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.
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
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.
Python/2.7.12-foss-2016b, the software name is
2.7.12) that is built with the
foss toolchain version
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
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.
foss/2018a is a parent toolchain to
foss includes GCC 6.4.0 as well as OpenMPI 2.1.2.
GCCcore - GCC compiler
iccifort - Intel compiler (GCCcore is actually a also sub-toolchain of
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.
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