| [5d30c1] | 1 | #!/usr/bin/env perl
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| 2 | #eval 'exec perl $0 $*'
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| 3 | # if 0;
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| 4 |
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| 5 | $prefix = '@prefix@';
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| 6 | $exec_prefix = "@exec_prefix@";
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| 7 | $bindir = "@bindir@";
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| 8 | $scdatadir = "@scdatadir@";
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| 9 |
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| 10 | $pwd = `pwd`;
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| 11 | chomp $pwd;
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| 12 | $pwd =~ s/\/$//;
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| 13 |
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| 14 | use POSIX;
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| 15 |
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| 16 | # The path to the ccaffiene executable
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| 17 | $ccafe = "@CCAFE_BIN@/ccafe-batch";
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| 18 |
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| 19 | # The threadgrp specialization
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| 20 | $threadgrp = "none";
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| 21 |
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| 22 | # The mpi launch command
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| 23 | $launch = "@CCALAUNCH@";
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| 24 |
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| 25 | # The number of tasks
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| 26 | $ntask = 1;
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| 27 |
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| 28 | # A filename with a list of nodes.
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| 29 | $nodefile = "";
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| 30 |
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| 31 | # A command line argument with a list of nodes.
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| 32 | $nodes = "";
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| 33 |
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| 34 | # A format string to convert a node number to a node name
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| 35 | $nodename = "%d";
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| 36 |
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| 37 | # The number of nodes each job will use.
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| 38 | $nnodeperjob = "nnode";
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| 39 |
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| 40 | # The number of threads each process will use.
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| 41 | $nthreadperproc = 1;
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| 42 |
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| 43 | # The number of processes to run on each node.
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| 44 | $nprocpernode = 1;
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| 45 |
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| 46 | # The directory where the input file is to be found.
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| 47 | $inputprefix = "";
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| 48 |
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| 49 | # The directory where the output file is to be placed.
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| 50 | $outputprefix = "";
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| 51 |
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| 52 | # If true, then print out help info and exit
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| 53 | $help = 0;
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| 54 |
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| 55 | # If true, then don't actually run anything
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| 56 | $debug = 0;
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| 57 |
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| 58 | # If true, then print out extra info.
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| 59 | $verbose = 0;
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| 60 |
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| 61 | # If true, then overwrite output files that seem up-to-date
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| 62 | $rerun = 0;
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| 63 |
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| 64 | # If true, then do not overwrite any output file.
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| 65 | $onlynew = 0;
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| 66 |
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| 67 | ######################################################################
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| 68 |
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| 69 | use Getopt::Long;
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| 70 |
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| 71 | if (!GetOptions("launch=s" => \$launch,
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| 72 | "threadgrp=s" => \$threadgrp,
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| 73 | "nnodeperjob=i" => \$nnodeperjob,
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| 74 | "nthreadperproc=i" => \$nthreadperproc,
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| 75 | "nprocpernode=i" => \$nprocpernode,
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| 76 | "outputprefix=s" => \$outputprefix,
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| 77 | "inputprefix=s" => \$inputprefix,
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| 78 | "nodefile=s" => \$nodefile,
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| 79 | "nodes=s" => \$nodes,
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| 80 | "nodename=s" => \$nodename,
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| 81 | "help!" => \$help,
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| 82 | "rerun!" => \$rerun,
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| 83 | "onlynew!" => \$onlynew,
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| 84 | "debug!" => \$debug,
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| 85 | "verbose!" => \$verbose,
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| 86 | )) {
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| 87 | $help=1;
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| 88 | }
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| 89 |
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| 90 | if ("$launch" eq "@" . "CCALAUNCH@") {
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| 91 | $launch = "mpirun [-hf %NODEFILE%] -n %NPROC% %CCARUNPROC% %CCAFE% --ccafe-rc %INPUT% --ccafe-remap-stdio --ccafe-outputdir %OUTPUT%";
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| 92 | }
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| 93 |
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| 94 | $outputprefix =~ s/\/$//;
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| 95 | $inputprefix =~ s/\/$//;
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| 96 |
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| 97 | ######################################################################
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| 98 |
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| 99 | if ($help) {
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| 100 | print "Usage: $ARGV[0] [options] [rcfile1.in] [rcfile2.in] ...\n";
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| 101 | print "Options:\n";
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| 102 | print " --nnodeperjob n run with n nodes per job (value: $nnodeperjob)\n";
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| 103 | print " --nprocpernode n run with n procs per node (value: $nprocpernode)\n";
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| 104 | print " --nthreadperproc n use n threads per process (value: $nthreadperproc)\n";
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| 105 | print " --threadgrp grp use the given threading layer (value: $threadgrp)\n";
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| 106 | print " none: uses MPQC's default\n";
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| 107 | print " proc: does a single threaded run\n";
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| 108 | print " posix: use POSIX threads\n";
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| 109 | printf " --launch cmd use the given cmd to launch jobs--see below (value: %s)\n",
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| 110 | (($launch eq "")?"<not set>":$launch);
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| 111 | printf " --nodefile file a file listing nodes to use (value: %s)\n",
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| 112 | (($nodefile eq "")?"<not set>":$nodefile);
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| 113 | printf " --nodes nodes a command line list of machines to use (value: %s)\n",
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| 114 | (($nodes eq "")?"<not set>":$nodes);
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| 115 | printf " groups can be given as 8-10,12,15-17 for example\n";
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| 116 | printf " --nodename fmt converts node num to name (value: %s)\n", $nodename;
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| 117 | print " --rerun overwrite output file, even if up-to-date\n";
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| 118 | print " --onlynew do not overwrite output file, even if not up-to-date\n";
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| 119 | print " --inputprefix dir path to prefix input files with\n";
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| 120 | print " --outputprefix dir path to prefix output files with\n";
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| 121 | print " --debug don't actually run mpqc\n";
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| 122 | print " --help print this help\n";
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| 123 | print "\n";
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| 124 | print "The launch command can contain special strings that will be substituted.\n";
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| 125 | print "These are:\n";
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| 126 | print " %NPROC% The number of processes to start.\n";
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| 127 | print " %NODEFILE% The name of a file containing the node names.\n";
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| 128 | print " %NODELIST% A comma separated list of node names.\n";
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| 129 | print " For these last two, if they are contained within square brackets\n";
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| 130 | print " and a substitution is not available, then everything within the\n";
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| 131 | print " the brackets is removed.\n";
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| 132 | print "Examples of the launch argument:\n";
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| 133 | print " mpirun [-hf %NODEFILE%] -n %NPROC% %CCAFE% --ccafe-rc %INPUT% --ccafe-remap-stdio --ccafe-outp
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| 134 | utdir %OUTPUT%\n";
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| 135 | print " mpirun [-H %NODELIST%] -n %NPROC% %CCAFE% --ccafe-rc %INPUT% --ccafe-remap-stdio --ccafe-outp
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| 136 | utdir %OUTPUT%\n";
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| 137 | exit 0;
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| 138 | }
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| 139 |
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| 140 | ######################################################################
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| 141 |
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| 142 | @nodelist = ();
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| 143 | if ($nodes ne "") {
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| 144 | $nodes =~ s/-/../g;
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| 145 | foreach my $i (eval $nodes) {
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| 146 | $nodelist[$#nodelist + 1] = sprintf "$nodename", $i;
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| 147 | }
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| 148 | }
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| 149 | elsif ("$nodefile" eq "" && exists($ENV{"PBS_NODEFILE"})) {
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| 150 | $nodefile=$ENV{"PBS_NODEFILE"};
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| 151 | }
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| 152 | if ("$nodefile" ne "" && -f "$nodefile") {
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| 153 | my %nodesfound = {};
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| 154 | open(NODEFILE,"<$nodefile");
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| 155 | while(<NODEFILE>) {
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| 156 | if (/(\S+)/) {
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| 157 | my $nodename = $1;
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| 158 | if (!exists($nodesfound{$nodename})) {
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| 159 | $nodelist[$#nodelist + 1] = $nodename;
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| 160 | $nodesfound{$nodename} = 1;
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| 161 | }
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| 162 | }
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| 163 | }
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| 164 | close(NODEFILE);
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| 165 | }
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| 166 |
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| 167 | if ($#nodelist == -1) {
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| 168 | $nnode = 1;
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| 169 | }
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| 170 | else {
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| 171 | $nnode = $#nodelist + 1;
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| 172 | }
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| 173 |
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| 174 | if ($nnodeperjob eq "nnode") {
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| 175 | $nnodeperjob = $nnode;
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| 176 | }
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| 177 |
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| 178 | $nprocperjob = $nnodeperjob * $nprocpernode;
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| 179 |
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| 180 | $nnodeperjob = POSIX::ceil($nprocperjob / $nprocpernode);
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| 181 |
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| 182 | @jobnodes = ();
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| 183 | %jobnnodes = {};
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| 184 | %nodelist = {};
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| 185 | %nodefile = {};
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| 186 | $maxjobs = 0;
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| 187 | while (($maxjobs + 1) * $nnodeperjob <= $nnode) {
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| 188 | $jobnnodes[$maxjobs++] = $nnodeperjob;
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| 189 | }
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| 190 |
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| 191 | if ($maxjobs == 0) {
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| 192 | die "requested $nnodeperjob nodes but have $nnode nodes";
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| 193 | }
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| 194 |
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| 195 | $nodesbegin = 0;
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| 196 | foreach my $i (0..$maxjobs-1) {
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| 197 | my $nodesend = $nodesbegin + $jobnnodes[$i];
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| 198 | my @slice = (@nodelist)[$nodesbegin..($nodesend-1)];
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| 199 | $jobnodes{$i} = \@slice;
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| 200 | $nodesbegin = $nodesend;
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| 201 | foreach my $j (@slice) {
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| 202 | if ($nodelist{$i} eq "") { $nodelist{$i} = $j; }
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| 203 | else { $nodelist{$i} = sprintf "%s,%s", $nodelist{$i}, $j; }
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| 204 | }
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| 205 | $nodefile{$i} = ".tmp.nodefile.$$.$i";
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| 206 | open(NODEFILE,">" . $nodefile{$i});
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| 207 | foreach my $j (@slice) {
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| 208 | printf NODEFILE "%s\n", $j;
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| 209 | }
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| 210 | close(NODEFILE);
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| 211 | }
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| 212 |
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| 213 | ######################################################################
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| 214 |
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| 215 | if ($threadgrp eq "none" && $nthreadperproc > 1) {
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| 216 | $threadgrp = "posix";
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| 217 | }
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| 218 |
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| 219 | if ($threadgrp eq "proc") {
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| 220 | $ENV{"THREADGRP"} = "<ProcThreadGrp>:()";
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| 221 | }
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| 222 | elsif ($threadgrp eq "posix") {
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| 223 | $ENV{"THREADGRP"} = "<PthreadThreadGrp>:(num_threads=$nthreadperproc)";
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| 224 | }
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| 225 |
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| 226 | ######################################################################
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| 227 |
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| 228 | $usingthreads = 0;
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| 229 | if ($maxjobs > 1) {
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| 230 | require threads;
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| 231 | require threads::shared;
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| 232 | $usingthreads = 1;
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| 233 | }
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| 234 |
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| 235 | ######################################################################
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| 236 |
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| 237 | # autoflush output
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| 238 | $| = 1;
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| 239 |
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| 240 | @allfiles = reverse(get_file_list());
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| 241 |
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| 242 | my @seqfiles : shared = ();
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| 243 | my @files : shared = ();
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| 244 | foreach my $file (@allfiles) {
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| 245 | $files[$#files+1] = $file;
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| 246 | }
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| 247 |
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| 248 | printf "Running a maximum of %d jobs at a time.\n", $maxjobs;
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| 249 | printf "Running %d processes per job.\n", $nprocperjob;
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| 250 | printf "Running %d threads per process.\n", $nthreadperproc;
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| 251 | foreach my $i (0..$maxjobs-1) {
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| 252 | print "Nodes in slot $i:";
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| 253 | foreach my $j (@{$jobnodes{$i}}) {
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| 254 | printf " \"%s\"", $j;
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| 255 | }
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| 256 | print "\n";
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| 257 | }
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| 258 | printenvvar("MESSAGEGRP");
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| 259 | printenvvar("THREADGRP");
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| 260 | printenvvar("MEMORYGRP");
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| 261 | printenvvar("SCLIBDIR");
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| 262 | printenvvar("INTEGRAL");
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| 263 |
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| 264 | $thecount = 0;
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| 265 | $n = 0;
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| 266 |
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| 267 | if ($usingthreads) {
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| 268 | @threads = ();
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| 269 |
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| 270 | foreach my $jobnum (0..$maxjobs-1) {
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| 271 | my $thr = threads->new(\&jobrunner, $jobnum);
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| 272 | $threads[$#threads+1] = $thr;
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| 273 | }
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| 274 |
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| 275 | foreach my $thr (@threads) {
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| 276 | $thr->join();
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| 277 | }
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| 278 |
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| 279 | @threads = ();
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| 280 | }
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| 281 | else {
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| 282 | foreach my $jobnum (0..$maxjobs-1) {
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| 283 | jobrunner($jobnum);
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| 284 | }
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| 285 | }
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| 286 |
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| 287 | foreach $i (values(%nodefile)) {
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| 288 | unlink "$i";
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| 289 | }
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| 290 |
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| 291 | sub get_next_file {
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| 292 | my $jobnum = shift;
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| 293 | lock(@seqfiles) if ($usingthreads);
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| 294 | if ($#seqfiles >= 0 && $jobnum == 0) {
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| 295 | return pop(@seqfiles);
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| 296 | }
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| 297 | lock(@files) if ($usingthreads);
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| 298 | if ($#files >= 0) {
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| 299 | return pop(@files);
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| 300 | }
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| 301 | return "";
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| 302 | }
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| 303 |
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| 304 | sub jobrunner {
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| 305 | my $jobslot = shift;
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| 306 |
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| 307 | my $file;
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| 308 |
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| 309 | while ( ($file = get_next_file($jobslot)) ne "") {
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| 310 | $file =~ s/\.in//;
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| 311 | $tmp_out = "$pwd/$outputprefix/$file.tmp";
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| 312 | $ENV{"CCACHEM_RESULTS_DIR"} = "$tmp_out";
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| 313 | my $in = "$inputprefix/$file.in";
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| 314 | my $cmd = "$launch";
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| 315 | $cmd =~ s/%CCAFE%/$ccafe/;
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| 316 | $cmd =~ s/%NPROC%/$nprocperjob/;
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| 317 | $cmd =~ s/%INPUT%/$in/;
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| 318 |
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| 319 | my $ccarunproc = "$scdatadir/ccarunproc $ccafe";
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| 320 | if (exists($ENV{THREADGRP})) {
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| 321 | $ccarunproc = "$ccarunproc " . &isoencode("$ENV{THREADGRP}");
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| 322 | }
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| 323 | else {
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| 324 | $ccarunproc = "$ccarunproc none";
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| 325 | }
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| 326 | # no mem/message groups for now
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| 327 | $ccarunproc = "$ccarunproc none none";
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| 328 | #results dir
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| 329 | $ccarunproc = "$ccarunproc " . &isoencode("$ENV{CCACHEM_RESULTS_DIR}");
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| 330 |
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| 331 | $cmd =~ s|%CCARUNPROC%|$ccarunproc|;
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| 332 |
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| 333 | $cmd = substitute_optional_parameter($cmd, "%OUTPUT%", "$tmp_out");
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| 334 | $cmd = substitute_optional_parameter($cmd, "%NODELIST%", $nodelist{$jobslot});
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| 335 | $cmd = substitute_optional_parameter($cmd, "%NODEFILE%", $nodefile{$jobslot});
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| 336 |
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| 337 | mkdir $tmp_out;
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| 338 | printf "starting in slot %d: %s\n", $jobslot, "$cmd";
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| 339 | $cmd = "true" if ($debug);
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| 340 | $pid = fork();
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| 341 | if ($pid == 0) {
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| 342 | exec("$cmd");
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| 343 | die "exec returned";
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| 344 | }
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| 345 | waitpid($pid,'');
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| 346 |
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| 347 | rename "$tmp_out/pOut0", "$pwd/$outputprefix/$file.out";
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| 348 | unlink "$tmp_out/pErr0";
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| 349 | rename "$tmp_out/results.txt", "$pwd/$outputprefix/$file.results";
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| 350 | rmdir "$tmp_out";
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| 351 | }
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| 352 | }
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| 353 |
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| 354 | sub get_file_list {
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| 355 | my @dirfiles;
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| 356 | my @argfiles;
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| 357 |
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| 358 | if ($readdir ne "") {
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| 359 | opendir(DIR,"$readdir");
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| 360 | @tdirfiles = sort(readdir(DIR));
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| 361 | foreach my $j (@tdirfiles) {
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| 362 | if ($j =~ /\.in$/) {
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| 363 | $dirfiles[$#dirfiles+1] = $j;
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| 364 | }
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| 365 | }
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| 366 | closedir(DIR);
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| 367 | }
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| 368 |
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| 369 | @argfiles = sort(@ARGV);
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| 370 |
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| 371 | my @allfiles = (@dirfiles, @argfiles);
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| 372 |
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| 373 | my @files;
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| 374 |
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| 375 | foreach my $infile (@allfiles) {
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| 376 | my $out = outfile("$infile");
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| 377 | $out = "$outputprefix$out";
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| 378 | $in = "$inputprefix$infile";
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| 379 | if (!$rerun
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| 380 | && (-f "$out")
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| 381 | && ($onlynew
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| 382 | || (-M "$out" < -M "$in" && (! -f "$ccafe" || -M "$out" < -M "$mpqc")))) {
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| 383 | if ($verbose) {
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| 384 | print "$in: skipping: $out up-to-date\n";
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| 385 | }
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| 386 | }
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| 387 | else {
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| 388 | if ($verbose) {
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| 389 | print "$in: will be run\n";
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| 390 | }
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| 391 | $files[$#files+1] = "$infile";
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| 392 | }
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| 393 | }
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| 394 |
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| 395 | return @files;
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| 396 | }
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| 397 |
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| 398 | sub outfile {
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| 399 | my $in = shift;
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| 400 |
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| 401 | my $outbase = "$in";
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| 402 | $outbase =~ s/\.[^.]*$//;
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| 403 | $outbase = sprintf "%s.out", "$outbase";
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| 404 | my $out;
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| 405 |
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| 406 | if ($uniqout) {
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| 407 | $out = "$outbase";
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| 408 | my $outversion = 1;
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| 409 | while (-f "$out") {
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| 410 | $outversion++;
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| 411 | $out = sprintf "%s.%02d", "$outbase", $outversion;
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| 412 | }
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| 413 | }
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| 414 |
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| 415 | return "$out";
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| 416 | }
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| 417 |
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| 418 | sub printenvvar {
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| 419 | my $envvar = shift;
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| 420 | if (exists($ENV{$envvar})) {
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| 421 | printf "Using %s = \"%s\"\n", $envvar, $ENV{$envvar};
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| 422 | }
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| 423 | }
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| 424 |
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| 425 | sub substitute_optional_parameter {
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| 426 | my $str = shift;
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|---|
| 427 | my $name = shift;
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|---|
| 428 | my $value = shift;
|
|---|
| 429 | if ($value ne "") {
|
|---|
| 430 | $str =~ s/\[([^[]*$name[^[]*)\]/$1/;
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| 431 | $str =~ s/$name/$value/;
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|---|
| 432 | }
|
|---|
| 433 | else {
|
|---|
| 434 | $str =~ s/\[([^[]*$name[^[]*)\]//;
|
|---|
| 435 | }
|
|---|
| 436 | return $str;
|
|---|
| 437 | }
|
|---|
| 438 |
|
|---|
| 439 | sub isoencode {
|
|---|
| 440 | my $str = shift;
|
|---|
| 441 | $str =~ s/ /%20/g;
|
|---|
| 442 | $str =~ s/\</%3c/g;
|
|---|
| 443 | $str =~ s/\>/%3e/g;
|
|---|
| 444 | $str =~ s/\[/%5b/g;
|
|---|
| 445 | $str =~ s/\]/%5d/g;
|
|---|
| 446 | $str =~ s/\$/%24/g;
|
|---|
| 447 | $str =~ s/:/%38/g;
|
|---|
| 448 | $str =~ s/\(/%28/g;
|
|---|
| 449 | $str =~ s/\)/%29/g;
|
|---|
| 450 | return $str;
|
|---|
| 451 | }
|
|---|
