HTC Application Environment

Lmod will be used by cluster administrators to provide optimized builds of commonly used software. Applications be available to users through the Lmod modular environment commands. There are no default modules loaded when you log in.

Installed packages

Use the command "module spider" to list all installed applications. The architecture for the HTC Cluster is called haswell, which means that codes have been compiled to utilize the AVX2 instruction set as best as possible.

We have implemented a hierarchical structure of module files. Use "module avail" to list "core" modules

[fangping@login0a ~]$ module avail
 -------------------------------------------- /ihome/crc/modules/Core --------------------------------------------
   abaqus/2016-vandegeest                    matlab/R2017a                       (D)
   abaqus/2017-general                       matlab/R2018a
   abaqus/2017-vandegeest             (D)    maven/3.5.0
   adf/2017.108                              medea/2.22.3
   admixmap/3.8.3103                         meerkat/0.189
   afni/18.0.22                              meme/5.0.3

To load modules compiled using GCC 8.2.0, run "module load gcc/8.2.0" then "module avail".

Module environment files have been created for each of these packages and can be easily loaded into your shell with "module load <packagename>" for "core" modules. To load modules compiled using GCC 8.2.0, for example r/3.5.1, use "module load gcc/8.2.0 r/3.5.1"

In the example below I have loaded the HISAT package into my environment. The executables, such as hisat2, hisat2-build is now in my PATH.

[fangping@login0a ~]$ module load hisat2/2.1.0
[fangping@login0a ~]$ which hisat2
[fangping@login0a ~]$ which hisat2-build

You can check which modules are “loaded” in your environment by using the command module list

[fangping@login0a ~]$ module list
Currently Loaded Modules:
  1) hisat2/2.1.0

To unload or remove a module, just use the unload option with the module command, but you have to specify the complete name of the environment module:

[fangping@login0a ~]$ module unload hisat2/2.1.0
[fangping@login0a ~]$ module list
No modules loaded

Alternatively, you can unload all loaded environment modules using module purge.

  • Several reference genome data are available at /mnt/mobydisk/pan/genomics/refs