{"id":4411,"date":"2020-03-14T22:17:02","date_gmt":"2020-03-14T21:17:02","guid":{"rendered":"https:\/\/cnrm.uniri.hr\/?page_id=4411"},"modified":"2023-03-07T22:09:51","modified_gmt":"2023-03-07T21:09:51","slug":"software","status":"publish","type":"page","link":"https:\/\/cnrm.uniri.hr\/hr\/software\/","title":{"rendered":"Programska podr\u0161ka"},"content":{"rendered":"<p><\/p>\n<style>\nul {list-style-position: inside;}\n<\/style>\n<div style=\"text-align: justify;\">\nProgramski paketi otvorenog koda kao i paketi s licencama u vlasni\u0161tvu CNRM-a integrirani su kao dio osnovne programske podr\u0161ke Superra\u010dunala. Predinstalirani temeljni programski paketi dostupni korisnicima navedeni su u nastavku:<\/p>\n<p><strong>Programski paketi otvorenog koda<\/strong><\/p>\n<ul class=\"simple\">\n<li><a class=\"reference external\" href=\"https:\/\/www.abinit.org\/\">ABINIT<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/alphafold.ebi.ac.uk\/\">AlphaFold<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/ambermd.org\/AmberTools.php\">AmberTools<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/wiki.fysik.dtu.dk\/ase\/\">Atomic Simulation Environment<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/vina.scripps.edu\/\">AutodocVINA<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/\">BLAST<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.blender.org\/\">Blender<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/\">Bowtie 2<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/bio-bwa.sourceforge.net\/\">Burrows-Wheeler Aligner<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.calculix.de\/\">CalculiX<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.cp2k.org\/\">CP2K<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/dealii.org\/\">deal.II<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/eigen.tuxfamily.org\/\">Eigen<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.freecadweb.org\/\">FreeCAD<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/freefem.org\/\">FreeFEM<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.gromacs.org\/\">GROMACS<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/pachterlab.github.io\/kallisto\/\">kallisto<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.lammps.org\/\">LAMMPS<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/nwchemgit.github.io\/\">NWChem<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/sourceforge.net\/projects\/foam-extend\/\">OpenFOAM ESI<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.openfoam.com\/\">OpenFOAM EXTEND<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.openfoam.org\/\">OpenFOAM ORG<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.paraview.org\/\">ParaView<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.plumed.org\/\">PLUMED<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/pytorch.org\/\">PyTorch<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.quantum-espresso.org\/\">Quantum ESPRESSO<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/root.cern\/\">ROOT<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/rdock.sourceforge.net\/\">rDock<\/a>\/<a class=\"reference external\" href=\"https:\/\/rxdock.gitlab.io\/\">RxDock<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.rosettacommons.org\/software\">Rosetta<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/samtools.sourceforge.net\/\">SAMtools<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/singularity.lbl.gov\/\">Singularity<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/github.com\/alexdobin\/STAR\">STAR<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.tensorflow.org\/\">TensorFlow<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/ccb.jhu.edu\/software\/tophat\/\">TopHat<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/github.com\/bcgsc\/transabyss\">Trans-ABySS<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.mmm.ucar.edu\/weather-research-and-forecasting-model\">Weather Research and Forecasting Model<\/a><\/li>\n<\/ul>\n<p><strong>Licencirani programski paketi<\/strong><\/p>\n<ul class=\"simple\">\n<li><a class=\"reference external\" href=\"https:\/\/www.altair.com\/resource\/altair-acusolve-datasheet\">Altair AcuSolve<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.altair.com\/resource\/altair-nanofluidx-datasheet\">Altair nanoFluidX<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.altair.com\/optistruct\/\">Altair OptiStruct<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.altair.com\/radioss\/\">Altair Radioss<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.altair.com\/altair-cfd-capabilities\/\">Altair ultraFluidX<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.diracprogram.org\/\">DIRAC<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.msg.ameslab.gov\/gamess\/\">GAMESS<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.gromos.net\/\">GROMOS<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.mathworks.com\/products\/matlab.html\">MATLAB<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.momap.net.cn\/\">MOMAP<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.ks.uiuc.edu\/Research\/namd\/\">NAMD<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.vapor.ucar.edu\/\">VAPOR<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.ks.uiuc.edu\/Research\/vmd\/\">VMD<\/a><\/li>\n<\/ul>\n<p>&nbsp;<br \/>\n<strong>Instalacija dodatnih paketa<\/strong><br \/>\nDodatna se programska podr\u0161ka mo\u017ee osigurati na zahtjev korisnika. Za instalaciju vlasni\u010dkih programskih paketa korisnik mora posjedovati odgovaraju\u0107u licencu za rad u superra\u010dunalnom okru\u017eenju. Op\u0107enito, programski paketi moraju biti namjenjeni za Linux te kompatibilni s Red Hat Enterprise Linux 7.<\/p>\n<p><strong>Razvoj programske podr\u0161ke<\/strong><br \/>\nNa Sveu\u010dili\u0161tu u Rijeci djeluju istra\u017eiva\u010dke skupine koje razvijaju znanstvenu programsku podr\u0161ku za potrebe vlastitih istra\u017eivanja te u okviru projekata razvoja programske podr\u0161ke, a specijaliziranu za izvo\u0111enje na superra\u010dunalu. Spomenute grupe djeluju na sastavnicama Sveu\u010dili\u0161ta:<\/p>\n<ul class=\"simple\" style=\"list-style-position: outside; text-align: justify;\">\n<li><a class=\"reference external\" href=\"https:\/\/www.biotech.uniri.hr\/\">Odjel za biotehnologiju<\/a>, <a class=\"reference external\" href=\"https:\/\/svedruziclab.github.io\/\">Laboratorij za strukturu i funkciju biomolekula<\/a>, voditelj\u00a0<a class=\"reference external\" href=\"https:\/\/www.svedruziclab.com\/people\/zeljko\/\">doc. dr. sc. \u017deljko Svedru\u017ei\u0107<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.phy.uniri.hr\/\">Odjel za fiziku<\/a>, <a class=\"reference external\" href=\"https:\/\/www.phy.uniri.hr\/hr\/ustroj\/29-hr\/ustroj\/laboratoriji\/1314-laboratorij-za-astrocesticnu-fiziku.html\">Laboratorij za astro\u010desti\u010dnu fiziku<\/a>, voditelj\u00a0<a class=\"reference external\" href=\"https:\/\/www.phy.uniri.hr\/hr\/djelatnici\/28-hr\/djelatnici\/183-tomislavterzi.html\">doc. dr. sc. Tomislav Terzi\u0107<\/a><\/li>\n<li><a class=\"reference external\" href=\"http:\/\/www.riteh.uniri.hr\/\">Tehni\u010dki fakultet<\/a>, <a class=\"reference external\" href=\"http:\/\/www.riteh.uniri.hr\/ustroj\/zavodi\/zmfri\/\">Zavod za mehaniku fluida i ra\u010dunarsko in\u017eenjerstvo<\/a>, voditelj\u00a0<a class=\"reference external\" href=\"http:\/\/www.riteh.uniri.hr\/osoba\/lado-kranjcevic\">izv. prof. dr. sc. Lado Kranj\u010devi\u0107<\/a><\/li>\n<\/ul>\n<\/div>\n<p><\/p>","protected":false},"excerpt":{"rendered":"<p>Programski paketi otvorenog koda kao i paketi s licencama u vlasni\u0161tvu CNRM-a integrirani su kao dio osnovne programske podr\u0161ke Superra\u010dunala. Predinstalirani temeljni programski paketi dostupni korisnicima navedeni su u nastavku: Programski paketi otvorenog koda ABINIT AlphaFold AmberTools Atomic Simulation Environment&hellip;&nbsp;<a href=\"https:\/\/cnrm.uniri.hr\/hr\/software\/\" class=\"more-link\">Read More<\/a><\/p>\n","protected":false},"author":14,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"templates\/builder.php","meta":{"_links_to":"","_links_to_target":""},"categories":[],"tags":[],"_links":{"self":[{"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/pages\/4411"}],"collection":[{"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/users\/14"}],"replies":[{"embeddable":true,"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/comments?post=4411"}],"version-history":[{"count":77,"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/pages\/4411\/revisions"}],"predecessor-version":[{"id":7767,"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/pages\/4411\/revisions\/7767"}],"wp:attachment":[{"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/media?parent=4411"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/categories?post=4411"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/cnrm.uniri.hr\/hr\/wp-json\/wp\/v2\/tags?post=4411"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}