This list may not be complete; run module av on UAHPC for an up to date list.

How to use centrally installed software on UAHPC by module.

Users can check for current software available on UAHPC by module av command.

To check the currently loaded modules in your current terminal environment, do module list

Load a software, module load a specific software

Unload a software, module unload a specific software

Unload all modules, module purge (recommended before starting a new simulation)

If you are submitting a job that uses a software by module load, users need to put these module load commands into sbatch script in order to use the software to run your job.

If you find a software you want to install centrally, but cannot find it on UAHPC, you can submit a software request through UAHPC portal.

Note:

  1. Please cite the publication related to the software you are using for your research, to recognize the significant efforts of scientific software developers.
  2. To ensure you are using the desired software with the specific version, you might need to pay attention to the following situation about the order of module load.

Suppose you want to module load the software with two different versions.

>>> situation 1: module load gaussian_1; module load gaussian_2,

Then gaussian_2 would be the one actually used.

>>> situation 2: However, if you have previously did module load gaussian_2,

This means that gaussian_2 will always be “loaded” in your current terminal environment unless you log out.  In the current terminal session, if you do module load gaussian_1; module load gaussian_2,  since the gaussian_2 has previously been loaded, then the 2nd module load gaussian_2 will be ignored because the environment set-up by module software considers gaussian_2 to be loaded already. But because gaussian_1 wasn’t already loaded, it does get loaded at this point and would be the one actually used.


How to install user’s private software on user’s own home dir to use it for submitting a job.

UAHPC users can also consider the option of installing their own software by themselves, under their home dir or under purchased /grps2 space for shared usage in their linux group.  This give users more control over what specific features they want to use and some privacy of their software. The software installed under your home can be accessed by all compute nodes. So if you submit a job that use the software just installed under your home, the software can run just like the software under central installation.

To install your software under your home dir, you may need to change the installation path to your home dir since many software set up the default installation path to system dir, such as /usr/bin, which only system admin can have access to.  In this case, you may need to check the configure file, the Makefile for the default prefix as default installation path, change the prefix to some directory path that you have access to.

In the following example, for a typical installation workflow of C/C++ software (not for all of them, check the specific installation guide), every user can install their own version of a software on their home dir

by

cd ~

wget the_specific_http_link or git clone XXXXX (--recursive for git submodules)

#sometimes, it needs to run autogen.sh to automatically generate the system architecture information saved in the configure file

tar -xzf xxxxxxxxx.tar.gz
cd untar_gmap
./configure --help
.

# check this author’s customized configure file, the purpose is to generate Makefile, --prefix specified here will be feed into the Makefile

# the default prefix is /usr/local for most of them

./configure --prefix=/home/your_username/gmap_installed

#sometimes, you need to ./configure with other arguments that are available through the documentation in  ./configure --help

make

# this will build (compile and link) software using gcc most of the time, check if you need newer version of gcc (module load compilers/gcc/5.4.0), the #default gcc is 4.8.5

make install

# most of software has this install option depending on Makefile, this will usually, not always, copy /bin /include /lib into the #/home/your_username/gmap_installed you just specified

# check the Makefile, sometimes it allows a DESTDIR option to prepend more path in front of /home/your_username/gmap_installed as the final

# installation location

If you want to use files in /bin, /lib,/include, you need to add it into PATH , LD_LIBRARY_PATH (and possibly LIBRARY_PATH), CPATH, respectively. Most of the time, you need bin


Available Versions of Software

  • SLURM 18.08.7
  • Intel Cluster Studio (2 Seat License)
    • C++ Composer XE 12.0
    • Fortran Composer XE 12.0
    • Trace Analyzer and Collector 8.0 U1
    • Math Kernel Library 10.3
    • Integrated Performance Primitives 7.0 U1
    • Threading Building Blocks 3.0 U3
    • MPI Benchmarks 3.2.2
    • Debugger 12.0
  • PGI compilers 15.4 (2 seat license)
  • bcftools
  • bedtools
  • gmap
  • htslib
  • GCC with G77 (3.4.6)
  • GCC with C++ and Fortran (4.4.7-3, 4.3.5, 4.7.4, 4.8.4, and 5.4.0)
  • Perl 5.22.1
  • HDF5
  • openMPI 1.10.2 compiled with gcc 4.8.4 with SLURM support built-in
  • openMPI_intel 1.6.4
  • Python 2.6.6-36 (default), 2.7.11 [limited packages installed – no further expansion], 3.6.5 [actively adding packages]
    • biopython: 1.71
    • matplotlib: 2.2.2
    • mpi4py: 3.0.0
    • mpmath: 1.0.0
    • nanoPlot: 1.13.0
    • numpy: 1.14.2
    • pandas: 0.22.0
    • scipy: 1.0.1
    • sympy: 1.1.1
  • R 3.2.5, with Rmpi, doMPI, snow, plyr, data.table, reshape2, ggplot2, RSvgDevice, plotrix, RColorBrewer, Rmarkdown, qtl, onemap, and Bioconductor(Mfuzz, Rsamtools, DESeq, EdgeR, GenomicRanges,  GenomicFeatures, Biostrings, BSgenome, rtracklayer)
  • Octave 3.0.3
  • netcdf 4.3.2 build separately with Intel and GCC. Contains these libraries:
    • HDF5-1.8.9 parallel, szip 2.1, zlib 1.2.7, curl 7.27.0
  • udunits 2.1.24
  • For Genomics: Edena, bowtie (both in /share/apps/bin so no extra setup required)
  • Lammps 5Feb2018: (compiled against Intel with openmpi and GCC with openmpi)
  • PGI C/C++/Fortran 2-seat server license for specialized software compiles
  • NCL/NCARG graphics 6.0.2
  • Matlab 2016 (Engineering Only), 2014 (Math Only), 2015 (Physics only) and 2017 (MINT Only)
  • Ansys 18.2 with Fluent (Engineering Only)
    • Start Workbench on 1 core with “runwb2”
  • GSL (Gnu scientific library) 2.4
  • Tecplot
    • start on 1 core with “runtecplot”

How to use numpy, sys, scipy, cogent, and qiime

Enable your preferred version of python (see modules above).
type python to start the interpreter.
type import sys, numpy, scipy

To use Qiime and Cogent, you must run

module load python/python2/2.7shared
python
import sys, numpy, scipy, cogent, qiime

You may add other includes at this time.


Need other software installed?

Request it by logging in to the UAHPC Portal.