#!/usr/bin/perl # # sw_app-index -- Update values for sw_app indexing # Copyright 2014 University of Tennessee # Parts copyright 2006, 2007 Ohio Supercomputer Center # # License: GNU GPL v2; see ../COPYING for details. # Revision info: # $HeadURL$ # $Revision$ # $Date$ # # Usage: sw_app-index [-h system] [-s dbhost] [-d dbname] [-t dbtable] # [-u dbuser] [-p dbpasswd] [-F|-T] # -F -- full re-index (off by default, use with caution) # -T -- syntax check use strict; use POSIX; use DBI; # functions sub software_list() { my @list=( "3dcavity", "3dh", "3n_bound", "55_x", "a_out", "abaqus", "ABCsampler", "abinit", "accorrsf", "aces2", "aces3", "activeharmony", "adcprep", "adda", "adf", "aflow", "afma", "agk", "aims", "airebo", "AliEn", "amber", "amdat", "amg2006", "AnalyzePathP", "anolis", "ansys", "anton", "AraSim", "armcibench", "arps", "arts", "ash", "astrobear", "atat", "athena", "atmc", "ausam", "autodock", "awm", "bam", "beast", "beopest", "berkeleygw", "bgw", "bicg_solver", "bigdft", "blat", "bolztran", "boots", "bowtie", "brams-opt", "bugget", "cactus", "cafemol", "calc1", "calc_group_stats", "cam", "cando", "casino", "castro3d", "cbl", "ccsm", "cctm", "cdns", "cdo", "cdp", "cfd++", "cfd_postprocess", "cfl3d", "changa", "charmm", "charles", "chemkin", "chemshell", "chg", "chimera", "chroma", "cilk", "clover_inverter", "cluster", "clustalo", "clustalw", "cm1", "coarsen", "comm-bench", "compaware", "comsol", "condor", "consensus", "convectionimr", "cp2k", "cpmd", "cql3d", "crime", "crystal", "css2sld", "csurfs", "cube", "cudac", "cvm", "da_update_bc", "dalexec", "dam", "darshan", "dasquad", "decomp", #"decypher", "delphi", "delta5d", "desmond", "dfdx", "dghbc", "dgtd", "dhybrid", "dirac-pilot", "dissens", "distuf", "dlmonte", "dlpoly", "dns2d", "dock", "dolt", "doublebeta", "dplasma", "drone", "dtms", "dv72", "dws_mpi", "eddy", "eden", "eigen.x", "elk", "energyplus", "enkf", "ens4dvar", "enzo", "epfem", "episimdemics", "esmf", "esp", "eulacc", "ex_e", "examl", "f-plane", "falkon", "fastqc", "fd3d", "fdl3di", "featureComputation", "fedvr", "fidap", "firefly", "fit_exe", "flash2", "flash4", "flotran", "flowsolver", "flow3d", "fluent", "foam", "force_free", "foxexe", "fsc25221", "fsweep", "ftb", "ftes", "gaac", "gabe", "gadget", "gamess", "garli", "gaussian", "gc", "gdl", "gemc_x", "gen.v4", "geodict", "genlatmu", "geosgcm", "glast", "gop2pc", "gpaw", "GreenSolver", "grads", "grib", "grbplot", "grmhd", "gromacs", "gromov", "grouper", "gsi.exe", "gtc", "gvksx", "gyro", "h2mol", "h3d", "hadoop", "hall3d", "halo", "harness", "harris", "hchbm", "hd", "hd_nonuma", "hdfsubdomain", "hf", "hf2", "hfb", "hfodd", "hmc", "hmmer", "homme", "hoomd", "hpcc", "hpl", "hsi", "hsphere", "hwtpost", "hybrid-gsi", "hydro", "hy3s", "ice", "idl", "ifs", "imb", "imc", "inca", "intestine3d", "ior", "iplmcfd", "isodata", "jaguar", "jet_02", "jetxb", "jobgrd", "josephson", "jrmc", "k2r2", "ker_filter_par", "kmeans", "lammps", "lautrec", "les_mpi", "les_spike", "lesmpi", "lfm", "liso", "lkh", "lmf", "lobster", "lodn", "lsdyna", "lsms", "lsp", "lu_lesh", "m2md", "madness", "maestro", "makethemcross", "masa", "mathematica", "matlab", "mcnp", "mcrothers", "mcsim", "mctas", "md_ab21", "md_xx", "mddriver", "mdsim", "meamzilla", "measurements", "meep", "meta", "metgrid", "mfc", "mhd_1", "mhd3d", "mhdam", "milc", "mitgcmuv", "mkelly", "mkl_mm", "mlane", "mm5", "molaf3di", "molcas", "moldife", "moldive", "molpro", "mothur", "mpcugles", "mpi_dgels", "mpi_dgesv", "mpi_dpos", "mpi_helium", "mpi-multi", "mpiasm", "mpiblast", "mrbayes", "mrobb6dipzz", "mtrsassi", "music", "mustem", "mykim9dgt", "myq", "mysql", #"nag", "namd", "nb", "ncbi", "ncl", "nek5000", "nektar", "nemd", "nested", "newseriesrun", "nga_cfb", "nicam", "nmm3d", "npb", "npemd", "nplqcd", "nonpareil", "nsbsintheat", "nscale", "nsmpicuf", "ntsolve", "nu-segment", "nwchem", "ocore", "octave", "omega", "omen", "omgred", "onepartm", #"openeye", "opt_exe", "optics", "orca", "os2z", "overlap", "p3dfft", "p3ripple", "p4extract", "padc", "parallelEAM", "parallelqp", #"param", "paratec", "paraview", "parflow", "parody", "parsec", "partadv", "paup", "pbar", "pbohmd", "pcg", "pencil", "perseus", "phasta", "phits", "phonon", "phraider", "pic-star", "picard", "picrun", "pimd", "pkdgrav", "pluto", "pmcl3d", "polarpigs", "polly", "polmc", "pop", "preps", "preqx", "prog_ccm_sph", "prog_hf", "prop_rotation", "propagators", "proto2", "pse", "psi4", "psolve", "pstg", "pulsar", "pwscf", "python", "qb", "qchem", "qmc", "qrpacc", "qwalk", "R", "r_out", "radhyd", "raxml", "readall_parallel", "real_exe", "reduce", "reflect", "res", "rho_pion_corre", "root", "rosenbrock", "rosetta", "rotbouss", "roth", "rtp", "run_1kmd", "run_all_de_novo", "run_flexible", "run_hyd", "run_im", "run_lprlx", "run_xyzvort", "run1s-5th-NL", "s-param", "s3d", #"sable", "sam_adv_um5", "samtools", "sas", "sauron", "scalapack", "scattering", "sddt", "seissol", "sfeles", "sgf", "shadowfax", "sickle", "siesta", "sigma", "simfactory", "simpleio", "simu_pow", "sleuth", "sms", "sne3d", "SOAPdenovo", "sord", "sovereign", "spark", "sparkfuse", "spce", "spdcp", "srad", "sses", "stagyy", "starcd", "starccm", "stata", "stationaryAccretionShock3D", "sus", "swarthmore", "sweqx", "swh1b", "swift", "tacoma", "tantalus", "tbms", "tdcc2d", "tdse", "terachem", "testpio", "tetradpost", "tfe", "thickdisk", "tmdmpi", "tornado_friction", "track", "translate", "trinityrnaseq", "tristan-mp3d", "tsc", "ttmmdmpi", "turbo", "turbomole", "two_phase", "ukh2d", "upc", "vasp", "velvet", "vbc", "vdac", "vecadd", "vhone", "vida", "ViennaRNA", "visit", "vli", "vorpal", "vmd", "vnc", "vpic", "walksat", "wave_packet", "webmo", "wmc", "wrf", "xgc", "xmfdn", "xplot3d", "xtest", "xvicar3d", "xx", "yt", "zeus", "zk3", "zNtoM" ); return @list; } sub software_match_list() { my %pkgmatch; # default to "( script LIKE '%pkgname%' OR ( software IS NOT NULL AND software LIKE 'pkgname%' ) )" foreach my $pkg ( software_list() ) { $pkgmatch{$pkg}="( script LIKE '%".$pkg."%' OR ( software IS NOT NULL AND software LIKE '%".$pkg."%' ) )"; # $pkgmatch{$pkg}="( script LIKE '%".$pkg."%' )"; } # exceptions # REGEXP match is ***MUCH*** slower than regular LIKE matching # in MySQL, so don't use REGEXP unless you really need it. $pkgmatch{'3dh'} = "script LIKE '%./3dh%'"; $pkgmatch{'55_x'} = "script LIKE '%55.x%'"; $pkgmatch{'aims'} = "( script LIKE '%aims%' AND NOT ( script LIKE '%aims/vasp%' ) )"; $pkgmatch{'a_out'} = "( script LIKE '%a.out %' OR script LIKE '%a.out\n%' )"; $pkgmatch{'abinit'} = "( script LIKE '%abinit%' OR script LIKE '%abinis%' OR script LIKE '%abinip%' )"; $pkgmatch{'aces2'} = "script LIKE '%xaces2%'"; $pkgmatch{'adda'} = "( script LIKE '%adda%' AND NOT ( script LIKE '%FindRadDat%' ) )"; $pkgmatch{'adf'} = "( script LIKE '%adf%' AND NOT ( script LIKE '%radfile%' ) AND NOT ( script LIKE '%adfs%' ) )"; $pkgmatch{'AliEn'} = "( script LIKE '%aliroot%' OR script LIKE '%agent.startup%' )"; $pkgmatch{'amdat'} = "script LIKE '%/AMDAT %'"; $pkgmatch{'arts'} = "( script LIKE '%arts%' AND script NOT LIKE '%starts%' )"; $pkgmatch{'ash'} = "( script LIKE '%ash_1%' OR script LIKE '%ash_2%' OR script LIKE '%ash_fd%' )"; $pkgmatch{'athena'} = "script LIKE '%/athena %'"; $pkgmatch{'blat'} = "script LIKE '%blat %'"; $pkgmatch{'boltztran'} = "(script LIKE '%boltzpar%')"; $pkgmatch{'boots'} = "( script LIKE '%boots%' AND NOT ( script LIKE '%bootstrap%' ) )"; $pkgmatch{'cbl'} = "( script LIKE '% cbl%' OR script LIKE '%pcbl%' OR script LIKE '%biolib%' )"; $pkgmatch{'charles'} = "script like '%charles.exe%'"; $pkgmatch{'chemshell'} = "script LIKE '%chemsh%'"; $pkgmatch{'chg'} = "script LIKE '%/chg %'"; $pkgmatch{'cluster'} = "script LIKE '%/cluster %'"; $pkgmatch{'crystal'} = "script LIKE '%Pcrystal%'"; $pkgmatch{'cube'} = "( script LIKE '%/cube %' OR script LIKE '%/intelcube %' )"; $pkgmatch{'dam'} = "script LIKE '%/dam %'"; $pkgmatch{'decomp'} = "script LIKE '%/decomp %'"; $pkgmatch{'decypher'} = "script REGEXP '(decypher|dc_(target|make|blast|phrap)|TimeLogic)'"; $pkgmatch{'desmond'} = "( script LIKE '%desmond%' AND NOT ( username LIKE '%desmond%' ) )"; $pkgmatch{'dipole'} = "script LIKE '%.cxx.op%'"; $pkgmatch{'dissens'} = "script LIKE '%dissens.x%'"; $pkgmatch{'dns2d'} = "( script LIKE '%DNS2d.x%' OR script LIKE '%DNS2d_%.x%' OR script LIKE '%code2.x%' OR script LIKE '%spcal2d.x%' )"; $pkgmatch{'dock'} = "( script LIKE '%dock5%' OR script LIKE '%dock6%' OR script LIKE '%sphgen%' OR script LIKE '%mopac%' )"; $pkgmatch{'esp'} = "script LIKE '%/esp %'"; $pkgmatch{'ex_e'} = "script LIKE '%ex.e%'"; $pkgmatch{'fit_exe'} = "script LIKE '%fit.exe%'"; $pkgmatch{'fluent'} = "( script LIKE '%fluent%' OR ( software IS NOT NULL AND software LIKE '%fluent%' ) )"; $pkgmatch{'fsweep'} = "( script LIKE '%fsweep.exe%' OR script LIKE '%fsweep2.exe%' )"; $pkgmatch{'gabe'} = "script LIKE '%./gabe %'"; $pkgmatch{'gamess'} = "( script LIKE '%gamess%' OR script LIKE '%rungms%' OR script LIKE '%rungmx%' )"; $pkgmatch{'gaussian'} = "( script LIKE '%g98%' OR script LIKE '%g03%' OR script LIKE '%g09%' )"; $pkgmatch{'gc'} = "script LIKE '%kland_gc%'"; $pkgmatch{'gemc_x'} = "script LIKE '%gemc.x%'"; $pkgmatch{'glast'} = "( script LIKE '%glast%' OR script LIKE '%gp run%' )"; $pkgmatch{'harness'} = "script LIKE '%test_harness_driver.py%'"; $pkgmatch{'harris'} = "script LIKE '%harris.cxx.op%'"; $pkgmatch{'hd'} = "script LIKE '%/HD %'"; $pkgmatch{'hf'} = "script LIKE '%hf/hf%'"; $pkgmatch{'hf2'} = "script LIKE '%/hf2%'"; $pkgmatch{'hmmer'} = "( script LIKE '%hmmer%' OR script LIKE '%hmmp%' )"; $pkgmatch{'hpl'} = "script LIKE '%xhpl%'"; $pkgmatch{'hydro'} = "script LIKE '%./hydro %'"; $pkgmatch{'idl'}="( script LIKE '%module load idl%' OR script LIKE '%module add idl%' OR script LIKE '%\nidl%' OR ( software IS NOT NULL AND software LIKE '%idl%' ) )"; $pkgmatch{'hsi'} = "( script LIKE '%hsi%' OR script LIKE '%htar%' OR queue='hpss' )"; $pkgmatch{'ice'} = "script LIKE '%IceModule%'"; $pkgmatch{'imb'} = "script LIKE '%IMB-%'"; $pkgmatch{'imc'} = "script LIKE '%/imc.x%'"; $pkgmatch{'lammps'} = "( script LIKE '%lammps%' OR script LIKE '% lmp_%' OR script LIKE '%/lmp_%' )"; $pkgmatch{'liso'} = "script LIKE '%/liso %'"; $pkgmatch{'lsdyna'} = "( script LIKE '%lsdyna%' OR script LIKE '%ls-dyna%' OR script LIKE '%mpp-dyna%' OR script LIKE '%mpp971%' OR ( software IS NOT NULL AND software LIKE '%lsdyna%' ) )"; $pkgmatch{'lsp'} = "script LIKE '%/lsp.%'"; $pkgmatch{'madness'} = "( script LIKE '%m-a-d-n-e-s-s%' OR script LIKE '%slda%' )"; $pkgmatch{'md_xx'} = "script LIKE '%md.xx%'"; $pkgmatch{'meta'} = "( script LIKE '%anti.meta%' OR script LIKE '%para.meta%' OR script LIKE '%xray.meta%' )"; $pkgmatch{'mhd_1'} = "( script LIKE '%mhd_1%' OR script LIKE '%mhd_2%' OR script LIKE '%mhd_3%' OR script LIKE '%mhd_4%' OR script LIKE '%rmhd%' OR script LIKE '% mhd %' )"; $pkgmatch{'mhd_vec'} = "( script LIKE '%mhd_vec%' OR script LIKE '%mhd_pvec%' )"; $pkgmatch{'mm5'} = "( script LIKE '%mm5%' AND NOT SCRIPT LIKE '%womm5%' )"; $pkgmatch{'mrbayes'} = "( script LIKE '%mrbayes%' OR script LIKE '%mb-parallel%' )"; $pkgmatch{'nb'} = "script LIKE '%NB/CODES%'"; $pkgmatch{'ncbi'} = "( script LIKE '%ncbi%' OR script LIKE '%blastall%' OR script LIKE '%blastpgp%' OR script LIKE '%fastacmd%' OR script LIKE '%formatdb%' OR script LIKE '%rpsblast%' OR script LIKE '%seqtest%' )"; $pkgmatch{'nga_fb'} = "( script LIKE '%nga_fb%' OR script LIKE '%nga_cfb%' )"; $pkgmatch{'omega'} = "script LIKE '%omega.exe%'"; $pkgmatch{'openeye'} = "( script LIKE '%babel3%' OR script LIKE '%checkcff%' OR script LIKE '%chunker%' OR script LIKE '%fred2%' OR script LIKE '%fredPA%' OR script LIKE '%ligand_info%' OR script LIKE '%makefraglib%' OR script LIKE '%makerocsdb%' OR script LIKE '%nam2mol%' OR script LIKE '%omega2%' OR script LIKE '%szybki%' )"; $pkgmatch{'opt_exe'} = "( script LIKE '%opt_exe%' OR script LIKE '%scriptLaunchAll%' )"; $pkgmatch{'os2z'} = "( script LIKE '%/oS2x_%' OR script LIKE '%/oS2z_%' )"; $pkgmatch{'paraview'} = "( script LIKE '%paraview%' OR script LIKE '%pvserver%' )"; $pkgmatch{'pse'} = "( script LIKE '%/PSE\n' OR script LIKE '%/PSE2\n' )"; $pkgmatch{'psi4'} = "( script LIKE '%/psi4 %' OR script LIKE '%\npsi4%' )"; $pkgmatch{'pwscf'} = "( script LIKE '%pwscf%' OR script LIKE '%/pw.x %' OR script LIKE '%/ph.x %' )"; $pkgmatch{'r_out'} = "( script LIKE '%/r.out %' OR script LIKE '%/r.out\n%' )"; $pkgmatch{'radhyd'} = "( script LIKE '%radhyd%' OR script LIKE '%rhd_hyb%' OR script LIKE '%orion2%' )"; $pkgmatch{'real_exe'} = "script LIKE '%real.exe%'"; $pkgmatch{'reduce'} = "( script LIKE '%reduce_1%' OR script LIKE '%reduce_eta%' )"; $pkgmatch{'reflect'} = "script LIKE '%/reflect\n%'"; $pkgmatch{'root'} = "script LIKE '%\nroot -q%'"; $pkgmatch{'rosetta'} = "( script LIKE '%rosetta.%' OR script LIKE '%/rr %' )"; $pkgmatch{'roth'} = "script LIKE '%/ROTH%'"; $pkgmatch{'rtp'} = "( script LIKE '%rtp%' AND NOT ( script like '%RestartP%' ) AND NOT ( script LIKE '%addpertpath%' ) )"; $pkgmatch{'sable'} = "( script LIKE '%sable%' AND script NOT LIKE '%DISABLE%' )"; $pkgmatch{'sas'} = "( script LIKE '%\nsas%' OR ( software IS NOT NULL AND software LIKE '%sas%' ) OR queue LIKE '%sas%' )"; $pkgmatch{'scattering'} = "script LIKE '%/scattering %'"; $pkgmatch{'simu_pow'} = "( script LIKE '%simu_pow%' OR script LIKE '%simu_thres%' )"; $pkgmatch{'spark'} = "script LIKE '%spark-submit%'"; $pkgmatch{'tbms'} = "( script LIKE '%tbms%dvm%' OR script LIKE '%distr%dvm%' OR script LIKE '%jac%dvm%' OR script LIKE '%mt%dvm%' )"; $pkgmatch{'track'} = "script LIKE '%TRACKdir%'"; $pkgmatch{'turbo'} = "script LIKE '%pturbo.x%'"; $pkgmatch{'upc'} = "script LIKE '%upcrun%'"; $pkgmatch{'vasp'} = "script LIKE '%vasp%'"; $pkgmatch{'visit'} = "( script LIKE '%visit%' AND script NOT LIKE '%revisit%' )"; $pkgmatch{'vnc'} = "script LIKE '%vncserver%'"; $pkgmatch{'vpic'} = "( script LIKE '%npic%' OR script LIKE '%open.cxx.op%' )"; $pkgmatch{'xtest'} = "script LIKE '%/xtest%'"; $pkgmatch{'xx'} = "script LIKE '%./xx\n%'"; $pkgmatch{'zeus'} = "( script LIKE '%/zeus%' OR script LIKE '%/pglobal%' )"; $pkgmatch{'zNtoM'} = "( script LIKE '%z1to3%' OR script LIKE '%z4to6%' OR script LIKE '%z7to9%' OR script LIKE '%z10to12%' OR script LIKE '%z13to15%' )"; # package matches with dependencies on other package matches $pkgmatch{'R'} = "( ( script LIKE '%\nR %' OR script LIKE '%Rscript %' ) AND NOT ( ".$pkgmatch{'gaussian'}." ) AND NOT ( ".$pkgmatch{'adf'}." ) )"; $pkgmatch{'agk'} = "( script LIKE '%agk%' AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'mhd_1'}." ) )"; $pkgmatch{'amber'} = "( ( script LIKE '%amber%' OR script LIKE '%sander%' OR script LIKE '%pmemd%' OR script LIKE '%sviol%' OR script LIKE '%SingleJob%' OR script LIKE '%MINJob%' OR script LIKE '%run_md_mpi.csh%' ) AND NOT ( ".$pkgmatch{'cctm'}." ) AND NOT ( ".$pkgmatch{'cvm'}." ) AND NOT ( ".$pkgmatch{'idl'}." ) AND NOT ( ".$pkgmatch{'qmc'}." ) AND NOT ( ".$pkgmatch{'sigma'}." ) AND NOT ( ".$pkgmatch{'tantalus'}." ) AND NOT ( ".$pkgmatch{'tfe'}." ) )"; $pkgmatch{'arps'} = "( script LIKE '%arps%' AND NOT ( ".$pkgmatch{'adf'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'matlab'}." ) )"; $pkgmatch{'bugget'} = "( script LIKE '%bugget%' AND NOT ( ".$pkgmatch{'halo'}." ) AND NOT ( ".$pkgmatch{'simpleio'}." ) )"; $pkgmatch{'cactus'} = "( script LIKE '%cactus%' AND NOT ( ".$pkgmatch{'cdo'}." ) AND NOT ( ".$pkgmatch{'simfactory'}." ) )"; $pkgmatch{'cam'} = "( script LIKE '%cam%' AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'grads'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) )"; $pkgmatch{'ccsm'} = "( ( script LIKE '%ccsm%' OR script LIKE '%cpl%csim%clm%pop%cam%' ) AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'mm5'}." ) AND NOT ( ".$pkgmatch{'swift'}." ) )"; $pkgmatch{'charmm'} = "( script LIKE '%charmm%' AND NOT ( ".$pkgmatch{'chemshell'}." ) )"; $pkgmatch{'cpmd'} = "( script LIKE '%cpmd%' AND NOT ( ".$pkgmatch{'a_out'}." ) AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'inca'}." ) AND NOT ( ".$pkgmatch{'vasp'}." ) )"; $pkgmatch{'cvm'} = "( script LIKE '%cvm%' AND NOT ( ".$pkgmatch{'cpmd'}." ) AND NOT ( ".$pkgmatch{'psolve'}." ) )"; $pkgmatch{'eden'} = "( script LIKE '%eden%' AND NOT ( ".$pkgmatch{'matlab'}." ) )"; $pkgmatch{'enzo'} = "( script LIKE '%enzo%' AND NOT ( ".$pkgmatch{'rtp'}." ) )"; $pkgmatch{'f-plane'} = "( script LIKE '%f-plane%' AND NOT ( ".$pkgmatch{'hsi'}." ) )"; $pkgmatch{'foam'} = "( script LIKE '%foam%' AND NOT ( ".$pkgmatch{'lsdyna'}." ) )"; $pkgmatch{'gadget'} = "( script LIKE '%gadget%' AND NOT ( ".$pkgmatch{'hsi'}." ) )"; $pkgmatch{'gdl'} = "( script LIKE '%gdl%' AND NOT ( ".$pkgmatch{'rotbouss'}." ) )"; $pkgmatch{'grib'} = "( script LIKE '%grib%' AND NOT ( ".$pkgmatch{'cdo'}." ) AND NOT ( ".$pkgmatch{'mm5'}." ) AND NOT ( ".$pkgmatch{'sgf'}." ) AND NOT ( ".$pkgmatch{'sigma'}." ) )"; $pkgmatch{'gromacs'} = "( ( script LIKE '%gromacs%' OR script LIKE '%grompp%' OR script LIKE '%mdrun%' OR script LIKE '%rgmx%' ) AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'cpmd'}." ) AND NOT ( ".$pkgmatch{'sigma'}." ) AND NOT ( ".$pkgmatch{'tantalus'}." ) )"; $pkgmatch{'gtc'} = "( ( script LIKE '%gtc%' OR script LIKE '%gts%' ) AND NOT ( ".$pkgmatch{'cctm'}." ) AND NOT ( ".$pkgmatch{'pmcl3d'}." ) )"; $pkgmatch{'halo'} = "( script LIKE '%halo%' AND NOT ( ".$pkgmatch{'enzo'}." ) AND NOT ( ".$pkgmatch{'gadget'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'simpleio'}." ) AND NOT ( ".$pkgmatch{'yt'}." ) )"; $pkgmatch{'hfb'} = "( script LIKE '%hfb%' AND NOT ( ".$pkgmatch{'vbc'}." ) )"; $pkgmatch{'hfodd'} = "( script LIKE '%hfodd%' AND NOT ( ".$pkgmatch{'cdo'}." ) )"; $pkgmatch{'hmc'} = "( script LIKE '%hmc%' AND NOT ( ".$pkgmatch{'chroma'}." ) AND NOT ( ".$pkgmatch{'gadget'}." ) AND NOT ( ".$pkgmatch{'nplqcd'}." ) AND NOT ( ".$pkgmatch{'tantalus'}." ) AND NOT ( ".$pkgmatch{'terachem'}." ) )"; $pkgmatch{'hsphere'} = "( script LIKE '%hsphere%' AND NOT ( ".$pkgmatch{'lfm'}." ) )"; $pkgmatch{'hy3s'} = "( ( script LIKE '%SSA%' OR script LIKE '%HyJCMSS-%' ) AND NOT ( ".$pkgmatch{'arps'}." ) AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'bugget'}." ) AND NOT ( ".$pkgmatch{'cactus'}." ) AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'ccsm'}." ) AND NOT ( ".$pkgmatch{'cdo'}." ) AND NOT ( ".$pkgmatch{'charmm'}." ) AND NOT ( ".$pkgmatch{'energyplus'}." ) AND NOT ( ".$pkgmatch{'enzo'}." ) AND NOT ( ".$pkgmatch{'grmhd'}." ) AND NOT ( ".$pkgmatch{'halo'}." ) AND NOT ( ".$pkgmatch{'hchbm'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'milc'}." ) AND NOT ( ".$pkgmatch{'ncl'}." ) AND NOT ( ".$pkgmatch{'nwchem'}." ) AND NOT ( ".$pkgmatch{'simpleio'}." ) AND NOT ( ".$pkgmatch{'sses'}." ) AND NOT ( ".$pkgmatch{'tfe'}." ) )"; $pkgmatch{'ifs'} = "( script LIKE '%ifsMASTER%' AND NOT ( ".$pkgmatch{'cdp'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) )"; $pkgmatch{'inca'} = "( script LIKE '%inca%' AND NOT ( ".$pkgmatch{'vasp'}." ) )"; $pkgmatch{'ior'} = "( script LIKE '%ior%' AND NOT ( username LIKE '%ior%' ) AND NOT ( script LIKE '%prior%' ) AND NOT ( ".$pkgmatch{'a_out'}." ) AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'lammps'}." ) AND NOT ( ".$pkgmatch{'swift'}." ) )"; $pkgmatch{'meep'} = "( script LIKE '%meep%' AND NOT ( ".$pkgmatch{'sigma'}." ) )"; $pkgmatch{'milc'} = "( ( script LIKE '%milc%' OR script LIKE '%su3_%' OR script LIKE '%switch%.csh%' ) AND NOT ( ".$pkgmatch{'nicam'}." ) AND NOT ( ".$pkgmatch{'hmc'}." ) )"; $pkgmatch{'measurements'} = " ( script LIKE '%measurements%' ) AND NOT ( ".$pkgmatch{'milc'}." )"; $pkgmatch{'nag'} = "( script LIKE '%nag%' AND NOT ( ".$pkgmatch{'cctm'}." ) AND NOT ( ".$pkgmatch{'mpi_helium'}." ) )"; $pkgmatch{'namd'} = "( ( script LIKE '%namd%' OR script LIKE '%md.sh%' OR SCRIPT LIKE '%rem_mono_npt4.sh%') AND NOT ( ".$pkgmatch{'a_out'}." ) AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'cactus'}." ) AND NOT ( ".$pkgmatch{'charmm'}." ) AND NOT ( ".$pkgmatch{'cdo'}." ) AND NOT ( ".$pkgmatch{'gromacs'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'hmc'}." ) AND NOT ( ".$pkgmatch{'hy3s'}." ) AND NOT ( ".$pkgmatch{'ior'}." ) )"; $pkgmatch{'ncl'} = "( script LIKE '%ncl%' AND NOT ( script LIKE '%include%' ) AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'gen.v4'}." ) AND NOT ( ".$pkgmatch{'grmhd'}." ) AND NOT ( ".$pkgmatch{'swift'}." ) )"; $pkgmatch{'nested'} = "( script LIKE '%nested%' AND NOT ( ".$pkgmatch{'enzo'}." ) AND NOT ( ".$pkgmatch{'grib'}." ) )"; $pkgmatch{'nicam'} = "( script LIKE '%nicam%' AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'grads'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'hy3s'}." ) )"; $pkgmatch{'npb'} = "( script LIKE '%npb%' AND NOT ( script LIKE '%npbs.%' ) AND NOT ( script LIKE '%snsnpb%' ) AND NOT ( ".$pkgmatch{'milc'}." ) AND NOT ( ".$pkgmatch{'vorpal'}." ) )"; $pkgmatch{'omen'} = "( script LIKE '%omen%' AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'GreenSolver'}." ) AND NOT ( ".$pkgmatch{'milc'}." ) )"; $pkgmatch{'overlap'}="( script LIKE '%overlap_%' AND NOT ( ".$pkgmatch{'grib'}." ) AND NOT ( ".$pkgmatch{'hfb'}." ) AND NOT ( ".$pkgmatch{'nicam'}." ) AND NOT ( ".$pkgmatch{'simfactory'}." ) )"; $pkgmatch{'paratec'} = "( script LIKE '%paratec%' AND NOT ( ".$pkgmatch{'sigma'}." ) )"; $pkgmatch{'pcg'} = "( script LIKE '%pcg%' AND script NOT LIKE '%request%' AND NOT ( ".$pkgmatch{'gen.v4'}." ) )"; $pkgmatch{'pop'} = "( script LIKE '%pop%' AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'ccsm'}." ) AND NOT ( ".$pkgmatch{'cp2k'}." ) AND NOT ( ".$pkgmatch{'charmm'}." ) AND NOT ( ".$pkgmatch{'grib'}." ) AND NOT ( ".$pkgmatch{'gromacs'}." ) AND NOT ( ".$pkgmatch{'hmc'}." ) AND NOT ( ".$pkgmatch{'namd'}." ) AND NOT ( ".$pkgmatch{'nwchem'}." ) AND NOT ( ".$pkgmatch{'run_im'}." ) AND NOT ( ".$pkgmatch{'sses'}." ) )"; $pkgmatch{'propagators'} = "( script LIKE '%propagators%' AND NOT ( ".$pkgmatch{'milc'}." ) )"; $pkgmatch{'python'} = "( script LIKE '%python%' AND NOT ( ".$pkgmatch{'hoomd'}." ) )"; $pkgmatch{'qb'} = "( script LIKE '%qb%' AND NOT ( ".$pkgmatch{'hfb'}." ) AND NOT ( ".$pkgmatch{'milc'}." ) AND NOT ( ".$pkgmatch{'amber'}." ) )"; $pkgmatch{'qrpacc'} = "( script LIKE '%qrpacc%' AND NOT ( ".$pkgmatch{'vbc'}." ) )"; $pkgmatch{'quest'} = "( script LIKE '%quest%' AND script NOT LIKE '%request%' AND NOT ( ".$pkgmatch{'gen.v4'}." ) )"; $pkgmatch{'radhyd'} = "( script LIKE '%radhyd%' AND NOT ( ".$pkgmatch{'chimera'}." ) )"; $pkgmatch{'res'} = "( script LIKE '%/res_%' AND NOT ( ".$pkgmatch{'enzo'}." ) AND NOT ( ".$pkgmatch{'grib'}." ) AND NOT ( ".$pkgmatch{'lammps'}." ) )"; $pkgmatch{'run_im'} = "( script LIKE '%run_im%' AND NOT ( ".$pkgmatch{'aims'}." ) AND NOT ( ".$pkgmatch{'flash4'}." ) AND NOT ( ".$pkgmatch{'ncl'}." ) AND NOT ( ".$pkgmatch{'wrf'}." ) )"; $pkgmatch{'run_xyzvort'} = "( ( script LIKE '%run_xvort%' OR script LIKE '%run_yvort%' OR script LIKE '%run_zvort%' OR script LIKE '%run_thpert%' OR script LIKE '%run_u%' OR script LIKE '%run_v%' OR script LIKE '%run_w%' OR script LIKE '%run_dBZ%' ) AND NOT ( ".$pkgmatch{'beopest'}." ) AND NOT ( ".$pkgmatch{'lobster'}." ) AND NOT ( ".$pkgmatch{'paraview'}." ) AND NOT ( ".$pkgmatch{'vasp'}." ) AND NOT ( ".$pkgmatch{'vnc'}." ) AND NOT ( ".$pkgmatch{'wrf'}." ) )"; $pkgmatch{'s3d'} = "( script LIKE '%s3d%' AND NOT ( ".$pkgmatch{'adf'}." ) AND NOT ( ".$pkgmatch{'arps'}." ) AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'cctm'}." ) )"; $pkgmatch{'sgf'} = "( script LIKE '%sgf%' AND NOT ( ".$pkgmatch{'lsdyna'}." ) AND NOT ( ".$pkgmatch{'sigma'}." ) )"; $pkgmatch{'sord'} = "( script LIKE '%sord%' AND NOT ( ".$pkgmatch{'namd'}." ) )"; $pkgmatch{'sses'} = "( script LIKE '%sses%' AND NOT ( script LIKE '%subprocess%' ) AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'arps'}." ) AND NOT ( ".$pkgmatch{'cactus'}." ) AND NOT ( ".$pkgmatch{'cdo'}." ) AND NOT ( ".$pkgmatch{'enzo'}." ) AND NOT ( ".$pkgmatch{'grib'}." ) AND NOT ( ".$pkgmatch{'milc'}." ) AND NOT ( ".$pkgmatch{'namd'}." ) AND NOT ( ".$pkgmatch{'python'}." ) AND NOT ( ".$pkgmatch{'qb'}." ) AND NOT ( ".$pkgmatch{'vasp'}." ) AND NOT ( ".$pkgmatch{'vbc'}." ) )"; $pkgmatch{'sus'} = "( script LIKE '%sus%' AND NOT ( ".$pkgmatch{'cam'}." ) AND NOT ( ".$pkgmatch{'consensus'}." ) AND NOT ( ".$pkgmatch{'stata'}." ) )"; $pkgmatch{'tsc'} = "( script LIKE '%tsc%' AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'arps'}." ) AND NOT ( ".$pkgmatch{'cactus'}." ) AND NOT ( ".$pkgmatch{'foam'}." ) AND NOT ( ".$pkgmatch{'simfactory'}." ) AND NOT ( ".$pkgmatch{'swift'}." ) )"; $pkgmatch{'turbomole'} = "( script LIKE '%turbomole%' AND NOT ( ".$pkgmatch{'chemshell'}." ) )"; $pkgmatch{'ukh2d'} = "( ( script LIKE '%ukh2d%' OR script LIKE '%ukh.cxx.op%' ) AND NOT ( ".$pkgmatch{'h3d'}." ) )"; $pkgmatch{'wrf'} = "( script LIKE '%wrf%' AND NOT ( ".$pkgmatch{'arps'}." ) AND NOT ( ".$pkgmatch{'ccsm'}." ) AND NOT ( ".$pkgmatch{'grib'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'hy3s'}." ) AND NOT ( ".$pkgmatch{'milc'}." ) AND NOT ( ".$pkgmatch{'mm5'}." ) AND NOT ( ".$pkgmatch{'sgf'}." ) AND NOT ( ".$pkgmatch{'sigma'}." ) )"; $pkgmatch{'vmd'} = "( script LIKE '%vmd%' AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'cpmd'}." ) AND NOT ( ".$pkgmatch{'cvm'}." ) AND NOT ( ".$pkgmatch{'gromacs'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'hmc'}." ) AND NOT ( ".$pkgmatch{'namd'}." ) AND NOT ( ".$pkgmatch{'pop'}." ) )"; $pkgmatch{'xgc'} = "( script LIKE '%xgc%' AND NOT ( ".$pkgmatch{'agk'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) )"; $pkgmatch{'yt'} = "( script LIKE '%yt%' AND NOT ( ".$pkgmatch{'amber'}." ) AND NOT ( ".$pkgmatch{'cactus'}." ) AND NOT ( ".$pkgmatch{'cdo'}." ) AND NOT ( ".$pkgmatch{'gen.v4'}." ) AND NOT ( ".$pkgmatch{'grib'}." ) AND NOT ( ".$pkgmatch{'grmhd'}." ) AND NOT ( ".$pkgmatch{'hoomd'}." ) AND NOT ( ".$pkgmatch{'hsi'}." ) AND NOT ( ".$pkgmatch{'hy3s'}." ) AND NOT ( ".$pkgmatch{'lammps'}." ) AND NOT ( ".$pkgmatch{'lfm'}." ) AND NOT ( ".$pkgmatch{'matlab'}." ) AND NOT ( ".$pkgmatch{'namd'}." ) AND NOT ( ".$pkgmatch{'nwchem'}." ) AND NOT ( ".$pkgmatch{'pop'}." ) AND NOT ( ".$pkgmatch{'python'}." ) AND NOT ( ".$pkgmatch{'stata'}." ) AND NOT ( ".$pkgmatch{'sses'}." ) AND NOT ( ".$pkgmatch{'sord'}." ) AND NOT ( ".$pkgmatch{'swift'}." ) AND NOT ( ".$pkgmatch{'sus'}." ) AND NOT ( ".$pkgmatch{'vasp'}." ) AND NOT ( ".$pkgmatch{'vorpal'}." ) )"; return %pkgmatch; } # # Main program starts here # my $dbhost="localhost"; my $dbuser="pbsacct"; my $dbpasswd="pbsRroxor"; my $dbname="pbsacct"; my $dbtable="Jobs"; my $hostname='hostname'; my $fullreindex = 0; my $syntaxcheck = 0; my $domultimatch = 0; my $start_date; my $end_date; my $minjobs = 1000; my $mincpuhours = 100000; my $singlepkg; while ( $ARGV[0] =~ /^-.*/ ) { if ( $ARGV[0] eq "-d" ) { $dbname=$ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-h" ) { $hostname=$ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-p" ) { $dbpasswd=$ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-s" ) { $dbhost=$ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-t" ) { $dbtable=$ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-u" ) { $dbuser=$ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-C" ) { $mincpuhours = $ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-E" ) { $end_date = $ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-F" ) { $fullreindex = 1; } elsif ( $ARGV[0] eq "-J" ) { $minjobs = $ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-M" ) { $domultimatch = 1; } elsif ( $ARGV[0] eq "-P" ) { $singlepkg = $ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-S" ) { $start_date = $ARGV[1]; shift(@ARGV); } elsif ( $ARGV[0] eq "-T" ) { $syntaxcheck = 1; } shift(@ARGV); } # connect to DB my $dsn = "DBI:mysql:database=$dbname;host=$dbhost;"; my $dbh = DBI->connect($dsn,$dbuser,$dbpasswd) || die "$0: unable to connect to DB!\n"; # iterate over sw pkg patterns my %pkgmatch = software_match_list(); if ( $domultimatch==0 ) { my @pkglist; if ( defined($singlepkg) ) { @pkglist = ( $singlepkg ); } else { @pkglist = software_list(); } for my $pkg ( @pkglist ) { my $sql; if ( $syntaxcheck==0 ) { $sql = "UPDATE Jobs SET sw_app='".$pkg."'"; } else { $sql = "SELECT COUNT(jobid) FROM Jobs"; } $sql .= " WHERE system='".$hostname."' AND script IS NOT NULL AND ( ".$pkgmatch{$pkg}." )"; if ( $fullreindex==0 ) { $sql .= " AND sw_app IS NULL"; } if ( defined($start_date) ) { $sql .= " AND submit_date>='".$start_date."'"; } if ( defined($end_date) ) { $sql .= " AND submit_date<='".$end_date."'"; } $sql .= ";"; #print "$sql\n"; $dbh->do($sql) || die "$sql\n$0: query for pkg $pkg failed -- ".$dbh::errstr; } } else { # do multi-match analysis my %done; for my $pkg1 ( software_list() ) { for my $pkg2 ( software_list() ) { if ( $pkg1 ne $pkg2 && !defined($done{$pkg1}{$pkg2}) ) { #print "$pkg1:$pkg2\n"; my $sql = "SELECT '".$pkg1."' AS pkg1, '".$pkg2."' AS pkg2, COUNT(jobid) AS jobs, SUM(nproc*TIME_TO_SEC(walltime))/3600.0 AS cpuhours FROM Jobs WHERE system='".$hostname."' AND ( ( sw_app='".$pkg1."' AND ( ".$pkgmatch{$pkg2}." ) ) OR ( sw_app='".$pkg2."' AND ( ".$pkgmatch{$pkg1}." ) ) )"; if ( defined($start_date) ) { $sql .= " AND submit_date>='".$start_date."'"; } if ( defined($end_date) ) { $sql .= " AND submit_date<='".$end_date."'"; } $sql .= ";"; #print "$sql\n"; my $sth = $dbh->prepare($sql); $sth->execute() || die "Can't execute SQL statement: ", $sth->errstr(), "\n"; my @row = $sth->fetchrow_array(); if ( $row[2]>=$minjobs || $row[3]>=$mincpuhours ) { print "@row\n"; } $done{$pkg1}{$pkg2} = 1; $done{$pkg2}{$pkg1} = 1; } } } } # disconnect from DB $dbh->disconnect();