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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, 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 / 4.8.2 ((Modulefiles ''gcc/*'')) +Compilers are available when loading a module file associated with a toolchain. To 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'')) / Intel Composer 2013 ((Modulefile ''intel/composer/2013_4_183'' or ''intel-cluster-studio-2013.0.028'')) +
-  * Open64 4.5.1 / 4.5.2 ((Modulefiles ''open64/*'')) +
-  * PGI 12.4 / 13.10 / 14.1 ((Modulefiles ''pgi/*''))+
  
-==== MPIs ====+<code bash> 
 +$ module load compiler/[TAB] 
 +</code>
  
-See [[mpi|MPI]]. 
  
-==== Libraries ====+==== MPIs ==== 
 + 
 +Using MPI-Modules can be special. Please refer to our [[mpi|MPI wiki page]].
  
-  * [[software:acml|AMD Core Math Library]] (ACML) 5.1.0 / 5.2.0 / 5.3.0 (DO NOT USE 5.3.1, ITS BROKEN) ((Modulefiles ''acml/*/<compiler>{,_fma4}{,_mp}'')) +==== Licensed Software / Proprietary Software ====
-    * Available with ''fma4'' instructions, which are supported by the Mogon CPUs (recommended) +
-    * Available with multiprocessing (''mp'') support +
-  * [[software:mkl|Intel Math Kernel Library]] (MKL) 2011 SP1 ((Modulefile ''intel/mkl/2011_sp1.10.319'' or ''intel-studio-2011-sp1-10'')) / 2013 ((Modulefile ''intel/mkl/2013_4_183'' or ''intel-cluster-studio-2013.0.028'')) +
-    * [[http://software.intel.com/sites/products/mkl/|Math Kernel Library Link Line Advisor]]+
  
-==== Applications ====+For software which is associated with a restricted software, we have a number of options:
  
-Mostly to be found under ''/cluster/Apps/'', please load suitable modulefiles based on the available compiler, mpi, library-variants.+  - if the software anticipates a license server, we can setup the software (install + connect to the license server) for or with you. 
 +  - 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. 
 +  - If your case is special and not yet listed, get in touch with us.
  
-  * [[software:CDO|CDO (Climate Data Operators)]] +<WRAP center round info 90%> 
-  * [[software:cp2k|CP2K]] +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.
-  * [[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]] +
-  * [[software:Matlab]] +
-  * [[software:Mathematica]] +
-  * [[software:Nwchem]] +
-===== Soon available =====+
  
-  * Ferret 6.82 +When doing so, please include: 
-  * netCDF 4.2-C++ +  * your name 
-  * 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 Version (if not already stated on the license agreement)
  
-  * Rosetta +Multiple users may sign a single license agreement if the agreement in question permits this. 
-  * VASP +</WRAP>
-  * AceMD +
-  * Molden or any molecule visualizer+
  
-===== List of Compiler+Software ===== 
  
-==== GCC ====+===== Topical Software =====
  
-=== GCC 4.8.1 + MPI 1.6.5 ===+We have [[software:topical:|gathered]] a few additional descriptions on area specific software (packages). You will find more information at the specific pages.
  
-^ 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 ==== 
  
-=== Intel Studio 2011 SP1 10 (incl. intelmpi) === 
  
-^ name ^ version ^ module ^ 
-| udunits | 2.1.24 | software/udunits/intel/2.1.24 | 
  • software.1410417229.txt.gz
  • Last modified: 2014/09/11 08:33
  • by henkela