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software [2014/09/11 08:33] henkela |
software [2020/01/24 10:37] (current) meesters [Non-Canonical Installation Helpers] |
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====== Software ====== | ====== Software ====== | ||
- | ===== Installed Software ===== | + | On the mogon clusters we install a broad variety of software (libraries and applications) for our users. We seek to install all software in optimized form - as far as possible. |
+ | |||
+ | ===== Non-Canonical Installation Helpers ===== | ||
+ | |||
+ | <WRAP center round important 60%> | ||
+ | Many users feel tempted to install software themselves. This is perfectly fine, yet support for self-installed software cannot be granted. | ||
+ | |||
+ | Particularly, | ||
+ | </ | ||
+ | |||
+ | ===== EasyBuild and Software Installation on Mogon Clusters ===== | ||
+ | |||
+ | If some application or library or a flavor of it is missing you can [[https:// | ||
+ | |||
+ | You may install software independently, | ||
+ | |||
+ | If an EasyBuild configuration is missing, but the desired software is of interest to a handful of people, we might write the missing EasyBuild together. Please approach us in this case. | ||
+ | |||
+ | ===== Easybuild Toolchains ===== | ||
+ | |||
+ | When looking in the list of installed modules you see abbreviations as '' | ||
+ | |||
+ | When compiling or using software, please ensure that matching compilers and libraries have been used or loaded. Otherwise software might just crash for a variety of reasons. Please report, if a desired library is missing for a given toolchain. | ||
+ | |||
+ | ===== Installed Software | ||
+ | |||
+ | All software installed by the HPC team for users is available within so-called [[https:// | ||
+ | |||
==== Compilers ==== | ==== Compilers ==== | ||
- | * GCC 4.4.6 ((From | + | Compilers are available when loading a module file associated with a toolchain. To obtain only a compiler, you can load any module in the '' |
- | * Intel Composer 2011 SP1 ((Modulefile '' | + | |
- | * Open64 4.5.1 / 4.5.2 ((Modulefiles '' | + | |
- | * PGI 12.4 / 13.10 / 14.1 ((Modulefiles | + | |
- | ==== MPIs ==== | + | <code bash> |
+ | $ module load compiler/ | ||
+ | </ | ||
- | See [[mpi|MPI]]. | ||
- | ==== Libraries | + | ==== MPIs ==== |
+ | |||
+ | Using MPI-Modules can be special. Please refer to our [[mpi|MPI wiki page]]. | ||
- | * [[software: | + | ==== Licensed Software |
- | * Available with '' | + | |
- | * Available with multiprocessing ('' | + | |
- | * [[software: | + | |
- | * [[http:// | + | |
- | ==== Applications ==== | + | For software which is associated with a restricted software, we have a number of options: |
- | Mostly | + | - if the software anticipates a license server, we can setup the software (install + connect |
+ | - if the software may be run by anyone who has signed a license, we can install | ||
+ | | ||
- | * [[software: | + | <WRAP center round info 90%> |
- | * [[software: | + | In the 2nd case (a software |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | * [[software: | + | |
- | ===== Soon available ===== | + | |
- | | + | When doing so, please include: |
- | * netCDF 4.2-C++ | + | |
- | * BLAST+ | + | * your username |
- | ===== Software-Wishlist ===== | + | * your email address (in case we need to approach you) |
+ | * Software (if not already stated on the license agreement) | ||
+ | * Software | ||
- | * Rosetta | + | Multiple users may sign a single license agreement if the agreement in question permits this. |
- | * VASP | + | </ |
- | * AceMD | + | |
- | * Molden or any molecule visualizer | + | |
- | ===== List of Compiler+Software ===== | ||
- | ==== GCC ==== | + | ===== Topical Software ===== |
- | === GCC 4.8.1 + MPI 1.6.5 === | + | We have [[software: |
- | ^ name ^ version ^ module ^ | ||
- | | OpenFoam | 2.2.2 | software/ | ||
- | | PetsC | 3.3-p2 | software/ | ||
- | | PetsC | 3.4.2 | software/ | ||
- | | PetsC | 3.4.3 | software/ | ||
- | | Phylobayes | - | software/ | ||
- | === GCC 4.7.0 + MPI 1.6.1 (may not work in batch system) === | ||
- | ^ name ^ version ^ module ^ | ||
- | | Allpaths lg | 46652 | software/ | ||
- | | Blast | 2.2.28 | software/ | ||
- | | Bowtie | - | software/ | ||
- | | Bowtie2 | - |software/ | ||
- | | bwa | 0.7.4 | software/ | ||
- | | celera | 7.0 | software/ | ||
- | | cufflinks | 2.1.1 | software/ | ||
- | | fastgc | 0.10.1 | software/ | ||
- | | oases | 0.28 | software/ | ||
- | | samtools | 0.1.19 | software/ | ||
- | | solexaga | 2.2 | software/ | ||
- | | star | 2.3.0e | software/ | ||
- | | tophat | 2.0.8b | software/ | ||
- | | velvet | 1.2.09 | software/ | ||
- | | CDO | 1.5.8 | software/ | ||
- | | HDF5 | 1.8.10 | software/ | ||
- | | NCL | 6.1.2 | software/ | ||
- | | NCO | 4.2.1 | software/ | ||
- | | netCDF | 4.1.3 | software/ | ||
- | | netCDF | 4.2-c | software/ | ||
- | | Parallel netCDF | 1.3.1 | software/ | ||
- | | octave | 3.6.4 | software/ | ||
- | | orca | 2.9.1 | software/ | ||
- | | Paraview | 3.14.1 | software/ | ||
- | | udunits | 2.1.24 | software/ | ||
- | ==== Intel ==== | ||
- | === Intel Studio 2011 SP1 10 (incl. intelmpi) === | ||
- | ^ name ^ version ^ module ^ | ||
- | | udunits | 2.1.24 | software/ |