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 While our software is consistent and stable, it is no longer current.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	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
Intel Compilers	11.1, 2012	[56]	Programming, Compilers
Iprscan	4.8	[57]	BIology, Genomics
Kent	20120524	[58]	Biology, NGS
Kmer	1934	[59]	Biology, NGS
LAMMPS	25Jul12	[60]	Simulation
Last	193, 247	[61]	Biology, Sequence alignment
Lastz	1.02.00	[62]	Biology, NGS
MACS	1.4.2	[63]	Biology, ChIP-Seq
mafft	6.903	[64]	Biology, Multiple sequence alignment
Maker	2.10, 2.25b	[65]	Biology, Annotation, Genomics
Maq	0.7.1	[66]	Biology, NGS
Matlab	2012a	[67]	Math, Simulation, Programming
MATS	2.1.0	[68]	BIology, NGS
MCNP	5, 6b2	[69]	Physics
MCNPX	2.7.0, 2.7.0-i8	[70]	Physics
Meme	4.8.1	[71]	Biology, Motifs, Sequence analysis
MetaGeneMark	2012.04	[72]	Biology, Genomics
Midnight Commander	4.6.1	[73]	Tools, Utilities
Migrate-n	3.3.0	[74]	Biology, Population
MISO	0.4.4	[75]	Biology, NGS
MOLDEN	5.0	[76]	Molecular, electronic structure
mosaik	2.1.33	[77]	Biology,NGS
MrBayes	3.2.1	[78]	Biology, Phylogenetics
MUMmer	3.23	[79]	Biology, Genomics
MUSCLE	3.8.31	[80]	Biology, Genomics
NAMD	2.9	[81]	Simulation, Chemistry, Biology
NETCDF	in process	[82]	Data exchange, Tools
Newbler	2.6, 2.7	[83]	Biology, NGS
Novoalign	2.08.02	[84]	Biology, NGS
Parflow	v615	[85]	Ecology, Modeling
PASA	1.5, r20120625	[86]	Biology, Genomics
PeakSplitter	1.0	[87]	Biology, Chip-Seq
Perl	5.16.0	[88]	Programming, Language
PerM	0.4.0	[89]	Biology, NGS
Picard	1.69, 1.72	[90]	Biology, NGS
Proteinortho	4.26	[91]	Biology, Genomics
python	2.6.8, 2.7.3	[92]	Programming, scripting, language
QIIME	1.5.0	[93]	Biology, Ecology
R	2.15.0, 2.15.0-mpi, Rmpi/2.15.1	[94]	Statistics, Programming
R8S	1.71	[95]	Biology, Evolution
RAxML	7.3.2.0705	[96]	Biology, Phylogenetics
RepeatMasker	3.3.0	[97]	Biology, Genomics
Reptile	1.1	[98]	Biology, NGS, error correction
riboPicker	0.4.3	[99]	Biology, Sequence
samtools	0.1.16, 0.1.18	[100]	Biology, NGS
SAS	9.3	[101]	Statistics, Graphing
Schrodinger	2012	[102]	Simulation, chemistry
SeqPrep	0.5	[103]	Biology, NGS
SEQuel	1.0.1	[104]	Biology, NGS
Sickle	1.200	[105]	Biology, NGS, quality filter
Siesta	3.0b	[106]	Simulation, Physics, Ab Initio
SIFT	4.0.3b	[107]	Biology, Genomics
Silo	4.7	[108]	Library, Data
Snap	20100728	[109]	Biology, Genomics
SOAPdenovo	1.05	[110]	Biology, NGS
SOAPdenovo-Trans	1.01	[111]	Biology, NGS
SpliceTrap	0.90.5	[112]	Biology, NGS, RNA-Seq
Sputnik	1.0	[113]	Biology, Genomics
SRA	2.1.10	[114]]	biology, NGS
Stacks	0.9995	[115]	Biology, Genomics, NGS
Structure	2.3.3	[116]	Biology, Population
tgicl	2.1	[117]	Biology, sequencing, clustering
Tophat	1.4.1, 2.0.1	[118]	Biology, NGS
TRF	4.04	[119]	Biology, Genomics
Trinity	r20120518, r20120608, r20120905	[120]	Biology, RNA-Seq
Twinscan	4.1.2	[121]	Biology, Genomics
usearch	5.2.32	[122]	Biology, Sequence analysis
VASP	4.6.34, 5.2.12	[123]	Quantum Chemistry, Ab Initio
VCFtools	0.1.9	[124]	Biology, SNPs
velvet	1.2.06	[125]	Biology, NGS
vmd	1.9.1	[126]	Biology, Visualization
WebLogo	3.3	[127]	Biology, Genomics
WDSSII		[128]	Meteorology
wgs	7.0.1.22	[129]	Biology, NGS
wublast	2.0	[130]	Biology, Sequence Alignment

To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.