly other stuff.

/usr/local/package/lib/*

: Primary wrappers for individual packages.

/usr/local/package/admin/config

: Definition of binaries provided and optional shortcuts.

BUGS

See GitHub Issues: https://github.molgen.mpg.de/mariux64/mxtools

AUTHORS

D.Buczek, P.Marquardt, M.Tolzmann

SEE ALSO

ptype(1), pman(1), bash(1), ld.so(8)