Toolchains and EasyBuild
When we install software, we use pre-defined build environments called toolchains. These are modules that include core compilers and libraries (e.g.
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. The two common toolchains you will interact with are
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 to us and to the module system what should be compatible. An example would be
Python/2.7.12-foss-2016b, where the software name is
2.7.12, 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
The takeaway here is that you should try to use modules that match their
If you ever want 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