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Toolchains and EasyBuild

We use a build and installation framework called EasyBuild that connects the software we compile and maintain on the clusters with the module system that makes it available to you.

Toolchains

When we install software, we use pre-defined build environments called toolchains. These are modules that include core compilers and libraries (e.g. GCC, OpenMPI, zlib). We do this for two main reasons. One is to try to keep our build process simpler. The other is so that you can load two different modules for software built with the same toolchain and expect everything to work (see below for details on Toolchain Trees). The two common toolchains you will interact with are foss and intel. Each of these have module versions corresponding to the year they were built. Toolchain name and version information is appended to the name of a module so it is clear what will be compatible. For example Python/2.7.12-foss-2016b, the software name is Python (version 2.7.12) that is built with the foss toolchain version 2016b. The easiest way to see what software a toolchain includes is to load it and then list loaded modules.

[be59@farnam2 ~]$ module load foss/2016b
[be59@farnam2 ~]$ module list

Currently Loaded Modules:
  1) StdEnv                        (S)   7) OpenMPI/1.10.3-GCC-5.4.0-2.26
  2) GCCcore/5.4.0                       8) OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1
  3) binutils/2.26-GCCcore-5.4.0         9) gompi/2016b
  4) GCC/5.4.0-2.26                     10) FFTW/3.3.4-gompi-2016b
  5) numactl/2.0.11-GCC-5.4.0-2.26      11) ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1
  6) hwloc/1.11.3-GCC-5.4.0-2.26        12) foss/2016b

  Where:
   S:  Module is Sticky, requires --force to unload or purge

To summarize, you should try to use modules that use matching foss, iomkl or intel identifiers.

Toolchain Trees

The one place toolchains can be a little complicated is that there are various levels to a given toolchain depending on how many libraries are included. For example, foss/2018a is a parent toolchain to GCCcore/6.4.0 since foss includes GCC 6.4.0 as well as OpenMPI 2.1.2.

Base toolchains:

GCCcore - GCC compiler
iccifort - Intel compiler (GCCcore is actually a also sub-toolchain of iccifort)

Toolchains with MPI:

gompi - GCCcore + OpenMPI
iimpi - iccifort + Intel MPI
iompi - iccifort + OpenMPI

Full toolchains (also include math libraries):

foss - gompi + OpenBLAS + ScalaPack
intel - iimpi + Intel MKL
iomkl- iompi + Intel MKL

For installations that where you will be loading additional dependencies beyond the toolchain module: 1. Choose a full toolchain and version. 1. Look for modules that contain that toolchain or its sub-toolchains to ensure compatibility. You can run module display foss/2016b to see which versions of the compiler and libraries it includes.

Environment Variables

To refer to the directory where the software from a module is stored, you can use the environment variable $EBROOTMODULENAME where modulename is the name of the module in all caps with no spaces. This can be useful for finding the executables, libraries, or readme files that are included with the software:

[be59@farnam2 ~]$ module load SAMtools/1.9-foss-2016b
[be59@farnam2 ~]$ ls $EBROOTSAMTOOLS
bin  easybuild  include  lib  share
[be59@farnam2 ~]$ ls $EBROOTSAMTOOLS/bin
ace2sam        interpolate_sam.pl  md5sum-lite    r2plot.lua   seq_cache_populate.pl  wgsim
blast2sam.pl   maq2sam-long        novo2sam.pl    sam2vcf.pl   soap2sam.pl            wgsim_eval.pl
bowtie2sam.pl  maq2sam-short       plot-bamstats  samtools     varfilter.py           zoom2sam.pl
export2sam.pl  md5fa               psl2sam.pl     samtools.pl  vcfutils.lua

Last update: October 22, 2019