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PostgreSQLTranslator.java
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gmantele authored
[ADQL,TAP] Add geometry format in output and correct upload of STC-S regions. Geometrical type conversion from and into a DB type is now required in all JDBCTranslator. This allows formatting of geometrical column value coming from the database, but also the translation of STC-S expressions provided in uploaded table into geometrical column values.
gmantele authored[ADQL,TAP] Add geometry format in output and correct upload of STC-S regions. Geometrical type conversion from and into a DB type is now required in all JDBCTranslator. This allows formatting of geometrical column value coming from the database, but also the translation of STC-S expressions provided in uploaded table into geometrical column values.
numa.c 12.05 KiB
#include "allvars.h"
#include "proto.h"
#include <stdio.h>
#include <unistd.h>
#include <limits.h>
map_t Me;
MPI_Comm COMM[HLEVELS];
char *LEVEL_NAMES[HLEVELS] = {"NUMA", "ISLAND", "myHOST", "HOSTS", "WORLD"};
MPI_Aint win_host_master_size = 0;
MPI_Aint win_ctrl_hostmaster_size;
MPI_Win win_ctrl_hostmaster;
int win_ctrl_hostmaster_disp;
void *win_ctrl_hostmaster_ptr;
MPI_Aint win_hostmaster_size;
MPI_Win win_hostmaster;
int win_hostmaster_disp;
void *win_hostmaster_ptr;
int numa_build_mapping( int, int, MPI_Comm *, map_t *);
int numa_map_hostnames( MPI_Comm *, int, int, map_t *);
int get_cpu_id( void );
int compare_string_int_int( const void *, const void * );
int numa_init( int Rank, int Size, MPI_Comm *MYWORLD, map_t *Me )
{
/*
* build up the numa hierarchy
*/
numa_build_mapping( global_rank, size, MYWORLD, Me );
/*
* initialize the persistent shared windows
*/
int SHMEMl = Me->SHMEMl;
MPI_Info winfo;
MPI_Info_create(&winfo);
MPI_Info_set(winfo, "alloc_shared_noncontig", "true");
// -----------------------------------
// initialize the flow control windows
// -----------------------------------
Me->win_ctrl.size = sizeof(int);
MPI_Win_allocate_shared(Me->win_ctrl.size, 1, winfo, *Me->COMM[SHMEMl],
&(Me->win_ctrl.ptr), &(Me->win_ctrl.win));
MPI_Aint wsize = sizeof(int);
MPI_Win_allocate_shared(wsize, 1, winfo, *Me->COMM[SHMEMl],
&win_ctrl_hostmaster_ptr, &win_ctrl_hostmaster);
Me->scwins = (win_t*)malloc(Me->Ntasks[SHMEMl]*sizeof(win_t) );
// get the addresses of all the windows from my siblings
// at my shared-memory level
//
for( int t = 0; t < Me->Ntasks[SHMEMl]; t++ )
{
//if( t != Me->Rank[SHMEMl] )
MPI_Win_shared_query( Me->win_ctrl.win, t, &(Me->scwins[t].size),
&(Me->scwins[t].disp), &(Me->scwins[t].ptr) );
}
if( Me->Rank[SHMEMl] != 0 )
MPI_Win_shared_query( win_ctrl_hostmaster, 0, &(win_ctrl_hostmaster_size),
&win_ctrl_hostmaster_disp, &win_ctrl_hostmaster_ptr );
return 0;
}
int numa_allocate_shared_windows( map_t *me, MPI_Aint size, MPI_Aint host_size )
{
int SHMEMl = me->SHMEMl;
MPI_Info winfo;
MPI_Info_create(&winfo);
MPI_Info_set(winfo, "alloc_shared_noncontig", "true");
// -----------------------------------
// initialize the data windows
// -----------------------------------
MPI_Aint win_host_size;
if( host_size == 0 )
win_hostmaster_size = WIN_HOST_MASTER_SIZE_DFLT*1024*1024;
else
win_hostmaster_size = host_size;
if( size == 0 )
win_host_size = WIN_HOST_SIZE_DFLT*1024*1024;
else
win_host_size = size;
me->win.size = win_host_size;
MPI_Win_allocate_shared(me->win.size, 1, winfo, *me->COMM[SHMEMl], &(me->win.ptr), &(me->win.win));
MPI_Aint wsize = ( me->Rank[SHMEMl] == 0 ? win_hostmaster_size : 0);
MPI_Win_allocate_shared(wsize, 1, winfo, *me->COMM[SHMEMl], &win_hostmaster_ptr, &win_hostmaster);
me->swins = (win_t*)malloc(me->Ntasks[SHMEMl]*sizeof(win_t) );
me->swins[me->Rank[SHMEMl]] = me->win;
// me->swins = (win_t*)malloc(me->Ntasks[SHMEMl]*sizeof(win_t));
// get the addresses of all the windows from my siblings
// at my shared-memory level
//
for( int t = 0; t < me->Ntasks[SHMEMl]; t++ )
if( t != me->Rank[SHMEMl] )
MPI_Win_shared_query( me->win.win, t, &(me->swins[t].size), &(me->swins[t].disp), &(me->swins[t].ptr) );
if( me->Rank[SHMEMl] != 0 )
MPI_Win_shared_query( win_hostmaster, 0, &(win_hostmaster_size), &win_hostmaster_disp, &win_hostmaster_ptr );
return 0;
}
int numa_shutdown( int Rank, int Size, MPI_Comm *MYWORLD, map_t *me )
{
// free every shared memory and window
//
MPI_Win_free(&(me->win.win));
// free all the structures if needed
//
free(me->Ranks_to_host);
free(me->swins);
// anything else
//
// ...
return 0;
}
int numa_build_mapping( int Rank, int Size, MPI_Comm *MYWORLD, map_t *me )
{
COMM[WORLD] = *MYWORLD;
me->Ntasks[WORLD] = Size;
me->Rank[WORLD] = Rank;
me->COMM[WORLD] = &COMM[WORLD];
me->mycpu = get_cpu_id();
// --- find how many hosts we are running on;
// that is needed to build the communicator
// among the masters of each host
//
numa_map_hostnames( &COMM[WORLD], Rank, Size, me );
me->MAXl = ( me->Nhosts > 1 ? HOSTS : myHOST );
// --- create the communicator for each host
//
MPI_Comm_split( COMM[WORLD], me->myhost, me->Rank[WORLD], &COMM[myHOST]);
MPI_Comm_size( COMM[myHOST], &Size );
MPI_Comm_rank( COMM[myHOST], &Rank );
me->COMM[myHOST] = &COMM[myHOST];
me->Rank[myHOST] = Rank;
me->Ntasks[myHOST] = Size;
// with the following gathering we build-up the mapping Ranks_to_hosts, so that
// we know which host each mpi rank (meaning the original rank) belongs to
//
MPI_Allgather( &me->myhost, sizeof(me->myhost), MPI_BYTE,
me->Ranks_to_host, sizeof(me->myhost), MPI_BYTE, COMM[WORLD] );
me -> Ranks_to_myhost = (int*)malloc(me->Ntasks[myHOST]*sizeof(int));
MPI_Allgather( &global_rank, sizeof(global_rank), MPI_BYTE,
me->Ranks_to_myhost, sizeof(global_rank), MPI_BYTE, *me->COMM[myHOST]);
// --- create the communicator for the
// masters of each host
//
int Im_host_master = ( me->Rank[myHOST] == 0 );
MPI_Comm_split( COMM[WORLD], Im_host_master, me->Rank[WORLD], &COMM[HOSTS]);
//
// NOTE: by default, the Rank 0 in WORLD is also Rank 0 in HOSTS
//
if (Im_host_master)
{
me->COMM[HOSTS] = &COMM[HOSTS];
me->Ntasks[HOSTS] = me->Nhosts;
MPI_Comm_rank( COMM[HOSTS], &(me->Rank[HOSTS]));
}
else
{
me->COMM[HOSTS] = NULL;
me->Ntasks[HOSTS] = 0;
me->Rank[HOSTS] = -1;
}
// --- create the communicator for the
// numa node //
MPI_Comm_split_type( COMM[myHOST], MPI_COMM_TYPE_SHARED, me->Rank[myHOST], MPI_INFO_NULL, &COMM[NUMA]);
me->COMM[NUMA] = &COMM[NUMA];
MPI_Comm_size( COMM[NUMA], &(me->Ntasks[NUMA]));
MPI_Comm_rank( COMM[NUMA], &(me->Rank[NUMA]));
// check whether NUMA == myHOST and determine
// the maximum level of shared memory in the
// topology
//
if ( me->Ntasks[NUMA] == me->Ntasks[myHOST] )
{
// collapse levels from NUMA to myHOST
//
me->Ntasks[ISLAND] = me->Ntasks[NUMA]; // equating to NUMA as we know the rank better via MPI_SHARED
me->Rank[ISLAND] = me->Rank[NUMA];
me->COMM[ISLAND] = me->COMM[NUMA];
me->Rank[myHOST] = me->Rank[NUMA];
me->COMM[myHOST] = me->COMM[NUMA];
me->SHMEMl = myHOST;
}
else
{
// actually we do not care for this case
// at this moment
printf(">>> It seems that rank %d belongs to a node for which "
" the node topology does not coincide \n", Rank );
me->SHMEMl = NUMA;
}
int check_SHMEM_level = 1;
int globalcheck_SHMEM_level;
int globalmax_SHMEM_level;
MPI_Allreduce( &(me->SHMEMl), &globalmax_SHMEM_level, 1, MPI_INT, MPI_MAX, *MYWORLD );
check_SHMEM_level = ( (me->SHMEMl == myHOST) && (globalmax_SHMEM_level == me->SHMEMl) );
MPI_Allreduce( &check_SHMEM_level, &globalcheck_SHMEM_level, 1, MPI_INT, MPI_MAX, *MYWORLD );
if( globalcheck_SHMEM_level < 1 )
{
if( Rank == 0 ) {
printf("There was an error in determining the topology hierarchy, "
"SHMEM level is different for different MPI tasks\n");
return -1; }
}
return 0;
}
int numa_map_hostnames( MPI_Comm *MY_WORLD, // the communicator to refer to
int Rank, // the initial rank of the calling process in MYWORLD
int Ntasks, // the number of tasks in MY_WORLD
map_t *me) // address of the info structure for the calling task
{
// --------------------------------------------------
// --- init some global vars
me -> Ranks_to_host = (int*)malloc(Ntasks*sizeof(int));
me -> Nhosts = 0;
me -> myhost = -1;
// --------------------------------------------------
// --- find how many hosts we are using
char myhostname[HOST_NAME_MAX+1];
gethostname( myhostname, HOST_NAME_MAX+1 );
// determine how much space to book for hostnames
int myhostlen = strlen(myhostname)+1;
int maxhostlen = 0;
MPI_Allreduce ( &myhostlen, &maxhostlen, 1, MPI_INT, MPI_MAX, *MY_WORLD );
// collect hostnames
//
typedef struct {
char hostname[maxhostlen];
int rank;
} hostname_rank_t;
hostname_rank_t mydata;
hostname_rank_t *alldata = (hostname_rank_t*)calloc( Ntasks, sizeof(hostname_rank_t) );
mydata.rank = Rank;
sprintf( mydata.hostname, "%s", myhostname);
MPI_Allgather( &mydata, sizeof(hostname_rank_t), MPI_BYTE, alldata, sizeof(hostname_rank_t), MPI_BYTE, *MY_WORLD );
// sort the hostnames
// 1) set the lenght of string for comparison
int dummy = maxhostlen;
compare_string_int_int( NULL, &dummy );
// 2) actually sort
qsort( alldata, Ntasks, sizeof(hostname_rank_t), compare_string_int_int );
// now the array alldata is sorted by hostname, and inside each hostname the processes
// running on each host are sorted by their node, and for each node they are sorted
// by ht.
// As a direct consequence, the running index on the alldata array can be considered
// as the new global rank of each process
// --- count how many diverse hosts we have, and register each rank to its host, so that
// we can alway find all the tasks with their original rank
char *prev = alldata[0].hostname;
for ( int R = 0; R < Ntasks; R++ )
{
if ( strcmp(alldata[R].hostname, prev) != 0 ) {
me->Nhosts++; prev = alldata[R].hostname; }
if ( alldata[R].rank == Rank ) // it's me
me->myhost = me->Nhosts; // remember my host
}
me->Nhosts++;
free( alldata );
return me->Nhosts;
}
int compare_string_int_int( const void *A, const void *B )
// used to sort structures made as
// { char *s;
// int b;
// ... }
// The sorting is hierarchical by *s first, then b
// if necessary
// The length of *s is set by calling
// compare_string_int_int( NULL, len )
// before to use this routine in qsort-like calls
{
static int str_len = 0; if ( A == NULL )
{
str_len = *(int*)B + 1;
return 0;
}
// we do not use strncmp because str_len=0,
// i.e. using this function without initializing it,
// can be used to have a sorting only on
// strings
int order = strcmp( (char*)A, (char*)B );
if ( str_len && (!order) )
{
int a = *(int*)((char*)A + str_len);
int b = *(int*)((char*)B + str_len);
order = a - b;
if( !order )
{
int a = *((int*)((char*)A + str_len)+1);
int b = *((int*)((char*)B + str_len)+1);
order = a - b;
}
}
return order;
}
#define CPU_ID_ENTRY_IN_PROCSTAT 39
int read_proc__self_stat( int, int * );
int get_cpu_id( void )
{
#if defined(_GNU_SOURCE) // GNU SOURCE ------------
return sched_getcpu( );
#else
#ifdef SYS_getcpu // direct sys call ---
int cpuid;
if ( syscall( SYS_getcpu, &cpuid, NULL, NULL ) == -1 )
return -1;
else
return cpuid;
#else
int val;
if ( read_proc__self_stat( CPU_ID_ENTRY_IN_PROCSTAT, &val ) == -1 )
return -1;
return (int)val;
#endif // -----------------------
#endif
}
int read_proc__self_stat( int field, int *ret_val )
/*
Other interesting fields:
pid : 0
father : 1 utime : 13
cutime : 14
nthreads : 18
rss : 22
cpuid : 39
read man /proc page for fully detailed infos
*/
{
// not used, just mnemonic
// char *table[ 52 ] = { [0]="pid", [1]="father", [13]="utime", [14]="cutime", [18]="nthreads", [22]="rss", [38]="cpuid"};
*ret_val = 0;
FILE *file = fopen( "/proc/self/stat", "r" );
if (file == NULL )
return -1;
char *line = NULL;
int ret;
size_t len;
ret = getline( &line, &len, file );
fclose(file);
if( ret == -1 )
return -1;
char *savetoken = line;
char *token = strtok_r( line, " ", &savetoken);
--field;
do { token = strtok_r( NULL, " ", &savetoken); field--; } while( field );
*ret_val = atoi(token);
free(line);
return 0;
}