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Integraton of scientfc and engineering applicatons into CERN’s computng resources Markus Jylhänkangas Bachelor’s thesis May 2019 Informaton and communicaton technology Degree Programme in Sofware Engineering Description Author(s) Type of publication Date Jylhänkangas, Markus Bachelor’s thesis May 2019 Language of publication: English Number of pages Permission for web publi- 47 cation: x Title of publication Integration of scientific and engineering applications into CERN’s computing resources Degree programme Software Engineering Supervisor(s) Kokkonen, Tero Rantonen, Mika Assigned by CERN Abstract Following CERN’s strategy to consolidate all computing resources under Linux, it was planned to move the Windows HPC service to Linux-based infrastructure. The scientific and engineering applications that were running under Windows HPC were therefore assigned to be migrated to Linux HPC and HTC environments. The main objective is the migration of engineering applications to Linux-based computing resources. The first objective for the migration was to design a strategy to carry out the mi- gration by identifying potential risks and select target service HPC or HTC, to make efficient use of resources. Second objective was to implement templates, plugins and necessary changes to the HTC and HPC infrastructure. Migration was also going to be tested and vali- dates with users. The migration was implemented by first installing the applications on the Linux resources. Template script were written to submit applications to HPC or HTC. Modification to HPC were made with Puppet to make it possible to run the applications As a result, the applications were migrated to either HPC or HTC resources and the Win- dows HPC was deprecated. Authentication and security inside the Linux HPC cluster was also improved. Running complex scientific and engineering applications on Linux HPC and HTC resources is possible, but there are some compatibility problems with different parallel computing im- plementations. Keywords/tags (subjects) HPC, HTC, SLURM, HTCondor, Batch Miscellaneous (Confidential information) Kuvailulehti Tekijä(t) Julkaisun laji Päivämäärä Jylhänkangas, Markus Opinnäytetyö, AMK Toukokuu 2019 Sivumäärä Julkaisun kieli 47 Englanti Verkkojulkaisulupa myönnetty: x Työn nimi Integration of scientific and engineering applications into CERN’s computing resources Tutkinto-ohjelma Ohjelmistotekniikka Työn ohjaaja(t) Tero Kokkonen Mika Rantonen Toimeksiantaja(t) CERN Tiivistelmä CERNin strategiaa tietojenkäsittelyn vakauttamisesta seuraten Windows HPC-palvelu suun- niteltiin siirrettäväksi Linux-pohjaiseen infrastruktuuriin. Sen vuoksi tehtäväksi annettiin tieteellisten ja teknisten sovellusten siirtäminen Windows HPC-ympäristöstä Linux HPC ja HTC-ympäristöön. Päätehtävänä sovellusten siirrossa oli teknisten sovellusten siirto Linux-pohjaisiin tieto- jenkäsittelyresursseihin. Ensimmäisenä̈ tehtävänä siirrossa oli suunnitella strategia siirrosta ja siirtoon liittyvistä mahdollisista riskeistä sekä valita kohdeympäristö HPC tai HTC. Toi- senä tehtävänä oli toteuttaa ja kehittää sapluunat, lisäosat sekä tarvittavat muutokset HTC- ja HPC-infrastruktuureihin. Siirron lopputulokset testattiin ja vahvistettiin käyttäjien kanssa. Siirto suoritettiin ensin asentamalla sovellukset Linux resursseille. Sovellusten suoritta- mista varten kehitettiin sapluunat, joilla voitiin lähettää töitä Linux-resursseihin. Jotta so- vellukset saatiin toimimaan, muutoksia piti tehdä HPC-ympäristöön. Nämä muutokset suo- ritettiin Puppetilla. Tuloksena sovellukset siirrettiin joko HPC- tai HTC-resursseille ja Windows HPC-palvelu otettiin pois käytöstä. Käyttäjien identiteetin todennusta sekä turvallisuutta parannettiin Linux HPC-klusterissa. Monimutkaisten tieteellisten ja teknisten sovellusten suorittaminen Linux HPC- ja HTC- resursseilla on mahdollista, mutta näiden välillä on pieniä yhteensopivuusongelmia. Avainsanat (asiasanat) HPC, HTC, SLURM, HTCondor, Batch Muut tiedot (salassa pidettävät liitteet) 1 Contents Figures................................................................................................................. 3 Tables ................................................................................................................... 3 1 Introducton...................................................................................................... 5 1.1 Motvaton and background ............................................................. 5 1.2 CERN........................................................................................................... 5 1.3 Scope and objectves ........................................................................... 6 2 Research methodology................................................................................ 8 2.1 Constructve research.......................................................................... 8 2.2 Research process................................................................................... 8 3 Private cloud..................................................................................................... 10 3.1 Agile Infrastructure............................................................................... 10 3.2 OpenStack ................................................................................................ 11 3.3 Confguraton tools............................................................................... 12 3.4 Ceph............................................................................................................ 12 3.5 Version control ....................................................................................... 12 4 Computng systems ....................................................................................... 13 4.1 Computng at CERN.............................................................................. 13 4.2 High-Performance Computng......................................................... 13 4.2.1Windows HPC cluster ................................................................ 14 4.2.2Linux HPC cluster......................................................................... 15 4.3 Slurm .......................................................................................................... 17 4.4 Linux Control Groups........................................................................... 18 2 4.5 High-Throughput Computng ........................................................... 18 4.6 Scientfc and engineering applicatons........................................ 19 5 Migraton Plan ................................................................................................. 21 6 Development workfow............................................................................... 23 7 Migraton............................................................................................................ 25 7.1 HTC and HTCondor ............................................................................... 25 7.2 HPC and Slurm........................................................................................ 25 7.3 Slurm PAM................................................................................................ 27 7.3.1Puppet ............................................................................................. 29 7.4 Applicatons............................................................................................. 30 7.4.1CST..................................................................................................... 30 7.4.2Ansys................................................................................................. 31 7.4.3Ansys RSM HTCondor plugin .................................................. 33 7.5 AUKS ........................................................................................................... 36 7.5.1Puppet module............................................................................. 38 8 Results................................................................................................................. 40 9 Conclusions ....................................................................................................... 43 References ......................................................................................................... 47 3 Figures Figure 1. Agile infrastructure................................................................................ 10 Figure 2. Openstack .............................................................................................. 11 Figure 3. Windows cluster.................................................................................... 15 Figure 4. Linux cluster........................................................................................... 17 Figure 5. HPC or HTC migraton process.............................................................. 21 Figure 6. Development environment .................................................................. 23 Figure 7. Ansys Workbench update..................................................................... 32 Figure 8. Auks ........................................................................................................ 37 Tables Table 1. HPC node types ...................................................................................... 16 Table 2. HTC node types....................................................................................... 18 Table 3. What batch system applicaton should run.........................................
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