[Beowulf] Docker in HPC

Christopher Samuel samuel at unimelb.edu.au
Thu Nov 28 14:44:06 PST 2013


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On 28/11/13 23:13, Bogdan Costescu wrote:

> f.e. a single version of GROMACS 

But then you run into the issue of different users who say "but I must
have GROMACS x.y.z", hence why we've already got GROMACS 4.0.7, 4.5.7
and 4.6.3 installed on a system that was a clean install only a few
months ago. :-/   At least the person who uses GROMACS 3.x hasn't
asked for it (yet).

Then there are the ones who have a patch they want, or built with
different (mutually exclusive) options (for Ray).

We just install to:

/usr/local/$APP/$VERSION-$COMPILER

and use Modules to sort it out - a lot of times we can do it fairly
automatically with a generic file that extracts what it needs from
the name of the module:

#%Module1.0#####################################################################
##
## $name modulefile
##

set ver [lrange [split [ module-info name ] / ] 1 1 ]
set name [lrange [split [ module-info name ] / ] 0 0 ]
set subname [lrange [split $name - ] 0 0 ]
set compiler [lrange [split $name - ] 1 1 ]

proc ModulesHelp { } {
  puts stderr "\tThis module sets the environment for $name v$ver"
}

module-whatis   "Set environment variables to use $name version $ver"

if { ![ is-loaded $compiler ] } {
  module load $compiler
}

prepend-path --delim " " CPPFLAGS -I/usr/local/$subname/$ver-$compiler/include
prepend-path --delim " " LDFLAGS -L/usr/local/$subname/$ver-$compiler/lib

prepend-path LD_LIBRARY_PATH /usr/local/$subname/$ver-$compiler/lib
prepend-path MANPATH /usr/local/$subname/$ver-$compiler/share/man
prepend-path PATH /usr/local/$subname/$ver-$compiler/bin


- -- 
 Christopher Samuel        Senior Systems Administrator
 VLSCI - Victorian Life Sciences Computation Initiative
 Email: samuel at unimelb.edu.au Phone: +61 (0)3 903 55545
 http://www.vlsci.org.au/      http://twitter.com/vlsci

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