Installed Software
Cluster Software Upgrade (Update 09/07/12)
The transition from RHEL5/CentOS5 to RHEL6 is, for all practical purposes, complete. The "rhel5" queue has been stopped and is no longer accepting jobs and will be removed once the few remaining jobs complete. The interactive nodes test01, test04, and test05 will be upgraded by the end of the day on Friday, September 7 (today).
A majority of applications have been recompiled or otherwise re-installed under RHEL6. There are still a few lightly used applications remaining that we should be able to finish next week. If the software you need is not available and you have not already submitted a support request to have it installed, you may do so at http://support.hpc.ufl.edu.
Cluster Software Upgrade
One of our goals is to provide our users with a consistent, stable, and current software environment. The compute, login, and interactive nodes within the HPC Center have been running CentOS EL 5 (with updates) for over four years. This is a long time in the open source software world. While our software is consistent and stable, it is no longer current. Thus, after more than four months of testing, we have begun the process of upgrading all of our servers to RedHat Enterprise Linux 6.3. The migration plan is outlined below.
1. Machines will be upgraded slowly over the next six weeks with a goal of having all servers running RHEL6 by the end of August.
2. Because this is a major upgrade, most applications - and *all* MPI-based applications - will have to be recompiled to work under RHEL6. We have already built and installed many packages for the new platform. However, we do not wish to spend time re-installing applications that are out-dated and no longer used. Therefore, we will not necessarily reinstall all of the existing EL5 applications. You can see which applications have been installed for RHEL6 on our installed software wiki page (http://wiki.hpc.ufl.edu/index.php/Installed_Software).
If you do not see the software you need, don't panic. File a support request at https://support.hpc.ufl.edu and ask us to install your application under EL6. We will do so as soon as we can. In the meantime, you may continue to run using the EL5 version.
3. If the software you need is already available under EL6, you may submit jobs to servers running EL6 via the "rhel6" queue or the "parallel" queue. Note that the parallel queue is restricted to specific groups and is intended for jobs using 64 processors or more.
4. By the end of July, we should reach a point where there are more servers running EL6 than EL5. When we reach that point, we will reconfigure the default queue so that jobs will go to EL6 servers and the "rhel6" queue will be replaced with a "rhel5" queue. Those users wishing to run their older EL5-based applications will need to submit directly to the EL5 queue. We will announce this change again before it takes place.
5. There is a RHEL6 test node available that can be reached via ssh from the login servers (submit1/submit2). It is aptly named, "rhel6". This is the machine you should use if you want to to rebuild and test any of your own applications.
Significant Changes:
1. Switching to the "module" system for configuring software execution environments. See http://wiki.hpc.ufl.edu/index.php/Modules for more information
2. New versions of MPI. All MPI applications will have to be rebuilt (compiled and linked). Please submit a help request if you would like us to rebuild your applications under RHEL6 or help you do it.
3. New versions of the Intel and Gnu compiler suites.
Table
The following is a list of the installed software at the UF HPC Center.
Last updated 2012-09-07.
Note: Click on the icons to the right of the column headings to sort the table.
| Name | Version [1] | Website | Category |
|---|---|---|---|
| Abyss | 1.3.3, 1.3.4, 1.3.4-mpi | [1] | Biology, NGS |
| ALLPATHS-LG | 42316 | [2] | Biology, NGS |
| Amber | 11, 12 | [3] | Simulation, chemistry |
| Augustus | 2.6 | [4] | Biology, NGS |
| Bamtools | 2.1.1 | [5] | Biology, NGS |
| BamUtil | 1.0.2 | [6] | Biology, NGS |
| BayesRate | 1.3.43 | [7] | Biology, Phylogenetics |
| BEAST | 1.7.2 | [8] | Biology, Phylogenetics |
| BEDTools | 2.16.2 | [9] | Biology, NGS |
| BFAST | 0.7.0 | [10] | Biology, NGS |
| Bismark | 0.7.4 | [11] | Biology, Methylation, NGS |
| Bioconductor | Latest | [12] | Biology, R, Statistics |
| BioPerl | 1.006901 | [13] | Biology, Perl |
| BioPython | 1.59 | [14] | Biology, Python |
| NCBI BLAST | 2.2.26 (+ and legacy) | [15] | Biology, Sequence alignment |
| Blast2go | 2.5.0-20120705 | [16] | Biology, Annotation |
| BLAT | 20120524 | [17] | Biology, Sequence alignment |
| Boost | 1.49.0 | [18] | C++, Library |
| Bwa | 0.6.1 | [19] | Biology, NGS |
| Bowtie | 0.12.8, 2.0.0b6 | [20] | Biology, NGS |
| CAP3 | 20120705 | [21] | Biology, sequence assembly |
| CD-HIT | 4.6 | [22] | Biology, Genomics |
| CHARMM | 36a3 | [23] | Simulation, Chemistry |
| CisGenome | 2.0 | [24] | Biology, Genomics, Peak Calling |
| ClustalW | 2.1 | [25] | Biology, Genomics |
| CMake | 2.8.8 | [26] | Programming |
| Consed | 23.0 | [27] | Biology, Genomics |
| CUDA | 4.2 | [28] | Programming, Graphics |
| Cufflinks | 1.3.0, 2.0.0, 2.0.2 | [29] | Biology, NGS |
| Cutadapt | 1.1 | [30] | Biology, NGS |
| DIYABC | many | [31] | Biology, Genomics |
| Dlpoly | 4.03.4 | [32] | Simulation, Biology, Chemistry |
| DOCK | 6.5 | [33] | Chemistry, ligand binding prediction |
| emboss | 6.5.7 | [34] | Biology, multi-tool suite |
| ESPRESSO | 5.0.1 | [35] | Modeling, Physics |
| Exonerate | 2.2.0 | [36] | Biology, Genomics |
| FAR | 2.15 | [37] | Biology, Genomics |
| FASTA | 34.26.5 | [38] | Biology, Genomics |
| FastQC | 0.9.6, 0.10.1 | [39] | Biology, NGS |
| Fastx_toolkit | 0.0.13.2 | [40] | Biology, NGS |
| FreeBayes | 0.9.6 | [41] | Biology |
| Garli | 2.0 | [42] | Biology, Phylogenetics |
| GATK | 1.6.9 | [43] | Biology, NGS |
| Gaussian | E01, G03, G09-A.02, G09-C.01 | [44] | Modeling, Computational Chemistry |
| GeneMark | 2012.04 | [45] | Biology, Genomics, Metagenomics |
| Genewise | 2.2.0 | [46] | Biology, Genomics, Annotation |
| GMAP | 20070928, 20120712 | [47] | Biology, Genomics |
| GnuPlot | 4.6.0 | [48] | Graphics, Plotting, Programming |
| GRACE | 5.1.22 | [49] | Graphics, plotting, 2D |
| HaMStR | v8b | [50] | Biology, Genomics |
| HDF5 | 1.8.9 | [51] | Library, Data |
| HMMER3 | 3.0 | [52] | Biology, Genomics |
| HTSeq | 0.5.3p3 | [53] | Biology, NGS |
| HyPhy | 2.1.2.28 | [54] | Biology, Phylogenetics |
| Hypre | 2.8.0b | [55] | Library, Math, Physics |
| Iprscan | 4.8 | [56] | BIology, Genomics |
| Kent | 20120524 | [57] | Biology, NGS |
| Kmer | 1934 | [58] | Biology, NGS |
| LAMMPS | 25Jul12 | [59] | Simulation |
| Last | 193, 247 | [60] | Biology, Sequence alignment |
| Lastz | 1.02.00 | [61] | Biology, NGS |
| MACS | 1.4.2 | [62] | Biology, ChIP-Seq |
| mafft | 6.903 | [63] | Biology, Multiple sequence alignment |
| Maker | 2.10, 2.25b | [64] | Biology, Annotation, Genomics |
| Maq | 0.7.1 | [65] | Biology, NGS |
| Matlab | 2012a | [66] | Math, Simulation, Programming |
| MATS | 2.1.0 | [67] | BIology, NGS |
| MCNP | 5, 6b2 | [68] | Physics |
| MCNPX | 2.7.0, 2.7.0-i8 | [69] | Physics |
| Meme | 4.8.1 | [70] | Biology, Motifs, Sequence analysis |
| MetaGeneMark | 2012.04 | [71] | Biology, Genomics |
| Midnight Commander | 4.6.1 | [72] | Tools, Utilities |
| Migrate-n | 3.3.0 | [73] | Biology, Population |
| MISO | 0.4.4 | [74] | Biology, NGS |
| MOLDEN | 5.0 | [75] | Molecular, electronic structure |
| mosaik | 2.1.33 | [76] | Biology,NGS |
| MrBayes | 3.2.1 | [77] | Biology, Phylogenetics |
| MUMmer | 3.23 | [78] | Biology, Genomics |
| MUSCLE | 3.8.31 | [79] | Biology, Genomics |
| NAMD | 2.9 | [80] | Simulation, Chemistry, Biology |
| netcdf | in process | [81] | Data exchange, Tools |
| Newbler | 2.6, 2.7 | [82] | Biology, NGS |
| Novoalign | 2.08.02 | [83] | Biology, NGS |
| Parflow | v615 | [84] | Ecology, Modeling |
| PASA | 1.5, r20120625 | [85] | Biology, Genomics |
| PeakSplitter | 1.0 | [86] | Biology, Chip-Seq |
| Perl | 5.16.0 | [87] | Programming, Language |
| PerM | 0.4.0 | [88] | Biology, NGS |
| Picard | 1.69, 1.72 | [89] | Biology, NGS |
| Proteinortho | 4.26 | [90] | Biology, Genomics |
| python | 2.6.8, 2.7.3 | [91] | Programming, scripting, language |
| QIIME | 1.5.0 | [92] | Biology, Ecology |
| R | 2.15.0, 2.15.0-mpi, Rmpi/2.15.1 | [93] | Statistics, Programming |
| R8S | 1.71 | [94] | Biology, Evolution |
| RAxML | 7.3.2.0705 | [95] | Biology, Phylogenetics |
| RepeatMasker | 3.3.0 | [96] | Biology, Genomics |
| Reptile | 1.1 | [97] | Biology, NGS, error correction |
| riboPicker | 0.4.3 | [98] | Biology, Sequence |
| samtools | 0.1.16, 0.1.18 | [99] | Biology, NGS |
| SAS | 9.3 | [100] | Statistics, Graphing |
| Schrodinger | 2012 | [101] | Simulation, chemistry |
| SeqPrep | 0.5 | [102] | Biology, NGS |
| SEQuel | 1.0.1 | [103] | Biology, NGS |
| Sickle | 1.200 | [104] | Biology, NGS, quality filter |
| Siesta | 3.0b | [105] | Simulation, Physics, Ab Initio |
| SIFT | 4.0.3b | [106] | Biology, Genomics |
| Silo | 4.7 | [107] | Library, Data |
| Snap | 20100728 | [108] | Biology, Genomics |
| SOAPdenovo | 1.05 | [109] | Biology, NGS |
| SOAPdenovo-Trans | 1.01 | [110] | Biology, NGS |
| SpliceTrap | 0.90.5 | [111] | Biology, NGS, RNA-Seq |
| Sputnik | 1.0 | [112] | Biology, Genomics |
| SRA | 2.1.10 | [113]] | biology, NGS |
| Stacks | 0.9995 | [114] | Biology, Genomics, NGS |
| Structure | 2.3.3 | [115] | Biology, Population |
| tgicl | 2.1 | [116] | Biology, sequencing, clustering |
| Tophat | 1.4.1, 2.0.1 | [117] | Biology, NGS |
| TRF | 4.04 | [118] | Biology, Genomics |
| Trinity | r20120518, r20120608, r20120905 | [119] | Biology, RNA-Seq |
| Twinscan | 4.1.2 | [120] | Biology, Genomics |
| usearch | 5.2.32 | [121] | Biology, Sequence analysis |
| VASP | 4.6.34, 5.2.12 | [122] | Quantum Chemistry, Ab Initio |
| VCFtools | 0.1.9 | [123] | Biology, SNPs |
| velvet | 1.2.06 | [124] | Biology, NGS |
| WebLogo | 3.3 | [125] | Biology, Genomics |
| wgs | 7.0.1.22 | [126] | Biology, NGS |
| wublast | 2.0 | [127] | Biology, Sequence Alignment |
- ↑ Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.
To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.