hpc-docs

Status of Major Software Installations

Graphical or Browser Software

Please consult the onBunya User Guide to see which software is installed and how to run. RStudio, Jupyter Notebooks and Labs, Gaussview, Mathematica and many CVL apps are available through onBunya.

Licensed Software

Mathematica

[AVAILABLE]

Access is restricted to UQ users
See onBunya User Guide

SPSS Statistics

[AVAILABLE]
Access is restrcited to UQ users

See onBunya User Guide

STATA

Installation in progress

Ansys

[AVAILABLE]

Access is restricted to approved UQ EAIT users only.
The Ansys dependencies have been built and deployed as a single mega-module.
The issue with the system coupling component now appears to have been resolved following a system configuration patch.

To load the dependencies and set the environment for using Ansys:

module load ansys/2023.1 or module load ansys/2024.1

Additional Notes

You must use the 2024.1 version to utilise the H100 GPUs (only relevant for operations that can utilise a GPU).
Using Fluent across multiple servers requires that you override the default Intel-MPI behaviour of the software, and use the OpenMPI instead. The OpenMPI module is automatically loaded when you load the Ansys module, but you must ensure that the fluent command is invoked to use OpenMPI (instead of the default IntelMPI).

Please submit a support request via email to rcc-support@uq.edu.au if you experience any issues with Ansys.

Gurobi

[AVAILABLE]

The issue with accessing the Gurobi product license servers on campus has been resolved.
RCC is working with the vendor and ITS to faciliate access and use of the campus license server.
Version 9.5.0 has been installed.
Version 10.0.1 has been installed and configured.
Awaiting a patch to the license server to be applied.
The licensing patch has been applied.
Version 11.0.3 has been deployed and is the (current) default version. ``` [uq_user@bunya2 ~]$ module purge [uq_user@bunya2 ~]$ module load gurobi/11.0.3

[uq_user@bunya2 ~]$ alias | grep gurobi alias check_gurobi_lic=’/sw/local/rocky8.6/noarch/rcc/software/Gurobi/gurobi950/linux64/bin/gurobi_cl –license’

[uq_user@bunya2 ~]$ check_gurobi_lic Set parameter TokenServer to value “uq-gurobi.research.dc.uq.edu.au” Set parameter LogFile to value “gurobi.log” Using license file /sw/local/rocky8.6/noarch/rcc/software/Gurobi/gurobi.lic

___
### MATLAB 

#### UQ Users

[**AVAILABLE BUT UPDATES BEING TESTED**]

* The version of MATLAB (2022a) that is available does not support some Simulink functionality.
* The Update 6 of R2022a is installed.

Please test the updated version using

**`module load matlab/R2022a6`**

#### Non-UQ 

[**UNAVAILABLE**]

* The access to license servers at home institutions needs to be configured.
* Once that is established, software installation can occur.
___
### Star-CCM+

[**AVAILABLE FOR TESTING**]

* Access to the UQ license server for this product has been established.
* Several dependencies have been deployed.
* Some command line options are essential. Please refer to `module help starccm+/17.02.008`

To test functionality please either of these 

module load star-ccm+/15.06.008 module load star-ccm+/17.02.008

Please submit a support request via email to rcc-support@uq.edu.au if you experience any issues while testing Star-CCM+.
___
## CUDA Related Modules

The GPU nodes will have different modules available and users are advised to log onto a GPU node via an interactive session to see which modules are avialable for the specific GPU architectures. For example, CUDA modules will not be availalbe on CPU nodes, but will be available on the CUDA GPU nodes.<br>
The command that will load the default version of the cuda drivers etc. on a GPU node will be <br>
`module load cuda`<br>
An alternative to using an interactive session on a CUDA node, would be to interrogate the `/sw` filesystem for the versions of cuda that are available.<br>
`ls /sw/auto/rocky8*/*/modules/all/cuda/`

## Full Module List

### CPU Nodes

You should run **`module -I -w 120 --show-hidden overview`** on Bunya to get the up-to-date list of installed software.

—————————————— abricate (1) fastp alsa-lib (1) fastqc anaconda3 (2) fasttree ansys-dependencies (1) fermi-lite ant (2) ffmpeg any2fasta (1) ffnvcodec archive-zip (1) fftw.mpi archspec (1) fftw at-spi2-atk (1) file at-spi2-core (1) filevercmp atk (1) flac augustus (2) flex autoconf (4) flexiblas automake (4) flye autotools (4) fontconfig bamtools (2) foss bbmap (2) freebayes bcftools (2) freetype bcl2fastq2 (1) fribidi beagle-lib (2) fsom beagle (1) gatk beautifulsoup (1) gc bedtools (2) gcc binutils (6) gcccore bio-db-hts (1) gcta bio-searchio-hmmer (2) gdal bioperl (2) gdk-pixbuf biopython (2) geos bison (4) gettext blast+ (2) gfbf blast (1) gffcompare blat (1) gffread blis (3) ghostscript boost.python (2) giflib boost (2) git bowtie (1) gitpython bowtie2 (2) glib-networking brotli (2) glib busco (2) glpk bwa (2) gmap-gsnap bzip2 (3) gmp c-ares (1) gnuplot cairo (2) gnutls canu (2) go capnproto (1) cd-hit (2) gompi cellranger-arc (1) googletest cellranger (1) gperf cereal (1) graphite2 checkm-database (1) groff checkm (2) gromacs clang (3) gsl cmake (5) gtdb-tk compress-raw-zlib (1) gtk2 coordgenlibs (2) gtk3 cp2k (2) guile cppy (2) gzip cunit (1) h5py curl (3) harfbuzz cutadapt (2) hdf db (2) hdf5 db_file (2) help2man dbd-mysql (1) hifiasm dbus (2) hipsycl deeptools (2) hisat2 dendropy (2) hmmer diamond (2) htseq double-conversion (2) htslib doxygen (2) humann easybuild (2) hwloc eigen (2) hypothesis elfutils (2) icu elpa (2) iimpi expat (2) imagemagick fastahack (1) imkl-fftw fastani (1) imkl /sw/auto/rocky8c/epyc3/modules/all —————————————— (1) impi (3) lz4 (2) pybigwig (2) (1) intel-compilers (3) lzo (1) pybind11 (2) (1) intel (3) m4 (5) pycoqc (1) (1) interproscan (1) maeparser (2) pysam (2) (1) intervaltree (1) mafft (1) python-isal (2) (1) intltool (2) make (3) python (7) (2) ipython (2) makeinfo (1) pyyaml (2) (3) isa-l (2) mako (2) qhull (2) (2) jags (1) mariadb (1) qiime2 (1) (1) jansson (1) mash (1) qt5 (2) (2) jasper (2) matplotlib (2) quantumespresso (2) (7) java (1) maxquant (1) quast (2) (3) jbigkit (2) megahit (2) r (3) (1) jellyfish (2) mesa (2) rapidjson (2) (2) jemalloc (3) meson (2) re2c (2) (3) jsoncpp (1) metaeuk (2) rjags (1) (1) judy (1) metis (2) ruby (2) (2) julia (1) miller (1) rust (2) (2) jupyter-server (1) miniconda3 (2) salmon (2) (1) jupyterlab (1) minimap2 (1) samtools (3) (1) kallisto (2) mono (1) scafacos (1) (1) kim-api (1) motif (1) scalapack (3) (3) kraken2 (2) mpfr (2) scikit-build (1) (3) kronatools (1) mrbayes (2) scipy-bundle (2) (1) lame (2) mrtrix (1) sdl2 (1) (2) lammps (1) multichoose (1) sepp (2) (1) lapack (1) multiqc (2) seqlib (1) (2) libaio (1) mummer (2) seqtk (2) (4) libarchive (3) nasm (2) smithwaterman (1) (1) libcerf (2) ncbi-vdb (2) snakemake (2) (1) libdeflate (1) ncurses (6) snappy (2) (1) libdrm (2) netcdf (2) spaceranger (1) (2) libepoxy (1) nettle (2) spades (2) (1) libev (1) networkx (2) spectra (1) (2) libevent (3) nextflow (2) sqlite (3) (2) libfabric (3) nghttp2 (1) sra-toolkit (1) (1) libffi (3) nghttp3 (1) ssw (1) (2) libgd (2) ngs (1) star (2) (2) libgeotiff (2) ngtcp2 (1) stringtie (1) (1) libgit2 (2) ninja (2) suitesparse (2) (2) libglu (4) nlohmann_json (1) swig (2) (2) libglvnd (2) nlopt (2) szip (2) (1) libiconv (2) nodejs (2) tabixpp (1) (3) libidn (2) nspr (2) tbb (2) gobject-introspection (2) libidn2 (2) nss (2) tbl2asn (2) (3) libint (2) numactl (3) tcl (3) (1) libjpeg-turbo (2) openbabel (2) tk (2) (2) libnsl (1) openblas (3) tkinter (2) (1) libogg (2) openjpeg (1) tqdm (1) (2) libopus (1) openmpi (3) trimmomatic (1) (1) libpciaccess (3) openpgm (2) trinity (1) (2) libpng (2) openssl (1) ucc (2) (1) libpsl (1) p11-kit (1) ucx (3) (1) libreadline (3) pandoc (1) udunits (2) (1) libsndfile (2) pango (2) unzip (3) (1) libsodium (2) parallel (2) util-linux (2) (2) libsoup (1) pcre (2) vcflib (1) (1) libtasn1 (1) pcre2 (2) vcftools (2) (2) libtiff (2) perl (5) vep (1) (2) libtirpc (2) picard (1) voro++ (1) (2) libtool (4) pigz (2) wget (2) (3) libunistring (1) pillow (2) x11 (2) (1) libunwind (2) pixman (2) x264 (1) (1) libvorbis (2) pkg-config (2) x265 (1) (2) libwebp (1) pkgconf (3) xml-libxml (2) (2) libxc (2) pkgconfig (1) xorg-macros (3) (1) libxml2 (5) plink (1) xvfb (2) (2) libxslt (1) plotly.py (2) xxd (2) (1) libxsmm (2) plumed (2) xz (3) (3) libyaml (2) pmix (3) yasm (1) (2) littlecms (2) pocl (1) z3 (2) (2) llvm (2) popt (1) zeromq (2) (3) lmdb (3) pplacer (1) zip (1) (2) lpsolve (2) prodigal (2) zlib (6) (2) lua (2) proj (2) zstd (2) (3) lxml (1) prokka (2)

—————————————— /sw/local/rocky8/epyc3/rcc/modules —————————————— bolt-lmm (1) eagleimp (1) lisflood-fp (3) vasp (4)

—————————————– /sw/local/rocky8/noarch/rcc/modules —————————————— ansys (1) crisflash (1) huygens (2) mathematica (1) qctool (1) star-ccm+ (2) asreml-as (1) gaussian (1) ilastik (1) matlab (1) relion (3) wombat (1) basespace (1) gurobi (2) localcolabfold (1) orca (1) rstudio (1)

—————————————– /sw/local/rocky8/noarch/qcif/modules —————————————– 3d-dna (1) f5c (1) macs2 (1) pear (1) shpc (1) biobakery_workflows (1) fastool (1) maker (1) qapa (1) singlem (1) blast (1) gcta (1) medaka (1) qiime2-amplicon (1) snap (1) braker3 (1) gff3sort (1) mikado (1) qiime2-shotgun (1) sortmerna (1) cellbender (1) gmap (1) mira (1) racon (1) sqanti3 (1) celseq2 (1) gtdbtk (1) mixer (1) ratatosk (1) sra-tools (1) circlator (1) harvesttools (1) mlst (1) raxml (1) srst2 (1) dadi (1) hisat2 (1) mtag (1) regenie (1) star (1) dfam (1) ipyrad (2) nanocompore (1) repeatmasker (1) suppa (1) diamond (1) iqtree (1) nanopolish (1) repeatmodeler (1) transdecoder (1) dram (1) isoseq3 (1) nextpolish (1) rmats-turbo (1) trinity (1) drep (1) juicer (1) nextpolish2 (1) rsem (1) trinotate (1) edirect (1) kallisto (1) ont-fast5-api (1) salsa2 (1) unicycler (1) enrichm (1) kofamscan (1) parsnp (1) scvelo (1) xpore (1) exonerate (1) ldsc (1) pb-assembly (1) shovill (1)

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Software Survey Requests

In late 2022, we asked users to participate in the software survey to ascertain which tools were required on Bunya. The following table summarises the status of those requests.

|Name|Requests|Responsible|Completed| |:—|:——:|:–:|:——–| |Anaconda|96|RCC|YES| |R|95|RCC|YES| |GNU compilers (gcc and gfortran)|74|RCC|YES| |bedtools|56|RCC|YES| |bamtools|53|RCC|YES| |fastqc|53|RCC|YES| |samtools|50|RCC|YES| |Singularity|49|RCC|YES| |bcftools|47|RCC|YES| |OpenMPI (Intel and/or GNU)|46|RCC|YES| |blast2|45|RCC|YES| |bowtie2|43|RCC|YES| |Matlab|41|RCC|YES| |trimmomatic|36|RCC|YES| |Intel Compilers (icc and ifort)|29|RCC|YES| |curl|29|RCC|YES| |gatk4|27|RCC|YES| |BLAS|26|RCC|YES| |IntelMPI|26|RCC|YES| |gcta|25|RCC|YES| |LAPACK|24|RCC|YES| |cutadapt|24|RCC|YES| |STAR|24|QCIF|YES| |fastp|23|RCC|YES| |hisat2|22|QCIF|YES| |hmmer|22|RCC|YES| |Julia|20|RCC|YES| |Gaussian|20|RCC|YES| |busco|20|RCC|YES| |picard|20|RCC|YES| |trinity|20|QCIF/RCC|YES| |beagle|19|RCC|YES| |htseq|18|RCC|YES| |seqtk|18|RCC|YES| |sra-tools|18|QCIF|YES| |augustus|17|RCC|YES| |cellRanger|16|RCC|YES| |multiQC|16|RCC|YES| |OpenJDK|15|RCC|YES| |canu|15|RCC|YES| |jellyfish|15|RCC|YES| |RepeatMasker|15|QCIF|YES| |deeptools|14|RCC|YES| |Gromacs|13|RCC|YES| |cd-hit|13|RCC|YES| |guppy|13|User|YES … User must install personally licensed copy| |qiime2|13|RCC|YES| |transdecoder|13|QCIF|YES| |Orca|12|RCC|| |LAMMPS|12|RCC|YES| |gffcompare|12|RCC|YES| |hclust2|12|QCIF|| |kallisto|12|QCIF|YES| |pacbio|12|RCC/QCIF|| |snakemake|12|RCC|YES| |flye|11|RCC|YES| |interproscan|11|RCC|YES| |macs2|11|RCC|| |spades|11|RCC |YES| |trinotate|11|QCIF|YES| |VASP|10|RCC|YES| |diamond|10|RCC|YES| |gmap|10|QCIF|| |prokka|10|RCC|Has been reinstalled due to a dependency issue| |braker2|9|QCIF|YES but has issues ?| |checkm|9|RCC|YES| |htslib|9|RCC|YES| |kraken2|9|QCIF|YES| |mafft|9|RCC|YES| |maker|9|QCIF|| |nextflow|9|RCC|YES| |quast|9|RCC|YES| |pb-assembly|8|QCIF|| |repeatmodeler|8|QCIF|| |plink (inc plink 1.9)|8|RCC|YES| |exonerate|7|QCIF|| |iqtree|7|QCIF|| |VEP|7|RCC|| |ATLAS|6|RCC|| |Nimrod|6|RCC|| |krona|6|RCC|YES| |mauve|6|RCC|| |NextPolish|6|QCIF|| |SNAP|6|QCIF|| |StarCCM|6|RCC|NEARLY| |circlator|5|QCIF|| |isoseq3|5|QCIF|| |3d-dna|4|QCIF|YES| |edirect|4|QCIF|| |raxml|4|RCC|| |cp2k|4|RCC|YES| |eilmer4|4|User|| |plink2|4|RCC|YES| |neurodesk|4|User|| |abricate|3|RCC|YES| |celseq2|3|QCIF|| |dfam|3|QCIF|| |metaphlan|3|QCIF|YES| |mlst|3|QCIF|YES| |salsa|3|QCIF|YES| |spaceRanger|3|QCIF|| |pytorch/tensorflow/cuda|3|RCC|| |gtdb-tk|3|RCC|YES| |juicer|2|QCIF|| |maxquant|2|RCC |YES| |mira|2|QCIF|| |pear|2|QCIF|| |cmake|2|RCC|YES| |ansys|2|RCC|YES| |gurobi|2|RCC|YES| |AOCC|1||| |besst|1||| |dammit|1||| |NextDenovo|1||| |picrust2|1||| |rcorrector|1||| |shovill|1|QCIF|YES| |go (golang)|1|RCC|YES| |intel mkl|1|RCC|YES| |parallel|1|RCC|YES| |vcftools|1|RCC|YES| |mikado|0|QCIF|| |proovread|0|QCIF|| |ratatosk|0|QCIF|| |sortmerna|0|QCIF|| |humann|0|RCC|YES| |srst2|0|QCIF|| |rust|0|RCC|YES| ___

Post Software Survey Requests

These are requests that were not included in the software survey and have been requested since that time. They are necessarily lower priority.

Name	Requested	Ready?	Note
DIA-NN	202303	NO	Suitable download found. User is testing
Vienna RNA	202303	NO	Installation via EB mechanism yet to be done after initial attempts failed.
Mr Bayes	202303	YES	Installation by modified EB script mechanism successful. Submitting for deployment. Deployed!
VBZ Compression Tool		NO
FoldX, Rosetta and RFdiffusion		NO
LESYMAP	2023-06-01	YES	HackyHour. Identified suitable docker image to use with Apptainer on Bunya.
REEF3D		NO	Was installed on Tinaroo previously. User to install with RCC guidance.