lib/nonmem_subs.pm

   1 # {{{ include statements
   2
   3 start include statements
   4 use File::Copy 'cp';
   5 use PsN;
   6 use ext::Config::Tiny;
   7 use ext::IPC::Run3;
   8 use Config;
   9 end include statements
  10
  11 # }}}
  12
  13 # {{{ new
  14
  15 start new
  16     {
  17       unless( defined $this -> {'outputfile'} ){
  18         $this -> {'outputfile'} = $this -> {'modelfile'};
  19         $this -> {'outputfile'} =~ s/\.mod$/\.lst/;
  20       }
  21
  22       unless( defined $this -> {'nm_directory'} ){
  23         my $nmdir = $PsN::config -> { 'nm_versions' } -> { $this -> {'version'} };
  24
  25         unless( defined $nmdir ){
  26           print "Unknown NONMEM version ",$this -> {'version'}," specified.\n";
  27           my @nmkeys = keys %{$PsN::config -> { 'nm_versions' }};
  28           if ( $#nmkeys == 0 and
  29                defined $nmkeys[0] and
  30                defined $PsN::config -> { 'nm_versions' } -> {$nmkeys[0]} ) {
  31             print "Using ",$PsN::config -> { 'nm_versions' } -> {$nmkeys[0]}," instead\n";
  32             $nmdir = $PsN::config -> { 'nm_versions' } -> {$nmkeys[0]};
  33           }
  34         }
  35
  36         $this -> {'nm_directory'} = $nmdir;
  37
  38         unless( defined $PsN::config -> {'compiler'} and defined $PsN::config -> {'compiler'} -> {'name'} ){
  39           debug -> warn( level => 1,
  40                          message => "No compiler defined, assuming g77" );
  41           $this -> {'compiler'} = 'g77';
  42         } else {
  43           $this -> {'compiler'} = $PsN::config -> {'compiler'} -> {'name'};
  44           $this -> {'compiler_options'} = $PsN::config -> {'compiler'} -> {'options'};
  45         }
  46       }
  47     }
  48 end new
  49
  50 # }}}
  51
  52 # {{{ compile
  53
  54 start compile
  55     {
  56       my $version = $self -> {'version'};
  57       my $nmdir = $self -> {'nm_directory'};
  58       my $includes;
  59       my $nmlink;
  60
  61       if( -e "$nmdir/util/nmlink5.exe" ){
  62         $nmlink = "$nmdir/util/nmlink5.exe";
  63         $self -> {'version'} = 5;
  64         if( $self -> {'show_version'} ){
  65           $version = $self -> {'version'};
  66         } else {
  67           $version = '';
  68         }
  69       } elsif ( -e "$nmdir/util/nmlink6.exe" ){
  70         $self -> {'version'} = 6;
  71         if( $self -> {'show_version'} ){
  72           $version = $self -> {'version'};
  73         } else {
  74           $version = '';
  75         }
  76         $nmlink = "$nmdir/util/nmlink6.exe";
  77         if( $Config{osname} eq 'MSWin32' ){
  78           $includes = "-I$nmdir\\sizes";
  79         } else {
  80           $includes = "-I$nmdir/sizes";
  81         }
  82       } else {
  83         my $err_version = ( defined $nmdir and $nmdir ne '' ) ? $nmdir : 'undefined';
  84         debug -> die( message => "Unable to find a supported version of NONMEM\n".
  85                       "The NONMEM installation directory is $err_version for version ".
  86                       $self -> {'version'}." according to psn.conf" );
  87       }
  88
  89       # first clean up from old compile
  90       unlink( 'FCON', 'FDATA', 'FREPORT','FSUBS', 'FSUBS.f','LINK.LNK','FSTREAM', 'PRDERR', 'nonmem.exe', 'nonmem' );
  91
  92       my $nm;
  93
  94       if( $Config{osname} eq 'MSWin32' ){
  95         $nm="$nmdir\\nm";
  96       } else {
  97         $nm="$nmdir/nm";
  98       }
  99
 100       my $modelfile = $self -> {'modelfile'};
 101
 102       run3( "$nmdir/tr/nmtran.exe", $modelfile, \$self -> {'nmtran_message'}, \$self -> {'nmtran_message'} );
 103
 104       #$self -> {'nmtran_message'} = `$nmdir/tr/nmtran.exe < $modelfile 2>&1`;
 105
 106       open( NMMSG, '>compilation_output.txt' );
 107       print( NMMSG $self -> {'nmtran_message'}, "\n" );
 108
 109       unless(-e 'FREPORT'){
 110         $self -> {'error_message'} = "NMtran failed: \n" . $self -> {'nmtran_message'} ;
 111         return 0;
 112       }
 113
 114       my $nmlink_message;
 115       run3( "$nmlink", undef, \$nmlink_message, \$nmlink_message );
 116
 117       print( NMMSG $nmlink_message, "\n" );
 118
 119       my $fsub;
 120
 121       if(-e 'FSUBS'){
 122         if( $self -> {'compiler'} eq 'g77' ){
 123           cp("FSUBS", "FSUBS.f");
 124           $fsub='FSUBS.f';
 125         } else {
 126           cp("FSUBS", "FSUBS.for");
 127           $fsub='FSUBS.for';
 128         }
 129       }
 130
 131       if( defined $self -> {'fsubs'} ){
 132         foreach my $sub ( @{$self -> {'fsubs'}} ){
 133           $fsub .= " $sub";
 134         }
 135       }
 136
 137       open( FH, "<", 'LINK.LNK' );
 138       my @link;
 139       while( <FH> ){
 140         my $tmp = $_;
 141         $tmp =~ s/^\s+//;
 142         $tmp =~ s/\s+$//;
 143         push(@link, $tmp);
 144       }
 145
 146       my $compile_message;
 147       my $compile_command;
 148
 149       if( $self -> {'compiler'} eq 'g77' ){
 150
 151         my @nmlib = ("$nm/NONMEM.o", "$nm/BLKDAT.o", "$nm/nonmem.a");
 152         $compile_command = "g77 " . $self -> {'compiler_options'} . " -ononmem$version $includes $fsub @link @nmlib 2>&1";
 153
 154       } elsif( $self -> {'compiler'} eq 'df' or $self -> {'compiler'} eq 'fl32' ){
 155
 156         my @nmlib = ("$nm\\nonmem.obj", "$nm\\blkdat.obj", "$nm\\nonmem.lib");
 157 # <<<<<<< nonmem_subs.pm
 158 #       if( $fsub ){
 159 #         $compile_command = "df " . $self -> {'compiler_options'} . " /Fenonmem $fsub @nmlib @link";
 160 #       } else {
 161 #         $compile_command = "df " . $self -> {'compiler_options'} . " /Fenonmem @nmlib @link";
 162 #       }
 163 #       } elsif( $self -> {'compiler'} eq 'fl32' ){
 164 #       my @nmlib = ("$nm\\nonmem.obj", "$nm\\blkdat.obj", "$nm\\nonmem.lib");
 165 #       if( $fsub ){
 166 #         $compile_command = "fl32 " . $self -> {'compiler_options'} . " /Fenonmem $fsub @nmlib @link";
 167 #       } else {
 168 #         $compile_command = "fl32 " . $self -> {'compiler_options'} . " /Fenonmem @nmlib @link";
 169 #       }
 170 # =======
 171         $compile_command = $self -> {'compiler'}." " . $self -> {'compiler_options'} . " /Fenonmem $fsub @nmlib @link";
 172
 173 #>>>>>>> 1.27
 174       }
 175
 176       run3( "$compile_command", undef, \$compile_message, \$compile_message );
 177
 178       print( NMMSG $compile_message, "\n" );
 179
 180       close( NMMSG );
 181
 182       if( $self -> {'compiler'} eq 'df' or $self -> {'compiler'} eq 'fl32' ){
 183         unless(-e "nonmem.exe") {
 184           $self -> {'error_message'} = "Fortran Compilation failed: \n" . $compile_message ;
 185           return 0;
 186         }
 187       } else {
 188         unless(-e "nonmem$version") {
 189           $self -> {'error_message'} = "Fortran Compilation failed: \n" . $compile_message ;
 190           return 0;
 191         }
 192       }
 193     }
 194 end compile
 195
 196 # }}}
 197
 198 # {{{ execute
 199 start execute
 200     {
 201       my $version = $self -> {'version'};
 202       my $nmdir = $self -> {'nm_directory'};
 203       my $outputfile = $self -> {'outputfile'};
 204
 205       if( $Config{osname} eq 'MSWin32' ){
 206         run3( "nonmem.exe", undef, undef );
 207         if ( -e "output" ) {
 208           cp( "output", $outputfile );
 209           unlink( "output" );
 210         } elsif ( -e "OUTPUT" ) {
 211           cp( "OUTPUT", $outputfile );
 212           unlink( "OUTPUT" );
 213         }
 214       } else {
 215         unless( $self -> {'show_version'} ){
 216           $version = '';
 217         }
 218         run3( "nice -n " . $self -> {'nice'} . " ./nonmem$version", "FCON", $outputfile );
 219         open( OUTPUTFILE, '>>', $outputfile );
 220         print( OUTPUTFILE  "This file was created using the NONMEM version in directory $nmdir\n" );
 221         print( OUTPUTFILE  `date`, "\n" );
 222         close( OUTPUTFILE );
 223       }
 224     }
 225 end execute
 226 # }}}