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software [2013/11/08 14:09]
vormstep
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,​ we strongly discourage using any ''​*conda''​ or ''​brew''​ setup on one of our clusters: It has often been a source of messing up an existing environment only to be discovered at a source of interference when switching back our modules. 
 +</​WRAP>​ 
 + 
 +===== EasyBuild and Software Installation on Mogon Clusters ===== 
 + 
 +If some application or library or a flavor of it is missing you can [[https://​hpc.uni-mainz.de/​high-performance-computing/​service-angebot/​softwareinstallation/​|ask us with this little form]] to install it. We apologize, but at some point the need arose to be a somewhat formal. We use [[https://​easybuilders.github.io/​easybuild/​|EasyBuild]] as a framework to install software and control the module building process. In our form we ask to indicate an [[http://​easybuild.readthedocs.io/​en/​latest/​version-specific/​Supported_software.html|EasyBuild configuration file]], if applicable. 
 + 
 +You may install software independently,​ yet in this case our support has to be limited. 
 + 
 +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 ''​foss'',​ ''​gompi''​ or similar. These are the [[http://​easybuild.readthedocs.io/​en/​latest/​eb_list_toolchains.html|EasyBuid Toolchains]],​ matches of specific compilers and basic library versions bundled together. 
 + 
 +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 ​and Modulefiles ​===== 
 + 
 +All software installed by the HPC team for users is available within so-called [[https://​en.wikipedia.org/​wiki/​Environment_Modules_%28software%29|Environment Modules]]: Little scripts, which set the matching environment variables for the desired application or library. More on Modulefiles can be found [[setting_up_environment_modules|on our wiki page covering Modules]]. This page covers looking for area specific tools, too. 
 + 
  
 ==== Compilers ==== ==== Compilers ====
  
-  * GCC 4.4.6 ((From ​the SL base system, no modulefile needed)) / 4.6.2 / 4.7.0 ((Modulefiles ​''​gcc/*''​)) +Compilers are available when loading a module file associated with a toolchainTo obtain only a compiler, you can load any module in the ''​compiler'' ​trunk of our modulefiles:​ 
-  * Intel Composer 2011 SP1 ((Modulefile ''​intel/composer/​2011_sp1.10.319''​ or ''​intel-studio-2011-sp1-10''​)) + 
-  * Open64 4.5.1 4.5.2 ((Modulefiles ''​open64/​*''​)) +<code bash> 
-  * PGI 12.4 ((Modulefiles ''​pgi/​*''​))+$ module load compiler/[TAB] 
 +</code> 
  
 ==== MPIs ==== ==== MPIs ====
  
-See [[mpi|MPI]].+Using MPI-Modules can be special. Please refer to our [[mpi|MPI ​wiki page]]. 
 + 
 +==== Licensed Software / Proprietary Software ====
  
-==== Libraries ====+For software which is associated with a restricted software, we have a number of options:
  
-  ​* [[software:acml|AMD Core Math Library]] ​(ACML5.1.0 / 5.2.0 ((Modulefiles ''​acml/​*/<​compiler>​{,​_fma4}{,​_mp}''​)) +  ​- if the software anticipates a license server, we can setup the software (install + connect to the license serverfor or with you
-    * Available with ''​fma4''​ instructions,​ which are supported ​by the Mogon CPUs (recommended) +  - if the software may be run by anyone who has signed a license, we can install ​the software ​(an [[software:topical:​physics:​vmd_namd|example would be VMD + NAMD]]) and make it accessible to a particular user or group. 
-    * Available with multiprocessing (''​mp''​) support +  ​If your case is special and not yet listed, get in touch with us.
-  * [[software:mkl|Intel Math Kernel Library]] (MKL2011 SP1 ((Modulefile ''​intel/​mkl/​2011_sp1.10.319''​ or ''​intel-studio-2011-sp1-10''​)) +
-    * [[http://​software.intel.com/​sites/​products/​mkl/​|Math Kernel Library Link Line Advisor]]+
  
-==== Applications ====+<WRAP center round info 90%> 
 +In the 2nd case (a software which comes with a license, which prohibits us to "//​just install and everyone can use it//") we require you (individual users of a group, possible several signs on one form) to print and sign printed licenses. Subsequently,​ send it via internal mail ("​Hauspost"​) to "ZDV HPC group"​. We will then set the permissions accordingly.
  
-Mostly to be found under ''/​cluster/​Apps/''​, please ​load suitable modulefiles based on the available compiler, mpi, library-variants.+When doing so, please ​include: 
 +  * your name 
 +  * your username 
 +  * your email address (in case we need to approach you) 
 +  * Software (if not already stated ​on the license agreement) 
 +  * Software Version (if not already stated on the license agreement)
  
-  * [[software:​CDO|CDO (Climate Data Operators)]] +Multiple users may sign a single license agreement if the agreement in question permits this. 
-  * [[software:​cp2k|CP2K]] +</​WRAP>​
-  * [[software:​gromacs|Gromacs]] +
-  * [[software:​hdf5|HDF5 parallel version]] +
-  * [[software:​namd2|NAMD2]] +
-  * [[software:​nco|NCO (netCDF Operator)]] +
-  * [[software:​netcdf|netCDF]] | [[software:​pnetcdf|PnetCDF]] +
-  * [[software:​openfoam|OpenFOAM]] +
-  * [[software:​petsc|PETSc]] +
-  * [[software:​UDUNITS]] +
-  * [[software:​Darshan]] +
-  * Matlab +
-  * [[software:​Mathematica]] +
-  * [[software:​Nwchem]] +
-===== Soon available =====+
  
-  * Ferret 6.82 
-  * netCDF 4.2-C++ 
-  * BLAST+ 
-===== Software-Wishlist ===== 
  
-  * Rosetta +===== Topical Software =====
-  * VASP +
-  * AceMD +
-  * Molden or any molecule visualizer+
  
-===== List of Compiler+Software =====+We have [[software:​topical:​|gathered]] a few additional descriptions on area specific software (packages). You will find more information at the specific pages.
  
-==== GCC ==== 
  
-=== GCC 4.8.1 + MPI 1.6.5 === 
  
-^ name ^ version ^ module ^ 
-| OpenFoam | 2.2.2 | software/​openfoam/​2.2.2 | 
-| PetsC | 3.3-p2 | software/​petsc/​3.3-p2/​gcc_4.8.1_openmpi_1.6.5 | 
-| PetsC | 3.4.2 | software/​petsc/​3.4.2/​gcc_4.8.1_openmpi_1.6.5 | 
-| PetsC | 3.4.3 | software/​petsc/​3.4.3/​gcc_4.8.1_openmpi_1.6.5 | 
-| Phylobayes | - | software/​phylobayes-mpi/​openmpi-1.6.5/​gcc-4.8.1 | 
  
-=== GCC 4.7.0 + MPI 1.6.1 (may not work in batch system) === 
  
-^ name ^ version ^ module ^ 
-| Allpaths lg | 46652 | software/​bioinf/​allpaths-lg/​46652 | 
-| Blast | 2.2.28 | software/​bioinf/​blast/​2.2.28 | 
-| Bowtie | - | software/​bioinf/​bowtie | 
-| Bowtie2 | - |software/​bioinf/​bowtie2 | 
-| bwa | 0.7.4 | software/​bioinf/​bwa/​0.7.4 | 
-| celera | 7.0 | software/​bioinf/​celera/​7.0 | 
-| cufflinks | 2.1.1 | software/​bioinf/​cufflinks/​2.1.1 | 
-| fastgc | 0.10.1 | software/​bioinf/​fastqc/​0.10.1 | 
-| oases | 0.28 | software/​bioinf/​oases/​0.2.8 | 
-| samtools | 0.1.19 | software/​bioinf/​samtools/​0.1.19 | 
-| solexaga | 2.2 | software/​bioinf/​solexaqa/​2.2 | 
-| star | 2.3.0e | software/​bioinf/​star/​2.3.0e | 
-| tophat | 2.0.8b | software/​bioinf/​tophat/​2.0.8b | 
-| velvet | 1.2.09 | software/​bioinf/​velvet/​1.2.09 | 
-| CDO | 1.5.8 | software/​cdo/​1.5.8 | 
-| HDF5 | 1.8.10 | software/​hdf5/​1.8.10-parallel | 
-| NCL | 6.1.2 | software/​ncl/​6.1.2 | 
-| NCO | 4.2.1 | software/​nco/​4.2.1 | 
-| netCDF | 4.1.3 | software/​netcdf/​4.1.3 | 
-| netCDF | 4.2-c | software/​netcdf/​4.2-c | 
-| Parallel netCDF | 1.3.1 | software/​netcdf/​parallel_1.3.1 | 
-| octave | 3.6.4 | software/​octave/​gcc/​3.6.4 | 
-| orca | 2.9.1 | software/​orca/​2.9.1 | 
-| Paraview | 3.14.1 | software/​paraview/​3.14.1 | 
-| udunits | 2.1.24 | software/​udunits/​gcc/​2.1.24 | 
  
-==== Intel ==== 
  • software.1383916154.txt.gz
  • Last modified: 2013/11/08 14:09
  • by vormstep