Home
Systemutvecklare med inriktning mot storskalig lagring
Halvan needs to be restarted due to a memory overflow
SNIC Cloud Computing Course at UPPMAX, May 16
Available software
Below you will find a list of softwares available at the UPPMAX resources.
UPPMAX buys, supports and updates software for scientific computing of general interest for researchers at UU. The software is mainly made available on UPPMAX computer systems, but also on other computer systems within UU when license agreements allows it. Examples of software are compilers (C, C++, F90) and software for electronic structure calculations, GAUSSIAN03 and GAMESS-US.
For information on how to use and write MPI and OpenMP parallel programs on Kalkyl and Grad, see the tutorial.
List of software
| Software |
module |
Kalkyl |
Tintin | Grad |
license |
|---|---|---|---|---|---|
| Compilers |
|||||
| pgi |
pgi |
X |
x | X |
site license, 5 users |
| gcc |
gcc |
X |
x | X |
gpl |
| intel |
intel |
X |
x | X |
site license, 2 users |
| open64 | open64 | x | |||
|
|
|||||
| Chemistry/Physics |
|||||
| Gaussian |
g03 g09 |
X X |
X |
X |
UU site license |
| turbomole |
turbo |
X |
user group license |
||
| gamess |
gamess |
X |
X | X |
academic site license |
| VASP |
vasp |
X |
user group license |
||
| molcas |
molcas |
X |
user group license | ||
|
gromacs |
gromacs |
X |
X | gpl |
|
|
desmond |
desmond |
X |
gpl |
||
| Engineering |
|||||
| matlab |
matlab |
X |
site license |
||
| Statistics |
|||||
| R |
R |
X |
X |
gpl |
|
| Bioinformatics |
|||||
| blast |
blast |
X |
X |
||
| emboss |
emboss |
X |
gpl lgpl |
||
| MUMmer |
MUMmer |
X |
|||
| anfo |
anfo |
X |
|||
| bwa |
bwa |
X |
|||
| hmmer |
hmmer |
X |
|||
| maq |
maq |
X |
|||
| mosaik-aligner |
mosaik-aligner |
X |
|||
| mpiblast |
mpiblast |
X |
|||
| splitseek |
splitseek |
X |
|||
| Ray |
Ray |
X |
|||
| FastQC |
FastQC |
X |
|||
| biopython |
biopython |
X |
|||
| genometools |
genometools |
X |
|||
| htseq |
htseq |
X |
|||
| picard |
picard |
X |
|||
| samtools |
samtools |
X |
|||
| concaterpillar |
concaterpillar |
X |
|||
| garli |
garli |
X |
|||
| raxml |
raxml |
X |
|||
| ab_wtp |
ab_wtp |
X |
|||
| bowtie |
bowtie |
X |
|||
| cufflinks |
cufflinks |
X |
|||
| tophat |
tophat |
X |
|||
| BEDtools |
BEDtools |
X |
|||
| CASAVA |
CASAVA |
X |
|||
| GATK |
GATK |
X |
|||
| bioscope |
bioscope |
X |
|||
| blast+ |
blast+ |
X |
|||
| blat |
blat |
X |
|||
| abyss |
abyss |
X |
|||
| mira |
mira |
X |
|||
| velvet |
velvet |
X |
|||
| BclConverter |
BclConverter |
X |
|||
| BioPerl |
BioPerl |
X |
|||
| Fastx |
Fastx |
X |
|||
| emmax |
emmax |
X |
|||
| gcta |
gcta |
X |
|||
| mrbays |
mrbays |
X |
|||
| 454-dataanalysis |
454-dataanalysis |
X |
|||
| 454-dataprocessing |
454-dataprocessing |
X |
|||
| staden |
staden |
X |
|||
| Parallell |
|||||
| openmpi |
openmpi |
X |
X |
gpl |
|
For support, please, mail support@uppmax.uu.se.
