lib/nonmem_subs.pm

   1 # {{{ include statements
   2
   3 start include statements
   4 if( $0 =~ /nonmem.pm$/ ) {
   5   use FindBin qw($Bin);
   6   use lib "$Bin";
   7 }
   8 use File::Copy 'cp';
   9 #use ext::Config::Tiny;
  10 use ext::IPC::Run3;
  11 use Config;
  12 if( $0 =~ /nonmem.pm$/ ) {
  13   require PsN;
  14   my $nonmem = nonmem -> new( 'modelfile'       => $ARGV[0],
  15                               'outputfile'      => $ARGV[1],
  16                               'nice'            => $ARGV[2],
  17                               'version'         => $ARGV[3],
  18                               'fsubs'           => [split( /,/ , $ARGV[6] )],
  19                               'nm_directory'    => $ARGV[7],
  20                               'show_version'    => 0);
  21
  22   my $compile = $ARGV[4];
  23   my $execute = $ARGV[5];
  24
  25   if( $compile ){
  26     unless( $nonmem -> compile() ){
  27       debug -> die( message => $nonmem -> error_message );
  28     }
  29   }
  30
  31   if( $execute ){
  32     $nonmem -> execute;
  33   }
  34 }
  35 end include statements
  36
  37 # }}}
  38
  39 # {{{ new
  40
  41 start new
  42     {
  43       unless( defined $this -> {'outputfile'} ){
  44         $this -> {'outputfile'} = $this -> {'modelfile'};
  45         $this -> {'outputfile'} =~ s/\.mod$/\.lst/;
  46       }
  47
  48       unless( defined $this -> {'nm_directory'} ){
  49         my ($nmdir,$version) = split(/,/ , $PsN::config -> { 'nm_versions' } -> { $this -> {'version'} });
  50
  51         unless( defined $nmdir ){
  52           print "Unknown NONMEM version ",$this -> {'version'}," specified.\n";
  53           my @nmkeys = keys %{$PsN::config -> { 'nm_versions' }};
  54           if ( $#nmkeys == 0 and
  55                defined $nmkeys[0] and
  56                defined $PsN::config -> { 'nm_versions' } -> {$nmkeys[0]} ) {
  57             #print "Using ",$PsN::config -> { 'nm_versions' } -> {$nmkeys[0]}," instead\n";
  58             my( $nmdir, $version ) = split(/,/,$PsN::config -> { 'nm_versions' } -> {$nmkeys[0]});;
  59           }
  60         }
  61
  62         $this -> {'nm_directory'} = $nmdir;
  63
  64         unless( defined $PsN::config -> {'compiler'} and defined $PsN::config -> {'compiler'} -> {'name'} ){
  65           debug -> warn( level => 1,
  66                          message => "No compiler defined, assuming g77" );
  67           $this -> {'compiler'} = 'g77';
  68         } else {
  69           $this -> {'compiler'} = $PsN::config -> {'compiler'} -> {'name'};
  70           $this -> {'compiler_options'} = $PsN::config -> {'compiler'} -> {'options'};
  71         }
  72       }
  73     }
  74 end new
  75
  76 # }}}
  77
  78 # {{{ compile
  79
  80 start compile
  81     {
  82       my $version = $self -> {'version'};
  83       my $nmdir = $self -> {'nm_directory'};
  84       my $includes;
  85       my $nmlink;
  86       my $adaptive = $self -> {'adaptive'} ? '_adaptive' : '';
  87       if( -e "$nmdir/util/nmlink5.exe" ){
  88         $nmlink = "$nmdir/util/nmlink5.exe";
  89         $self -> {'version'} = 5;
  90         if( $self -> {'show_version'} ){
  91           $version = $self -> {'version'};
  92         } else {
  93           $version = '';
  94         }
  95       } elsif ( -e "$nmdir/util/nmlink6.exe" ){
  96         $self -> {'version'} = 6;
  97         if( $self -> {'show_version'} ){
  98           $version = $self -> {'version'};
  99         } else {
 100           $version = '';
 101         }
 102         $nmlink = "$nmdir/util/nmlink6.exe";
 103         if( $Config{osname} eq 'MSWin32' ){
 104           $includes = "-I$nmdir\\sizes";
 105         } else {
 106           $includes = "-I$nmdir/sizes";
 107         }
 108       } else {
 109         my $err_version = ( defined $nmdir and $nmdir ne '' ) ? $nmdir : '[not configured]';
 110         debug -> die( message => "Unable to find a supported version of NONMEM\n".
 111                       "The NONMEM installation directory is $err_version for version [".
 112                       $self -> {'version'}."] according to psn.conf." );
 113       }
 114
 115       # first clean up from old compile
 116       unlink( 'FLIB','FCON', 'FDATA', 'FREPORT','FSUBS', 'FSUBS.f','LINK.LNK','FSTREAM', 'PRDERR', 'nonmem.exe', 'nonmem', 'nonmem5', 'nonmem6', 'nonmem5_adaptive', 'nonmem6_adaptive' );
 117
 118       my $nm;
 119
 120       if( $Config{osname} eq 'MSWin32' ){
 121         $nm="$nmdir\\nm";
 122       } else {
 123         $nm="$nmdir/nm";
 124       }
 125
 126       my $modelfile = $self -> {'modelfile'};
 127
 128       if( $Config{osname} eq 'MSWin32' ){
 129         run3( "$nmdir/tr/nmtran.exe", $modelfile, \$self -> {'nmtran_message'}, \$self -> {'nmtran_message'} );
 130       } else {
 131         run3( 'nice -' . $self -> {'nice'} . " $nmdir/tr/nmtran.exe", $modelfile, \$self -> {'nmtran_message'}, \$self -> {'nmtran_message'} );
 132       }
 133
 134       open( NMMSG, '>compilation_output.txt' );
 135       print( NMMSG $self -> {'nmtran_message'}, "\n" );
 136
 137       unless(-e 'FREPORT'){
 138         close(NMMSG);
 139         $self -> {'error_message'} = "NMtran failed: \n" . $self -> {'nmtran_message'} ;
 140         return 0;
 141       }
 142
 143       my $nmlink_message;
 144       run3( "$nmlink", undef, \$nmlink_message, \$nmlink_message );
 145
 146       print( NMMSG $nmlink_message, "\n" );
 147
 148       my $fsub;
 149
 150       if(-e 'FSUBS'){
 151         if( $self -> {'compiler'} eq 'g77' or $self -> {'compiler'} eq 'g95' ){
 152           rename("FSUBS", "FSUBS.f");
 153           $fsub='FSUBS.f';
 154         } else {
 155           rename("FSUBS", "FSUBS.for");
 156           $fsub='FSUBS.for';
 157         }
 158       }
 159
 160       if( defined $self -> {'fsubs'} and $self -> {'version'} != 6 ){
 161         foreach my $sub ( @{$self -> {'fsubs'}} ){
 162           $fsub .= " $sub";
 163         }
 164       }
 165
 166       open( FH, "<", 'LINK.LNK' );
 167       my @link;
 168       while( <FH> ){
 169         my $tmp = $_;
 170         $tmp =~ s/^\s+//;
 171         $tmp =~ s/\s+$//;
 172         push(@link, $tmp);
 173       }
 174       close( FH );
 175
 176       my $compile_message;
 177       my $compile_command;
 178
 179       my @nmlib;
 180
 181       if( $Config{osname} eq 'MSWin32' ){
 182         @nmlib = ("$nm\\NONMEM.obj","$nm\\BLKDAT.obj","$nm\\nonmem.lib");
 183       } else {
 184         @nmlib = ("$nm/NONMEM.o", "$nm/BLKDAT.o", "$nm/nonmem.a");
 185       }
 186       $compile_command = "g77 " . $self -> {'compiler_options'} . " -ononmem$version$adaptive $includes $fsub @link @nmlib 2>&1";
 187
 188       if( $self -> {'compiler'} eq 'g77' ){
 189
 190         $compile_command = "g77 " . $self -> {'compiler_options'} . " -ononmem$version$adaptive $includes $fsub @link @nmlib 2>&1";
 191
 192       } elsif( $self -> {'compiler'} eq 'g95' ){
 193
 194         $compile_command = "g95 " . $self -> {'compiler_options'} . " -ononmem$version$adaptive $includes $fsub @link @nmlib 2>&1";
 195
 196       } elsif( $self -> {'compiler'} eq 'df' or $self -> {'compiler'} eq 'fl32' ){
 197         $compile_command = $self -> {'compiler'}." " . $self -> {'compiler_options'} . " /Fenonmem $fsub @nmlib @link";
 198
 199       } elsif( $self -> {'compiler'} eq 'ifort' ){
 200
 201         $compile_command = "ifort " . $self -> {'compiler_options'} . " -ononmem$version$adaptive $includes $fsub @link @nmlib 2>&1";
 202
 203       }
 204
 205       run3( "$compile_command", undef, \$compile_message, \$compile_message );
 206
 207       print( NMMSG $compile_message, "\n" );
 208
 209       close( NMMSG );
 210
 211       unless(-e "nonmem.exe" or -e "nonmem$version$adaptive" ) {
 212         $self -> {'error_message'} = "Fortran Compilation failed: \n" . $compile_message ;
 213         return 0;
 214       }
 215     }
 216 end compile
 217
 218 # }}}
 219
 220 # {{{ execute
 221
 222 start execute
 223     {
 224       my $version = $self -> {'version'};
 225       my $nmdir = $self -> {'nm_directory'};
 226       my $outputfile = $self -> {'outputfile'};
 227       my $adaptive = $self -> {'adaptive'} ? '_adaptive' : '';
 228
 229       my ( $start_time, $fin_time );
 230       if( $Config{osname} eq 'MSWin32' ){
 231         $start_time = `date /T`;
 232         chomp($start_time);
 233         $start_time = $start_time.' '.`time /T`;
 234         run3( "nonmem.exe", undef, \undef );
 235         $fin_time = `date /T`;
 236         chomp($fin_time);
 237         $fin_time = $fin_time.' '.`time /T`;
 238         if ( -e "output" ) {
 239           cp( "output", $outputfile );
 240           unlink( "output" );
 241         } elsif ( -e "OUTPUT" ) {
 242           cp( "OUTPUT", $outputfile );
 243           unlink( "OUTPUT" );
 244         }
 245       } else {
 246         unless( $self -> {'show_version'} ){
 247           $version = '';
 248         }
 249         $start_time = `date`;
 250         if ( -e "/proc/self/lock" ) {
 251           open (OUTFILE,">/proc/self/lock") || die "Could not unlock myself!\n";
 252           print OUTFILE "0";
 253           close (OUTFILE);
 254         }
 255         run3( "nice -n " . $self -> {'nice'} . " ./nonmem$version$adaptive", "FCON", $outputfile );
 256         if ( -e "/proc/self/lock" ) {
 257           open (OUTFILE,">/proc/self/lock") || die "Could not lock myself!\n";
 258           print OUTFILE "1";
 259           close (OUTFILE);
 260         }
 261         $fin_time = `date`;
 262       }
 263       open( OUT, '>>', $outputfile );
 264       print( OUT  "This file was created using the NONMEM version in directory $nmdir\n" );
 265       print( OUT "Started  $start_time" );
 266       print( OUT "Finished $fin_time" );
 267       close( OUT );
 268     }
 269 end execute
 270
 271 # }}}