Installed Software

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 While our software is consistent and stable, it is no longer current.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 2012-08-07.

Note: Click on the icons to the right of the column headings to sort the table.

Name	Version	Website	Category	EL5	EL6
Abaqus	6.6-1, 6.9-2	[1]	Simulation	X
Abyss	1.3.1, 1.3.4	[2]	Biology, NGS	X	X
ADMB	9.1, 10.0, 10.1	[3]	Modeling, math	X
ALLPATHS-LG	39099, 40122, 41655, 42316 (EL6)	[4]	Biology, NGS	X	X
Amber	10,11.old, 11, 12	[5]	Simulation, chemistry	X	X
Amos	3.0.0	[6]	Biology, Genomics	X
ANNOVAR	20120308	[7]	Biology, Genomics	X
Ansys	9.0, 10.0	[8]	Simulation, Engineering	X
antlr	2.7.7, 3.1.3	[9]	Linguistics, Parser	X
arachne	37618	[10]	Biology, Genomics	X
Augustus	2.6	[11]	Biology, NGS	X	X
Bamtools	2.1.0	[12]	Biology, NGS	X	X
BamUtil	1.0.2	[13]	Biology, NGS	X
BayesPhylogenies	2.0	[14]	Biology, Phylogenetics	X
BayesRate	1.3.43	[15]	Biology, Phylogenetics	X	X
beast	1.6.2, 1.7.0, 1.7.1, 1.7.2 (EL6)	[16]	Biology, Phylogenetics	X
BEDTools	2.16.2	[17]	Biology, NGS	X	X
BFAST	0.7.0	[18]	Biology, NGS	X	X
Bismark	0.7.4	[19]	Biology, Methylation, NGS	X	X
Bioconductor	2011-11-16	[20]	Biology, R, Statistics	X
BioPerl	1.006901	[21]	Biology, Perl	X	X
Biopython	1.59	[22]	Biology, Python	X	X
bioscope	1.0.1, 1.2.1	[23]	Biology, NGS	X
Blast	2.2.24, 2.2.25, 2.2.26	[24]	Biology, Sequence alignment	X	X
Blast2go	2.5.0-20120220, 2.5.0-20120705 (EL6)	[25]	Biology, Annotation	X	X
BLAT	34	[26]	Biology, Sequence alignment	X	X
Boost	1.38.0, 1.46.1, 1.48.0, 1.49.0	[27]	C++, Library	X	X
bwa	0.5.9, 0.5.10, 0.6.0 (default)	[28]	Biology, NGS	X	X
Bowtie	0.12.8 (default), 2.0.0-beta5	[29]	Biology, NGS	X	X
BreakDancer	1.1	[30]	Biology, NGS, Genomics	X
CAP3	20071015	[31]	Biology, sequence assembly	X	X
CASAVA	1.8.2	[32]	Biology, NGS	X
CD-HIT	4.5.7, 4.6 (EL6)	[33]	Biology, Genomics	X	X
CEGMA	2.4.010312	[34]	Biology, Genomics, Annotation	X
CGATools	1.5.0.31	[35]	Biology, Genomics	X
Charmm	35b2	[36]	Simulation, Chemistry	X
Circuit	3.5.1, 3.5.7	[37]	GIS	X
CisGenome	2.0	[38]	Biology, Genomics, Peak Calling	X	X
ClustalW	2.1	[39]	Biology, Genomics	X	X
CMake	2.8.5	[40]	Programming	X	X
CNV-seq	07.15.11	[41]	Biology, NGS	X
CNVnator	0.2.5	[42]	Biology, NGS	X
Consed	23.0	[43]	Biology, Genomics	X	X
CPMD	3.11.1	[44]	Simulation, Chemistry	X
Cufflinks	1.0.3, 1.1.0, 1.3.0, 2.0.2	[45]	Biology, NGS	X	X
Cutadapt	1.1	[46]	Biology, NGS	X	X
dar	2.3.9	[47]	Backup	X
deFuse	0.4.3	[48]	Biology, RNA-seq	X
Desmond	2.4.2.1	[49]	Simulation, Biology, Chemistry	X
Dindel	1.01	[50]	Biology, NGS, Genomics	X
dlpoly	3.0.9	[51]	Simulation, Biology, Chemistry	X
dock	6.3, 6.4, 6.5	[52]	Chemistry, ligand binding prediction	X
emacs	21.4.1, 23.4.1	[53]	The Emacs editor	X
EMAN2	2.04	[54]	Biology, image processing	X
emboss	6.4.0	[55]	Biology, multi-tool suite	X
espresso	3.0, 3.2.2, 4.0.4, 5.0	[56]	Modeling, Physics	X
Exonerate	2.2	[57]	Biology, Genomics	X	X
FAR	2.15	[58]	Biology, Genomics	X	X
FASTA	34.26.5	[59]	Biology, Genomics	X	X
FastQC	0.9.6, 0.10.0	[60]	Biology, NGS	X	X
fastx_toolkit	0.0.13.1	[61]	Biology, NGS	X	X
fftw	2.1.5, 3.1.2	[62]	Math, Library, C++	X
fluent	6.3.26	[63]	Simulation	X
FragGeneScan	1.16	[64]	Biology, NGS	X
FreeBayes	0.9.4	[65]	Biology	X	X
gadget	2.0.4, 2.0.5	[66]	Software Development	X
gamess	11-Aug11	[67]	Quantum Chemistry	X
garli	2.0	[68]	Biology, Phylogenetics	X
GATK	1.4.30	[69]	Biology, NGS	X
gulp	4.0.3	[70]	Modeling/simulation, Chemistry	X
gaussian	E01, G03, G09-A.02, G09-C.01	[71]	Modeling, Computational Chemistry	X	X
Geneid	1.4	[72]	Biology, Genomics, Annotation	X
GeneMark	2012.04	[73]	Biology, Genomics, Metagenomics	X	X
Genewise	2.2.3	[74]	Biology, Genomics, Annotation	X
GMAP	20070928, 20120712	[75]	Biology, Genomics	X	X
GnuPlot	4.4.3, 4.6.0 (EL6)	[76]	Graphics, Plotting, Programming	X	X
Grace	5.1.22	[77]	Graphics, plotting, 2D	X
Gromacs	4.0.4, 4.0.7	[78]	Physics, Modeling	X
HDF5	1.8.7, 1.8.8	[79]	Library, Data	X
HMMER3	3.0	[80]	Biology, Genomics	X
HTSeq	0.5.3p3	[81]	Biology, NGS	X
HugeSeq	1.0.1	[82]	Biology, NGS, Genomics	X
HyPhy	2.002..., 2.1.2.28 (EL6)	[83]	Biology, Phylogenetics	X	X
hypre	2.8.0	[84]	Library, Math, Physics	X	X
IM and IMa	2009.12.17	[85]	Biology, Population	X
IMa2	8.26.11	[86]	Biology, Population	X
Inelastica	1.1 (python/2.7.2)	[87]	Quantum Chemistry	X
IE3D	15.1	[88]	Simulation, Design	X
Iprscan	4.8	[89]	BIology, Genomics		X
JDK	1.6.0_12, 1.7.0	[90]	Java Development Kit	X
Kent	20120423	[91]	Biology, NGS	X	X
Khmer	20120321	[92]	Biology, NGS, Utilities	X
Kmer	r1909	[93]	Biology, NGS, genome alignment	X	X
LAMMPS	17-Sept11	[94]	Simulation	X	X (25Jul12)
Last	193	[95]	Biology, Sequence alignment	X
libxc	1.1.0	[96]	Math, funtionals	X
MACS	1.4.1, 1.4.2 (EL6)	[97]	Biology, ChIP-Seq	X	X
madness	1769	[98]	Math, DIff. Equation solving	X
mafft	6.859	[99]	Biology, Multiple sequence alignment	X	X
Maker	2.10	[100]	Biology, Annotation, Genomics	X	X
MapSplice	1.15.2	[101]	Biology, Genomics	X
Maq	0.7.1	[102]	Biology, NGS	X	X
Matlab	2009b	[103]	Math, Simulation, Programming	X
MATS	2.1.0	[104]	BIology, NGS	X
Mauve	2.3.1	[105]	Biology, Multiple genome alignments	X
MCL	11-335	[106]	Biology, Genomics, Clustering	X
MCNP	5, 6beta2	[107]	Physics		X
MCNPX	2.7.0	[108]	Physics		X
meme	3.0.13, 4.3.0	[109]	Biology, Motifs, Sequence analysis	X
MetaPhyler	1.13	[110]	Biology, Metagenomics	X
metis	4.0	[111]	Math, Graph partitioning	X
Migrate-n	3.2.16	[112]	Biology, Population	X
mira	3.2.0, 3.4.0.1	[113]	Biology, NGS	X
MISO	0.4.4	[114]	Biology, NGS		X
mosaik	1.1.0021	[115]	Biology,NGS	X	X
MPIBlast	1.6.0	[116]	Biology, Sequence alignment	X
MrBayes	3.1.2,3.2.1	[117]	Biology, Phylogenetics	X
MUMmer	3.22, 3.23	[118]	Biology, Genomics	X	X
MUSCLE	3.8.31	[119]	Biology, Genomics	X	X
NAMD	2.7b2	[120]	Simulation, Chemistry, Biology	X
NCO	4.0.9	[121]	Data exchange tools	X
netcdf	3.6.3, 4.1.2, 4.1.3	[122]	Data exchange, Tools	X
NetLogo	4.1.3	[123]	Modeling	X
Newbler	2.5.3, 2.6	[124]	Biology, NGS	X	X
NFFT	3.1.3	[125]	NDFT, library, math	X
Novoalign	2.07.15	[126]	Biology, NGS	X
NWChem	6.0	[127]	Simulation, Chemistry	X
Oases	0.2.04	[128]	Biology, NGS	X
OpenFOAM	1.7.1	[129]	Molecular Dynamics	X
OrthoMCL	2.0	[130]	Biology, Genomics	X
PAL2NAL	14	[131]	Biology, Genomics	X
PAML	4.4e	[132]	Biology, Phylogenetics	X
PAPI	4.1.2.1	[133]	CPU API	X
Parflow	v615	[134]	Ecology, Modeling		X
PASA	20110520	[135]	Biology, Genomics	X	X
PeakSplitter	1.0	[136]	Biology, Chip-Seq	X	X
PDT	3.16	[137]	Programming, Profiler	X
Perl	5.14.1	[138]	Programming, Language	X	X
PerM	0.3.6, 0.4.0 (EL6)	[139]	Biology, NGS	X	X
PETSc	2.3.3-p8, 3.0.0-p12	[140]	MPI toolkit	X
Phred	020425	[141]	Biology, Genomics, Sequencing	X
PhyloBayes	3.3b	[142]	Biology, Phylogenetics	X
PhyML	3.0	[143]	Biology, Phylogenetics	X
Picard	1.54	[144]	Biology, NGS	X	X
Pindel	0.2.8	[145]	Biology, NGS	X
PQS	3.3-19	[146]	Modeling, Chemistry	X
Prinseq	0.17	[147]	Biology, NGS	X
Proteinortho	4.26	[148]	Biology, Genomics	X	X
PyOpenCL	2012.04	[149]	python, parallel programming	X
python	2.6.5, 2.7.2, 2.7.3	[150]	Programming, scripting, language	X	X
QIIME	1.5.0	[151]	Biology, Ecology	X	X
R	2.14.1-MPI, 2.14.2, 2.15.0	[152]	Statistics, Programming	X	X
RAxML	7.3.0,7.3.2	[153]	Biology, Phylogenetics	X	X
RAxML-Light	1.0.5	[154]	Biology, Phylogenetics	X
RepeatMasker	3.3.0	[155]	Biology, Genomics	X	X
Reptile	1.1, 1.1-omp	[156]	Biology, NGS, error correction	X	X
riboPicker	0.4.2	[157]	Biology, Sequence	X
Rosetta	2.1.1, 2.1.2	[158]	Biology, Structural, Modeling	X
Ruby	1.9.3	[159]	Programming, Language, Scripting	X
RSMToolkit	2961	[160]	Math, Modeling, Geometry	X
samtools	0.1.16, 0.1.18	[161]	Biology, NGS	X	X
SAS	9.2, 9.3	[162]	Statistics, Graphing	X	X
SATe	2.1.0	[163]	Biology, Phylogenetics	X
Scala	2.9.1	[164]	Programming, language, java	X
Segminator	0.0.2	[165]	Biology, NGS	X
SeqPrep	0.4, 0.5 (EL6)	[166]	Biology, NGS	X	X
Siesta	2.0, 2.0.2, 3.0b	[167]	Simulation, physics, ab-initio	X
SIFT	4.0.3b	[168]	Biology, Genomics	X	X
Silo	4.7	[169]	Library, Data	X	X
Snap	20100728	[170]	Biology, Genomics	X	X
SOAPdenovo	1.05	[171]	Biology, NGS	X	X
SOAPdenovo-Trans	1.01	[172]	Biology, NGS	X	X
SPARTA+	2.60	[173]	Chemistry	X
Sputnik	1.0	[174]	Biology, Genomics	X	X
SRA	2.1.7	[175]]	biology, NGS	X	X
SRNAPredict	3.0	[176]	Biology, Genomics	X
SRNAScanner	200903	[177]	Biology, Genomics	X
Stacks	0.9995	[178]	Biology, Genomics, NGS		X
Staden	2.0.0b9	[179]	Biology, Genomics, Sequencing	X	X
Stata	10	[180]	Statistics, Data analysis	X
Structure	2.3.3	[181]	Biology, Population	X	X
TAU	2.20.1	[182]	Profiling, Tracing, Programming	X
tgicl	2.1	[183]	Biology, sequencing, clustering	X	X
TRF	4.04	[184]	Biology, Genomics	X	X
Trimal	1.2	[185]	Biology, NGS	X
Trinity	r20120125, r20120317 (EL5); r20120518, r20120608 (EL6)	[186]	Biology, RNA-Seq	X	X
Tophat	1.3.0, 1.3.3, 1.4.1	[187]	Biology, NGS	X	X
Twinscan	3.5,4.1.2	[188]	Biology, Genomics	X
usearch	5.0.151,5.1.221, 5.2.32 (EL6)	[189]	Biology, Sequence analysis	X	X
VASP	4.6.34,5.2.0	[190]	Quantum Chemistry, ab initio	X
VCFtools	0.1.7 (EL5), 0.1.9	[191]	Biology, SNPs	X	X
velvet	1.2.06,1.2.02,1.2.01,1.1.05	[192]	Biology, NGS	X	X
vmd	1.9	[193]	Biology, Visualization	X
WebLogo	3.1, 3.3 (EL6)	[194]	Biology, Genomics	X	X
weka	3.6.2	[195]	Data mining algorithms	X
wgs	6.1, 6.1-20110830	[196]	Biology,Assembler,Genome	X	X
wublast	2.0	[197]	Biology, Sequence Alignment	X	X

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