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           print "Configuration file is ",$PsN::config_file,"\n";
  54           my @nmkeys = keys %{$PsN::config -> { 'nm_versions' }};
  55           if ( $#nmkeys == 0 and
  56                defined $nmkeys[0] and
  57                defined $PsN::config -> { 'nm_versions' } -> {$nmkeys[0]} ) {
  58             print "Using the only defined version $nmkeys[0] in ",$PsN::config -> { 'nm_versions' } -> {$nmkeys[0]}," instead\n";
  59             my( $nmdir, $version ) = split(/,/,$PsN::config -> { 'nm_versions' } -> {$nmkeys[0]});;
  60           }
  61         }
  62
  63         $this -> {'nm_directory'} = $nmdir;
  64
  65         unless( defined $PsN::config -> {'compiler'} and defined $PsN::config -> {'compiler'} -> {'name'} ){
  66           debug -> warn( level => 1,
  67                          message => "No compiler defined, assuming g77" );
  68           $this -> {'compiler'} = 'g77';
  69         } else {
  70           $this -> {'compiler'} = $PsN::config -> {'compiler'} -> {'name'};
  71           $this -> {'compiler_options'} = $PsN::config -> {'compiler'} -> {'options'};
  72         }
  73       }
  74     }
  75 end new
  76
  77 # }}}
  78
  79 # {{{ compile
  80
  81 start compile
  82     {
  83       my $version = $self -> {'version'};
  84       my $nmdir = $self -> {'nm_directory'};
  85       my $includes;
  86       my $nmlink;
  87       my $adaptive = $self -> {'adaptive'} ? '_adaptive' : '';
  88       if( -e "$nmdir/util/nmlink5.exe" ){
  89         $nmlink = "$nmdir/util/nmlink5.exe";
  90         $self -> {'version'} = 5;
  91         if( $self -> {'show_version'} ){
  92           $version = $self -> {'version'};
  93         } else {
  94           $version = '';
  95         }
  96       } elsif ( -e "$nmdir/util/nmlink6.exe" ){
  97         $self -> {'version'} = 6;
  98         if( $self -> {'show_version'} ){
  99           $version = $self -> {'version'};
 100         } else {
 101           $version = '';
 102         }
 103         $nmlink = "$nmdir/util/nmlink6.exe";
 104         if( $Config{osname} eq 'MSWin32' ){
 105           $includes = "-I$nmdir\\sizes";
 106         } else {
 107           $includes = "-I$nmdir/sizes";
 108         }
 109       } else {
 110         my $err_version = ( defined $nmdir and $nmdir ne '' ) ? $nmdir : '[not configured]';
 111         debug -> die( message => "Unable to find a supported version of NONMEM\n".
 112                       "The NONMEM installation directory is $err_version for version [".
 113                       $self -> {'version'}."] according to psn.conf." );
 114       }
 115
 116       # first clean up from old compile
 117       unlink( 'FLIB','FCON', 'FDATA', 'FREPORT','FSUBS', 'FSUBS.f','LINK.LNK','FSTREAM', 'PRDERR', 'nonmem.exe', 'nonmem', 'nonmem5', 'nonmem6', 'nonmem5_adaptive', 'nonmem6_adaptive' );
 118
 119       my $nm;
 120
 121       if( $Config{osname} eq 'MSWin32' ){
 122         $nm="$nmdir\\nm";
 123       } else {
 124         $nm="$nmdir/nm";
 125       }
 126
 127       my $modelfile = $self -> {'modelfile'};
 128
 129       run3( "nice -19 $nmdir/tr/nmtran.exe", $modelfile, \$self -> {'nmtran_message'}, \$self -> {'nmtran_message'} );
 130
 131       #$self -> {'nmtran_message'} = `nice -19 $nmdir/tr/nmtran.exe < $modelfile 2>&1`;
 132
 133       open( NMMSG, '>compilation_output.txt' );
 134       print( NMMSG $self -> {'nmtran_message'}, "\n" );
 135
 136       unless(-e 'FREPORT'){
 137         close(NMMSG);
 138         $self -> {'error_message'} = "NMtran failed: \n" . $self -> {'nmtran_message'} ;
 139         return 0;
 140       }
 141
 142       my $nmlink_message;
 143
 144       run3( "$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' ){
 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'} ){
 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       if( $self -> {'compiler'} eq 'g77' ){
 180
 181         my @nmlib = ("$nm/NONMEM.o", "$nm/BLKDAT.o", "$nm/nonmem.a");
 182         $compile_command = "g77 " . $self -> {'compiler_options'} . " -ononmem$version$adaptive $includes $fsub @link @nmlib 2>&1";
 183
 184       } elsif( $self -> {'compiler'} eq 'df' or $self -> {'compiler'} eq 'fl32' ){
 185
 186         my @nmlib = ("$nm\\nonmem.obj", "$nm\\blkdat.obj", "$nm\\nonmem.lib");
 187         $compile_command = $self -> {'compiler'}." " . $self -> {'compiler_options'} . " /Fenonmem $fsub @nmlib @link";
 188
 189       } elsif( $self -> {'compiler'} eq 'ifort' ){
 190         my @nmlib = ("$nm/NONMEM.o", "$nm/BLKDAT.o", "$nm/nonmem.a");
 191         $compile_command = "ifort        " . $self -> {'compiler_options'} . " -ononmem$version$adaptive $includes $fsub @link @nmlib 2>&1";
 192       }
 193
 194       run3( "$compile_command", undef, \$compile_message, \$compile_message );
 195
 196       print( NMMSG $compile_message, "\n" );
 197
 198
 199       unless(-e "nonmem.exe" or -e "nonmem$version$adaptive" ) {
 200         $self -> {'error_message'} = "Fortran Compilation failed: \n" . $compile_message ;
 201         close( NMMSG );
 202         return 0;
 203       } else {
 204         print( NMMSG "Compilation done\n" );
 205         close( NMMSG );
 206       }
 207     }
 208 end compile
 209
 210 # }}}
 211
 212 # {{{ execute
 213
 214 start execute
 215     {
 216       my $version = $self -> {'version'};
 217       my $nmdir = $self -> {'nm_directory'};
 218       my $outputfile = $self -> {'outputfile'};
 219       my $adaptive = $self -> {'adaptive'} ? '_adaptive' : '';
 220
 221       my ( $start_time, $fin_time );
 222       if( $Config{osname} eq 'MSWin32' ){
 223         $start_time = `date /T`;
 224         chomp($start_time);
 225         $start_time = $start_time.' '.`time /T`;
 226         run3( "nonmem.exe", undef, \undef );
 227         $fin_time = `date /T`;
 228         chomp($fin_time);
 229         $fin_time = $fin_time.' '.`time /T`;
 230         if ( -e "output" ) {
 231           cp( "output", $outputfile );
 232           unlink( "output" );
 233         } elsif ( -e "OUTPUT" ) {
 234           cp( "OUTPUT", $outputfile );
 235           unlink( "OUTPUT" );
 236         }
 237       } else {
 238         unless( $self -> {'show_version'} ){
 239           $version = '';
 240         }
 241         $start_time = `date`;
 242         run3( "nice -n " . $self -> {'nice'} . " ./nonmem$version$adaptive", "FCON", $outputfile );
 243         $fin_time = `date`;
 244       }
 245       open( OUT, '>>', $outputfile );
 246       print( OUT  "This file was created using the NONMEM version in directory $nmdir\n" );
 247       print( OUT "Started  $start_time" );
 248       print( OUT "Finished $fin_time" );
 249       close( OUT );
 250     }
 251 end execute
 252
 253 # }}}