mpi_utilities.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 */
#include "cddefines.h"
#include "save.h"
#include "dynamics.h"
#include "grid.h"
#if defined(__unix) || defined(__APPLE__)
#include <cstddef>
#include <sys/types.h>
#include <sys/wait.h>
#include <unistd.h>
#else
#define pid_t int
#define fork() TotalInsanityAsStub<pid_t>()
#define wait(X) TotalInsanityAsStub<pid_t>()
#endif
#ifdef __linux__
#include <sys/vfs.h>
// these come from /usr/include/linux/magic.h, but from linux kernel 3.7
// onwards, the file seems to have moved to /usr/include/uapi/linux/magic.h...
// to avoid the mess we copy the constants here
static const long NFS_SUPER_MAGIC = 0x6969L;
static const long SMB_SUPER_MAGIC = 0x517BL;
static const long AUTOFS_SUPER_MAGIC = 0x0187L;
// this one is not included in my header file (sshfs is also based on fuse)
static const long FUSE_SUPER_MAGIC = 0x65735546L;
#endif

STATIC void GridGatherOutput(const string&,long,const vector<long>&);
STATIC void GridGatherOutputSequential(const string&,long);
STATIC void GridGatherOutputParallel(const string&,long,const vector<long>&);
STATIC bool lgIsRemote(const string&);
STATIC void check_grid_file(const string&,int,int);

#ifndef MPI_ENABLED

int MPI_MODE_RDONLY = 0;
int MPI_MODE_WRONLY = 0;
int MPI_MODE_CREATE = 0;
int MPI_MODE_APPEND = 0;

int MPI_SUCCESS = 0;
int MPI_ERR_INTERN = -1;
MPI_File MPI_FILE_NULL = 0;

int total_insanity(MPI_File, int, MPI_Status*)
{
        return TotalInsanityAsStub<int>();
}

#endif

int mpi_mode_r = MPI_MODE_RDONLY;
int mpi_mode_w = MPI_MODE_WRONLY | MPI_MODE_CREATE;
int mpi_mode_a = MPI_MODE_WRONLY | MPI_MODE_CREATE | MPI_MODE_APPEND;

// NB NB this routine cannot throw any exceptions as it is executed outside
// the try{} block -- this includes mechanisms like ASSERT and cdEXIT!
void load_balance::init( unsigned int nJobs, unsigned int nCPU )
{
        if( nJobs == 0 )
                return;

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

        p_jobs.resize( nJobs );
        p_rank = cpu.i().nRANK();
        p_ptr = p_rank;
        p_ncpu = min(nCPU,nJobs);
        // the master rank will now set up a random sequence for the jobs
        // this way we hope to get statistical load balancing of the ranks
        if( p_rank == 0 )
        {
                for( unsigned int i=0; i < nJobs; ++i )
                        p_jobs[i] = i;

                if( p_ncpu > 1 )
                {
                        // This may or may not seed the random number generator used by
                        // random_shuffle. There is no portable C++ interface to do this :-(
                        srand( unsigned( time(NULL) ) );
                        random_shuffle( p_jobs.begin(), p_jobs.end() );
                }
        }
        // now broadcast the random sequence to the other ranks...
        if( lgMPI )
                MPI_Bcast( &p_jobs[0], nJobs, MPI_type(p_jobs[0]), 0, MPI_COMM_WORLD );
        else
                for( unsigned int i=1; i < p_ncpu; ++i )
                {
                        fflush(NULL);
                        pid_t pid = fork();
                        if( pid < 0 )
                        {
                                fprintf( ioQQQ, "creating the child process failed\n" );
                                // this _should_ be exit() not cdEXIT()!
                                exit(EXIT_FAILURE);
                        }
                        else if( pid == 0 )
                        {
                                /* this is child process */
                                p_rank = i;
                                p_ptr = p_rank;
                                cpu.i().set_nRANK( p_rank );
                                return;
                        }
                }
}

void load_balance::finalize( exit_type exit_status )
{
        // wait for all jobs to finish
        if( cpu.i().lgMPI() )
                MPI_Barrier( MPI_COMM_WORLD );
        else
        {
                if( p_rank == 0 )
                        for( unsigned int i=1; i < p_ncpu; ++i )
                                (void)wait(NULL);
                else
                        // this _should_ be exit() not cdEXIT()!
                        exit(exit_status);
        }
}

void process_output()
{
        DEBUG_ENTRY( "process_output()" );

        // NOTE: when this routine is called all file handles have already been closed

        try
        {
                string main_input = save.chRedirectPrefix + ".in";
                string main_output = save.chRedirectPrefix + ".out";

                // balance work over the ranks
                // rank n will process file numbers i with bound[n] <= i < bound[n+1]
                // in non-MPI runs, this will result in:
                //    bound[0] = 0;   bound[1] = grid.totNumModels;
                int nCPU = cpu.i().lgMPI() ? cpu.i().nCPU() : 1;
                int nRANK = cpu.i().lgMPI() ? cpu.i().nRANK() : 0;
                long stride = grid.totNumModels/nCPU;
                vector<long> bound( nCPU+1, stride );
                long remainder = grid.totNumModels - stride*nCPU;
                for( long i=1; i <= remainder; ++i )
                        ++bound[i];
                bound[0] = 0;
                for( long i=1; i <= nCPU; ++i )
                        bound[i] += bound[i-1];

                ASSERT( bound[nCPU] == grid.totNumModels );

                // first process main output files
                if( !grid.lgKeepMainOutputSeparate )
                        GridGatherOutput( main_output, grid.totNumModels, bound );

                // remove input files for individual grid points
                for( long j=0; j < grid.totNumModels; ++j )
                {
                        if( j >= bound[nRANK] && j < bound[nRANK+1] )
                        {
                                string in_name = GridPointPrefix(j) + save.chRedirectPrefix + ".in";
                                remove( in_name.c_str() );
                        }
                }

                fstream main_input_handle;
                open_data( main_input_handle, main_input.c_str(), mode_r, AS_LOCAL_ONLY );
                string line;

                int ipPun = 0;

                while( getline( main_input_handle, line ) )
                {
                        string caps_line;
                        // create all caps version
                        string::const_iterator p = line.begin();
                        while( p != line.end() )
                                caps_line.push_back( toupper(*p++) );
                        if( caps_line.compare( 0, 4, "SAVE" ) == 0 || caps_line.compare( 0, 4, "PUNC" ) == 0 )
                        {
                                ASSERT( ipPun < save.nsave );
                                string fnam = save.chFilenamePrefix;
                                string::size_type p = line.find( '"' );
                                fnam += line.substr( ++p );
                                fnam.erase( fnam.find( '"' ) );
                                // first do a minimal check on the validity of the save files
                                for( int j=0; j < grid.totNumModels; ++j )
                                        if( j >= bound[nRANK] && j < bound[nRANK+1] )
                                                check_grid_file( fnam, j, ipPun );
                                // and concatenate the output if necessary
                                if( save.lgSaveToSeparateFiles[ipPun] )
                                {
                                        if( cpu.i().lgMaster() )
                                        {
                                                // open in binary mode in case we are writing a FITS file
                                                FILE *dest = open_data( fnam.c_str(), "ab" );
                                                // keep the save files for each grid point separate
                                                // the main save file contains the save header
                                                // salvage it by prepending it to the first save file
                                                // this gives the same behavior as in non-MPI runs
                                                string gridnam = GridPointPrefix(0) + fnam;
                                                append_file( dest, gridnam.c_str() );
                                                fclose( dest );
                                                // this will overwrite the old file gridnam
                                                rename( fnam.c_str(), gridnam.c_str() );
                                        }
                                }
                                else
                                {
                                        GridGatherOutput( fnam, grid.totNumModels, bound );
                                }
                                if( caps_line.find( "XSPE", 4 ) != string::npos )
                                {
                                        if( cpu.i().lgMaster() )
                                        {
                                                FILE *dest = open_data( fnam.c_str(), "ab" );
                                                // dest points to an empty file, so generate the complete FITS file now
                                                ASSERT( save.FITStype[ipPun] >= 0 &&
                                                        save.FITStype[ipPun] < NUM_OUTPUT_TYPES );
                                                saveFITSfile( dest, save.FITStype[ipPun] );
                                                fseek( dest, 0, SEEK_END );
                                                ASSERT( ftell(dest)%2880 == 0 );
                                                fclose( dest );
                                        }
                                }
                                ++ipPun;
                        }
                }
        }
        catch( ... )
        {
                fprintf( ioQQQ, "PROBLEM - an internal error occurred while post-processing the grid output\n" );
        }
}

STATIC void GridGatherOutput(const string& basenam,
                             long nfiles,
                             const vector<long>& bound)
{
        if( cpu.i().lgMPI() && !lgIsRemote(basenam) )
                GridGatherOutputParallel( basenam, nfiles, bound );
        else {
                if( cpu.i().lgMaster() )
                        GridGatherOutputSequential( basenam, nfiles );
        }
}

STATIC void GridGatherOutputSequential(const string& basenam,
                                       long nfiles)
{
        // open in binary mode in case we are writing a FITS file
        FILE* output_handle = open_data( basenam.c_str(), "ab" );
        for( long j=0; j < nfiles; ++j )
        {
                string gridnam = GridPointPrefix(j) + basenam;
                append_file( output_handle, gridnam.c_str() );
                remove( gridnam.c_str() );
        }
        fclose( output_handle );
}

STATIC void GridGatherOutputParallel(const string& basenam,
                                     long nfiles,
                                     const vector<long>& bound)
{
        // determine total amount of data each rank has to copy
        // by summing the individual file sizes -- also remove input files
        MPI_Offset mySize = 0;
        for( long j=0; j < nfiles; ++j )
        {
                if( j >= bound[cpu.i().nRANK()] && j < bound[cpu.i().nRANK()+1] )
                {
                        string gridnam = GridPointPrefix(j) + basenam;
                        FILE* fh = open_data( gridnam.c_str(), "r", AS_LOCAL_ONLY );
                        fseek( fh, 0, SEEK_END );
                        mySize += static_cast<MPI_Offset>( ftell(fh) );
                        fclose(fh);
                }
        }

        // broadcast the computed amounts to all ranks so that each
        // rank can compute the offset where it needs to start writing
        vector<MPI_Offset> offset(cpu.i().nCPU());
        for( int i=0; i < cpu.i().nCPU(); ++i )
        {
                MPI_Offset myCopy = mySize;
                // directly using &offset[i] below instead of the detour via
                // &myCopy leads to segfaults for reasons that I cannot fathom...
                MPI_Bcast( &myCopy, 1, MPI_type(myCopy), i, MPI_COMM_WORLD );
                offset[i] = myCopy;
        }

        MPI_File output_handle = open_data( basenam.c_str(), mpi_mode_a );

        // compute offset where each rank needs to start writing
        MPI_Offset totalSize = 0;
        (void)MPI_File_get_size( output_handle, &totalSize );
        for( int j=0; j < cpu.i().nCPU(); ++j )
        {
                MPI_Offset tmp = offset[j];
                offset[j] = totalSize;
                totalSize += tmp;
        }

        // now gather the output and remove the individual files
        (void)MPI_File_set_view( output_handle, offset[cpu.i().nRANK()],
                                 MPI_CHAR, MPI_CHAR, const_cast<char*>("native"),
                                 MPI_INFO_NULL );
        for( long j=0; j < nfiles; ++j )
        {
                if( j >= bound[cpu.i().nRANK()] && j < bound[cpu.i().nRANK()+1] )
                {
                        string gridnam = GridPointPrefix(j) + basenam;
                        append_file( output_handle, gridnam.c_str() );
                        remove( gridnam.c_str() );
                }
        }
        MPI_File_close( &output_handle );
}

// determine if a file resides on a remote share
// this is needed to determine if MPI-IO can operate safely on the file
#ifdef __linux__
STATIC bool lgIsRemote(const string& fnam)
{
        struct statfs buf;
        int res = statfs( fnam.c_str(), &buf );
        if( res != 0 )
                return true;
        // parallel file systems do not count as remote since MPI-IO is supported on those
        if( buf.f_type == NFS_SUPER_MAGIC ||
            buf.f_type == SMB_SUPER_MAGIC ||
            buf.f_type == AUTOFS_SUPER_MAGIC ||
            buf.f_type == FUSE_SUPER_MAGIC )
                return true;
        else
                return false;
}
#else
STATIC bool lgIsRemote(const string&)
{
        // we do not know how to determine this, so we assume the worst
        return true;
}
#endif

STATIC void check_grid_file( const string& fnam, int j, int ipPun )
{
        DEBUG_ENTRY( "check_grid_file()" );

        // these are binary files, don't touch them...
        if( save.lgFITS[ipPun] )
                return;

        bool lgForceNoDelimiter = false;
        // in these cases there should not be a GRID_DELIMIT string...
        if( !save.lgHashEndIter[ipPun] || !save.lg_separate_iterations[ipPun] ||
            dynamics.lgTimeDependentStatic || strcmp( save.chHashString , "TIME_DEP" ) == 0 || strcmp( save.chHashString , "\n" ) == 0 )
                lgForceNoDelimiter = true;

        bool lgAppendDelimiter = true;
        bool lgAppendNewline = false;
        string gridnam = GridPointPrefix(j) + fnam;
        fstream str;
        open_data( str, gridnam.c_str(), mode_r, AS_LOCAL_ONLY_TRY );
        if( str.is_open() )
        {
                str.seekg( 0, ios_base::end );
                if( str.good() && str.tellg() > 0 )
                {
                        // check if the file ends in a newline
                        str.seekg( -1, ios_base::cur );
                        char chr;
                        str.get( chr );
                        lgAppendNewline = ( chr != '\n' );
                        // check if the GRID_DELIMIT string is present
                        string line;
                        str.seekg( 0, ios_base::beg );
                        while( getline( str, line ) )
                        {
                                if( line.find( "GRID_DELIMIT" ) != string::npos )
                                        lgAppendDelimiter = false;
                        }
                }
                str.close();
        }
        if( lgForceNoDelimiter )
                lgAppendDelimiter = false;
        if( lgAppendNewline || lgAppendDelimiter )
        {
                open_data( str, gridnam.c_str(), mode_a, AS_LOCAL_ONLY_TRY );
                if( str.is_open() )
                {
                        if( lgAppendNewline )
                                str << endl;
                        if( lgAppendDelimiter )
                        {
                                str << save.chHashString << " GRID_DELIMIT -- grid";
                                str << setfill( '0' ) << setw(9) << j << endl;
                        }
                        str.close();
                }
        }
}

void append_file( FILE *dest, const char *source )
{
        DEBUG_ENTRY( "append_file()" );

        FILE *src = open_data( source, "rb", AS_LOCAL_ONLY_TRY );
        if( src == NULL )
                return;

        // limited testing shows that using a 4 KiB buffer should
        // give performance that is at least very close to optimal
        // tests were done by concatenating 10 copies of a 62.7 MiB file
        const size_t BUF_SIZE = 4096;
        char buf[BUF_SIZE];

        while( ! feof(src) )
        {
                size_t nb = fread( buf, sizeof(char), BUF_SIZE, src );
                fwrite( buf, sizeof(char), nb, dest );
        }
        fclose(src);
        return;
}

void append_file( MPI_File dest, const char *source )
{
        DEBUG_ENTRY( "append_file()" );

        FILE *src = open_data( source, "rb", AS_LOCAL_ONLY_TRY );
        if( src == NULL )
                return;

        // use larger buffer for parallel file systems
        const size_t BUF_SIZE = 32768;
        char buf[BUF_SIZE];

        while( ! feof(src) )
        {
                size_t nb = fread( buf, sizeof(char), BUF_SIZE, src );
                MPI_Status status;
                (void)MPI_File_write( dest, buf, nb, MPI_CHAR, &status );
        }
        fclose(src);
        return;
}