maincl.cpp

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/* This file is part of Cloudy and is copyright (C)1978-2017 by Gary J. Ferland and
 * others.  For conditions of distribution and use see copyright notice in license.txt */
/*main program that reads input and calls cloudy to compute a single model, or
 * try to optimize an observed model.  Routine returns 0 if model is ok, 
 * and 1 if problems occurred. */
#include "cddefines.h"
#include "cddrive.h"
#include "input.h"
#include "prt.h"
#include "save.h"
#include "called.h"
#include "monitor_results.h"
#include "grid.h"

exit_type cdMain( int argc, const char* argv[] );

inline void print_delimiter(long nOptimiz)
{
        fprintf( ioQQQ, " ************************************************** GRID_DELIMIT" );
        if( nOptimiz >= 0 )
                fprintf( ioQQQ, " -- grid%9.9ld", nOptimiz );
        fprintf( ioQQQ, "\n" );
}

int main( int argc, char *argv[] )
{
        exit_type exit_status = ES_SUCCESS;

        DEBUG_ENTRY( "main()" );

        bool lgMPI = cpu.i().lgMPI();

        cpu.i().set_used_nCPU( 1 );
        if( lgMPI )
        {
                MPI_Init( &argc, &argv );

                int nCPU = 1, nRANK = 0;
                MPI_Comm_size( MPI_COMM_WORLD, &nCPU );
                cpu.i().set_nCPU( nCPU );
                cpu.i().set_used_nCPU( nCPU );
                MPI_Comm_rank( MPI_COMM_WORLD, &nRANK );
                cpu.i().set_nRANK( nRANK );

                // MPI_Init() will have overwritten our signal handlers
                // so we need to set them again....
                cpu.i().set_signal_handlers();
        }

        // save headers are needed for sequential runs
        // saving headers during the initial parsing of grid runs is also OK
        save.SetSaveHeaderNeeded( true );

        // this will generate input files for each grid point,
        // or execute the Phymir run, whichever is appropriate
        exit_status = cdMain( argc, (const char**)argv );

        // wait for writing of input files to finish
        if( lgMPI )
                MPI_Barrier( MPI_COMM_WORLD );

        // process the individual grid points
        if( grid.lgGrid && exit_status == ES_SUCCESS )
        {
                // this was set to true after we wrote the last input script
                grid.lgGridDone = false;

                // from now on each rank will run its own model
                cpu.i().set_MPISingleRankMode( true );

                unsigned int nCPU;
                if( lgMPI )
                        nCPU = cpu.i().nCPU();
                else
                        nCPU = grid.lgParallel ? grid.useCPU : 1;
                cpu.i().set_used_nCPU( nCPU );

                load_balance lb( grid.totNumModels, nCPU );

                // Each MPI rank will get jobs assigned by lb and execute them.
                // If there are no jobs left, lb.next_job() will return -1.
                while( ( optimize.nOptimiz = lb.next_job() ) >= 0 )
                {
                        const char** mpi_argv = new const char*[argc+2];

                        string jobName = GridPointPrefix( optimize.nOptimiz );
                        for( int i=0; i < argc; ++i )
                                mpi_argv[i] = argv[i];
                        mpi_argv[argc] = "-g";
                        mpi_argv[argc+1] = jobName.c_str();

                        // only save header if we are calculating the first grid model
                        save.SetSaveHeaderNeeded( optimize.nOptimiz == 0 );

                        exit_type retval = cdMain( argc+2, mpi_argv );

                        exit_status = max( retval, exit_status );
                        delete[] mpi_argv;

                        ++grid.seqNum;
                }

                lb.finalize( exit_status );

                // gather the spectral information from all ranks for saving FITS files
                grid.lgGridDone = true;
                optimize.nOptimiz = grid.totNumModels;
                GridGatherInCloudy();

                // and concatenate the output
                process_output();
        }

        // remove empty output files from slave ranks
        if( lgMPI && cpu.i().lgMaster() )
        {
                for( long n=1; n < cpu.i().nCPU(); ++n )
                {
                        ostringstream oss;
                        oss << ".err" << setfill('0') << setw(2) << n;
                        string slave_output = save.chRedirectPrefix + oss.str();
                        FILE *io = open_data( slave_output.c_str(), "a" );
                        bool lgEmpty = ( ftell(io) == 0 );
                        fclose( io );
                        if( lgEmpty )
                                remove( slave_output.c_str() );
                }
        }

        if( lgMPI )
                MPI_Finalize();

        return exit_status;
}

exit_type cdMain( int argc, const char* argv[] )
{
        /* these will be used to count number of various problems */
        long int NumberWarnings, 
          NumberCautions, 
          NumberNotes, 
          NumberSurprises, 
          NumberTempFailures, 
          NumberPresFailures,
          NumberIonFailures, 
          NumberNeFailures;

        bool lgAbort_exit,
          lgEarly_exit=true,
          lgFileIO;
        /* number of lines we can still read in */
        int nread=0;

        int i;
        const char *s, 
          *prefix = "",
          *gprefix = "", // grid prefix
          *pprefix = "", // save prefix
          *rprefix = ""; // redirect prefix
        string infile("");

        /* the length of the following vector will be the longest line image
         * the code will be able to read here.  Cloudy itself will ignore anything 
         * beyond INPUT_LINE_LENGTH, and checks that no information exists beyond it. 
         * The code will stop if the input line is longer than INPUT_LINE_LENGTH
         * since extra characters would become a new command line due to buffer overrun */
        char chLine[INPUT_LINE_LENGTH];

        /* indicates that a command line flag to redirect I/O has been used */
        lgFileIO = false;

        exit_type exit_status = ES_SUCCESS;

        DEBUG_ENTRY( "cdMain()" );

        try {
                /* 
                 * Handle argument input -- written generally, but presently handles
                 * only `-p prefix' or `-pprefix' to set input file as `prefix.in',
                 * output file as `prefix.out' and the save prefix.
                 */
                for( i=1; i < argc; i++ ) 
                {
                        s = argv[i];
                        if( *s != '-' || s[1] == '\0' ) 
                        {
                                if (infile != "")
                                {
                                        fprintf( ioQQQ, "%s: only one input file argument allowed\n", argv[0] );
                                        cdEXIT(ES_FAILURE);
                                }
                                infile = s;
                                if( infile.find( cpu.i().chDirSeparator() ) != string::npos )
                                {
                                        fprintf( ioQQQ, "%s %s: read/write from subdirectories is not supported\n",
                                                                argv[0], infile.c_str() );
                                        cdEXIT(ES_FAILURE);
                                }
                                FILE *fp = open_data(infile.c_str(), "r", AS_LOCAL_ONLY);
                                if (!fp)
                                {
                                        fprintf( ioQQQ, "%s: input filename `%s' not found\n", argv[0], infile.c_str() );
                                        cdEXIT(ES_FAILURE);
                                }
                                fclose(fp);
                                size_t suffindex = infile.find_last_of(".");
                                if (suffindex != string::npos)
                                        infile = infile.substr(0,suffindex);
                                pprefix = rprefix = infile.c_str();
                                lgFileIO = true;
                        }
                        else
                        {
                                while( s != NULL && *(++s) )
                                {
                                        exit_type exit = ES_SUCCESS;
                                        switch( *s ) 
                                        {
                                        case 'a':
                                                cpu.i().setAssertAbort( true );
                                                break;
                                        case 'g':
                                        case 'p':
                                        case 'r':
                                                if( s[1] != '\0' )
                                                {
                                                        prefix = s+1;
                                                }                                       
                                                else
                                                {
                                                        if( ++i == argc || argv[i][0] == '-' )
                                                        {
                                                                fprintf( ioQQQ, "%s: no argument given for -%c flag\n",
                                                                         argv[0], *s );
                                                                cdEXIT(ES_FAILURE);
                                                        }
                                                        prefix = argv[i];
                                                        if( strchr(prefix, cpu.i().chDirSeparator()) != NULL )
                                                        {
                                                                fprintf( ioQQQ, "%s -%c %s: writing in subdirectories is not supported\n",
                                                                         argv[0], *s, prefix );
                                                                cdEXIT(ES_FAILURE);
                                                        }
                                                }
                                                if( *s == 'g' )
                                                        gprefix = prefix;
                                                else if( *s == 'p' )
                                                {
                                                        pprefix = prefix;
                                                        rprefix = prefix;
                                                }
                                                else if( *s == 'r' )
                                                {
                                                        // make sure we erase the effects of a possible earlier -p flag
                                                        pprefix = "";
                                                        rprefix = prefix;
                                                }
                                                else
                                                        TotalInsanity();
                                                s = NULL;
                                                lgFileIO = true;
                                                break;
                                        default:
                                                fprintf( ioQQQ, "%s: argument %d, `%s': flag -%c not understood\n",
                                                         argv[0], i, argv[i], *s );
                                                exit = ES_FAILURE;
                                        case 'h':
                                                fprintf( ioQQQ, "\nSupported flags are:\n\n" );
                                                fprintf( ioQQQ, "-p example\n" );
                                                fprintf( ioQQQ, "    Cloudy reads the input from the file example.in\n" );
                                                fprintf( ioQQQ, "    and writes the output to the file example.out.\n" );
                                                fprintf( ioQQQ, "    Additionally, all file names in SAVE commands are\n" );
                                                fprintf( ioQQQ, "    prepended with the string \"example\", e.g. the\n" );
                                                fprintf( ioQQQ, "    output of SAVE DR \".dr\" will be in example.dr.\n" );
                                                fprintf( ioQQQ, "-r example\n" );
                                                fprintf( ioQQQ, "    This does the same as the -p switch, except that\n" );
                                                fprintf( ioQQQ, "    the names used in SAVE commands are not altered.\n" );
                                                fprintf( ioQQQ, "-g example\n" );
                                                fprintf( ioQQQ, "    This switch is used internally in MPI grid runs.\n" );
                                                fprintf( ioQQQ, "    Normal users should not use this switch.\n" );
                                                fprintf( ioQQQ, "-a\n" );
                                                fprintf( ioQQQ, "    This switch is used in debugging. It causes the\n" );
                                                fprintf( ioQQQ, "    code to crash rather than exit gracefully after\n" );
                                                fprintf( ioQQQ, "    a failed assert. This flag is deprecated.\n" );
                                                fprintf( ioQQQ, "-h\n" );
                                                fprintf( ioQQQ, "    Print this message.\n" );
                                                cdEXIT(exit);
                                        }
                                }
                        }
                }

                /* initialize the code for this run */
                cdInit();

                save.chGridPrefix = gprefix;
                save.chFilenamePrefix = pprefix;
                save.chRedirectPrefix = rprefix;

                /* following should be set true to print to file instead of std output */
                if( lgFileIO )
                {
                        string Base = save.chGridPrefix + save.chRedirectPrefix;
                        string InName = Base + ".in";
                        string OutName;
                        if( cpu.i().lgMPI_talk() )
                                OutName = Base + ".out";
                        else
                        {
                                ostringstream oss;
                                oss << ".err" << setfill('0') << setw(2) << cpu.i().nRANK();
                                OutName = Base + oss.str();
                        }
                        cdInput( InName.c_str(), "r" );
                        cdOutput( OutName.c_str(), "w" );
                }

                if( optimize.nOptimiz == 0 && called.lgTalk && cpu.i().lgMPISingleRankMode() )
                        print_delimiter(-1);
                        
                nread = 1;
                /* keep reading input lines until end of file */
                while( read_whole_line(chLine, (int)sizeof(chLine), ioStdin)!= NULL )
                {
                        /* when running from command prompt, last line can be \n or 
                         * \r (this can happen with gcc under cygwin in windows) 
                         * or space, so check for each here, and break if present,
                         * check on chLine[23] is for case where we are reading cloudy output */
                        /*fprintf(ioQQQ,"DEBUG char0 %i\n", (int)chLine[0] );*/
                        if( chLine[0] == '\n' || chLine[0] == '\r' || 
                            ( chLine[0] == ' ' && chLine[23] != '*' ) ||
                            (strncmp( chLine , "***" , 3 )==0 ) )
                                break;
                        
                        /* read entire line of input - lgAbort set true if lines too long */
                        if( !lgInputComment(chLine) )
                        {
                                bool lgEscape=false, lgQuoted=false;
                                for (char *s=chLine; *s != '\0'; ++s)
                                {
                                        if (lgQuoted && *s == '\\')
                                        {
                                                lgEscape= true;
                                                continue;
                                        }
                                        if ( *s == '\"' && !lgEscape )
                                        {
                                                lgQuoted = !lgQuoted;
                                        }
                                        else if ( *s == '_' && !lgQuoted )
                                        {
                                                *s = ' ';
                                                input.lgUnderscoreFound = true;
                                        }
                                        else if ( (*s == '[' || *s == ']') && !lgQuoted )
                                        {
                                                *s = ' ';
                                                input.lgBracketFound = true;
                                        }
                                        lgEscape = false;
                                }
                        }

                        /* this is trick so that cloudy input can read cloudy output */
                        /* are first 25 char of input string equal to output? */
                        if( strncmp(chLine,"                       * ",25) == 0 )
                        {
                                /* reading cloudy output, send in shifted input */
                                nread = cdRead( chLine+25 );
                        }
                        else
                        {
                                /* stuff the command line into the internal stack */
                                nread = cdRead( chLine  );
                        }
                }

                if( lgAbort )
                {
                        /* input parser hit something REALLY bad */
                        cdEXIT(ES_CLOUDY_ABORT);
                }

                if( nread <= 0 )
                        fprintf(ioQQQ," Warning: limit to number of lines exceeded, %i\n", nread);

                // optimize.lgVaryOn catches both optimizer and grid runs
                if( ( cpu.i().lgMPI() || optimize.lgVaryOn ) && save.chRedirectPrefix.empty() )
                {
                        if( cpu.i().lgMaster() )
                        {
                                if( cpu.i().lgMPI() )
                                        fprintf( ioQQQ, " Please use the style \"mpirun -n np /path/to/cloudy.exe -r input\" when doing grid\n"
                                                " or optimizer runs.  See http://trac.nublado.org/wiki/RunCode for more information.\n" );
                                else
                                        fprintf( ioQQQ, " Please use the style \"/path/to/cloudy.exe -r input\" when doing grid\n"
                                                " or optimizer runs.  See http://trac.nublado.org/wiki/RunCode for more information.\n" );
                        }
                        // stop the grid from being executed any further
                        grid.lgGrid = false;
                        cdEXIT(ES_FAILURE);
                }

                /* actually call the code.  This routine figures out whether the code will do
                 * a single model or be used to optimize on a spectrum, by looking for the
                 * keyword VARY on command lines.  It will call routine cloudy if no vary commands
                 * occur, and lgOptimize_do if VARY does occur.  
                 * cdDrive returns 0 if calculation is ok, 1 if problems happened */
                if( cdDrive() )
                        exit_status = ES_FAILURE;

                /* the last line of output will contain some interesting information about the model*/
                cdNwcns(
                        /* abort status, this better be false, 0 */
                        &lgAbort_exit,
                        /* the number of warnings, cautions, notes, and surprises */
                        &NumberWarnings, 
                        &NumberCautions, 
                        &NumberNotes, 
                        &NumberSurprises, 
                        /* the number of temperature convergence failures */
                        &NumberTempFailures, 
                        /* the number of pressure convergence failures */
                        &NumberPresFailures,
                        /* the number of ionization convergence failures */
                        &NumberIonFailures, 
                        /* the number of electron density convergence failures */
                        &NumberNeFailures );

                ostringstream finalMsg;

                finalMsg << " Cloudy ends: " << nzone << " zone";
                if( nzone > 1 )
                        finalMsg << "s";

                finalMsg << ", " << iteration << " iteration";
                if( iteration > 1 )
                        finalMsg << "s";

                if( lgAbort_exit )
                        finalMsg << ", ABORT DISASTER PROBLEM";

                if( NumberWarnings > 0 )
                {
                        finalMsg << ", " << NumberWarnings << " warning";
                        if( NumberWarnings > 1 )
                                finalMsg << "s";
                        /* this indicates error */
                        exit_status = ES_FAILURE;
                }

                if( NumberCautions > 0 )
                {
                        finalMsg << ", " << NumberCautions << " caution";
                        if( NumberCautions > 1 )
                                finalMsg << "s";
                }

                /* this flag was set in lgCheckMonitors*/
                if( !lgMonitorsOK )
                {
                        finalMsg << ", ";
                        /* some botches were three sigma */
                        if( lgBigBotch  )
                                finalMsg << "BIG ";
                        finalMsg << "BOTCHED MONITORS!!!";
                        /* this indicates error */
                        exit_status = ES_FAILURE;
                }

                if( NumberTempFailures+NumberPresFailures+NumberIonFailures+NumberNeFailures > 0 )
                {
                        finalMsg << ". Failures: " << NumberTempFailures << " thermal, ";
                        finalMsg << NumberPresFailures << " pressure, ";
                        finalMsg << NumberIonFailures << " ionization, ";
                        finalMsg << NumberNeFailures << " electron density";
                }

                if( prt.lgPrintTime )
                {
                        if( !cpu.i().lgMPI() && cpu.i().used_nCPU() == 1 )
                        {
                                finalMsg << ". (single thread)";
                        }
                        else if( !cpu.i().lgMPI() )
                        {
                                finalMsg << ". (" << cpu.i().used_nCPU() << " forked threads)";
                        }
                        else if( cpu.i().lgMPI() )
                        {
                                finalMsg << ". (rank " << cpu.i().nRANK()  << " of " << cpu.i().used_nCPU() << " MPI ranks)";
                        }
                        if (0)
                                finalMsg << " Max memory used " << cdMemory() << "kB.";
                        /* NB DO NOT CHANGE ANY ASPECT OF THE FOLLOWING STRINGS - THEY ARE USED TO RECORD
                         * EXEC TIME BY A PERL SCRIPT */
                        /* print execution time [s] by default,
                         * need spaces around number so that logging perl script picks up correct number 
                         * ir_extime.pl script will delete through "ExecTime(s)" and remainder of line must be number */
                        finalMsg << " ExecTime(s) " << fixed << setprecision(2) << cdExecTime();
                }
                else
                {
                        finalMsg << ".";
                }

                if( called.lgTalk )
                        fprintf( ioQQQ, "%s\n", finalMsg.str().c_str() );

                lgEarly_exit = false;

                /* cdDrive returned 1 if something bad happened, and 0 if everything is ok.  We will
                 * return 0 if everything is ok, and a non-zero error code if something bad happened.*/
                cdEXIT(exit_status);
        }
        catch( bad_alloc )
        {
                fprintf( ioQQQ, " DISASTER - A memory allocation has failed. Most likely your computer "
                         "ran out of memory.\n Try monitoring the memory use of your run. Bailing out...\n" );
                exit_status = ES_BAD_ALLOC;
        }
        catch( out_of_range& e )
        {
                fprintf( ioQQQ, " DISASTER - An out_of_range exception was caught, what() = %s. Bailing out...\n",
                         e.what() );
                exit_status = ES_OUT_OF_RANGE;
        }
        catch( domain_error& e )
        {
                fprintf( ioQQQ, " DISASTER - A vectorized math routine threw a domain_error. Bailing out...\n" );
                fprintf( ioQQQ, " What() = %s", e.what() );
                exit_status = ES_DOMAIN_ERROR;
        }
        catch( bad_assert& e )
        {
                MyAssert( e.file(), e.line() , e.comment() );
                exit_status = ES_BAD_ASSERT;
        }
#ifdef CATCH_SIGNAL
        catch( bad_signal& e )
        {
                if( ioQQQ != NULL )
                {
                        if( e.sig() == SIGINT || e.sig() == SIGQUIT )
                        {
                                fprintf( ioQQQ, " User interrupt request. Bailing out...\n" );
                                exit_status = ES_USER_INTERRUPT;
                        }
                        else if( e.sig() == SIGTERM )
                        {
                                fprintf( ioQQQ, " Termination request. Bailing out...\n" );
                                exit_status = ES_TERMINATION_REQUEST;
                        }
                        else if( e.sig() == SIGILL )
                        {
                                fprintf( ioQQQ, " DISASTER - An illegal instruction was found. Bailing out...\n" );
                                exit_status = ES_ILLEGAL_INSTRUCTION;
                        }
                        else if( e.sig() == SIGFPE )
                        {
                                fprintf( ioQQQ, " DISASTER - A floating point exception occurred. Bailing out...\n" );
                                exit_status = ES_FP_EXCEPTION;
                        }
                        else if( e.sig() == SIGSEGV )
                        {
                                fprintf( ioQQQ, " DISASTER - A segmentation violation occurred. Bailing out...\n" );
                                exit_status = ES_SEGFAULT;
                        }
#                       ifdef SIGBUS
                        else if( e.sig() == SIGBUS )
                        {
                                fprintf( ioQQQ, " DISASTER - A bus error occurred. Bailing out...\n" );
                                exit_status = ES_BUS_ERROR;
                        }
#                       endif
                        else
                        {
                                fprintf( ioQQQ, " DISASTER - A signal %d was caught. Bailing out...\n", e.sig() );
                                exit_status = ES_UNKNOWN_SIGNAL;
                        }

                }
        }
#endif
        catch( cloudy_exit& e )
        {
                if( called.lgTalk )
                {
                        ostringstream oss;
                        oss << " [Stop in " << e.routine();
                        oss << " at " << e.file() << ":" << e.line();
                        if( e.exit_status() == 0 )
                                oss << ", Cloudy exited OK]";
                        else
                                oss << ", something went wrong]";
                        fprintf( ioQQQ, "%s\n", oss.str().c_str() );
                }

                if ( called.lgTalk && prt.lgPrintHTML )
                {
                        fprintf( ioQQQ,"</pre>\n");
                        fprintf( ioQQQ,"</body>\n");
                        fprintf( ioQQQ,"</html>\n");
                }
                
                exit_status = e.exit_status();
                if( exit_status == ES_FAILURE && !lgEarly_exit )
                {
                        // try to make the error code more descriptive
                        // when there is no early exit in the code, then these 3
                        // should be the only reasons for a non-zero exit code
                        if( NumberWarnings > 0 )
                                exit_status = ES_WARNINGS;
                        if( !lgMonitorsOK )
                                exit_status = ES_BOTCHES;
                        if( lgAbort_exit )
                                exit_status = ES_CLOUDY_ABORT;
                }
        }
        catch( std::exception& e )
        {
                fprintf( ioQQQ, " DISASTER - An unknown exception was caught, what() = %s. Bailing out...\n",
                         e.what() );
                exit_status = ES_UNKNOWN_EXCEPTION;
        }
        // generic catch-all in case we forget any specific exception above... so this MUST be the last one.
        catch( ... )
        {
                fprintf( ioQQQ, " DISASTER - An unknown exception was caught. Bailing out...\n" );
                exit_status = ES_UNKNOWN_EXCEPTION;
        }

        if( called.lgTalk && cpu.i().lgMPISingleRankMode() )
                print_delimiter(optimize.nOptimiz);

        cdPrepareExit(exit_status);

        return exit_status;
}