1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
|
/* Support for MPI parallelization.
*/
#ifndef eslMPI_INCLUDED
#define eslMPI_INCLUDED
#include "esl_config.h"
#if defined(HAVE_MPI)
#include <mpi.h>
#include "esl_alphabet.h"
#include "esl_msa.h"
#include "esl_sq.h"
#include "esl_stopwatch.h"
/* Many MPI implementations are not MPI2.2 compliant, and do not
* support new MPI2.2 datatypes; work around that absence. [J10/152]
* This configuration is better here than esl_config.h.in, because
* we need to #include <mpi.h> first to see if the system MPI does
* the right thing, and esl_config.h.in is intended to be included
* BEFORE any system includes.
*/
#if MPI_VERSION < 2 || MPI_SUBVERSION < 2
#ifndef MPI_INT64_T
#define MPI_INT64_T MPI_LONG_LONG_INT
#endif
#ifndef MPI_UINT64_T
#define MPI_UINT64_T MPI_UNSIGNED_LONG_LONG
#endif
#ifndef MPI_UINT32_T
#define MPI_UINT32_T MPI_UNSIGNED
#endif
#ifndef MPI_INT16_T
#define MPI_INT16_T MPI_SHORT
#endif
#ifndef MPI_UINT8_T
#define MPI_UINT8_T MPI_UNSIGNED_CHAR
#endif
#endif /*MPI_VERSION,MPI_SUBVERSION*/
/* 1. Communicating optional arrays */
extern int esl_mpi_PackOpt(void *inbuf, int incount, MPI_Datatype type, void *pack_buf,
int pack_buf_size, int *position, MPI_Comm comm);
extern int esl_mpi_PackOptSize(void *inbuf, int incount, MPI_Datatype type, MPI_Comm comm, int *ret_n);
extern int esl_mpi_UnpackOpt(void *pack_buf, int pack_buf_size, int *pos, void **outbuf,
int *opt_n, MPI_Datatype type, MPI_Comm comm);
/* 2. Communicating ESL_SQ (single sequences) */
extern int esl_sq_MPISend(ESL_SQ *sq, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc);
extern int esl_sq_MPIPackSize(ESL_SQ *sq, MPI_Comm comm, int *ret_n);
extern int esl_sq_MPIPack(ESL_SQ *sq, char *buf, int n, int *pos, MPI_Comm comm);
extern int esl_sq_MPIUnpack(const ESL_ALPHABET *abc, char *buf, int n, int *pos, MPI_Comm comm, ESL_SQ **ret_sq);
extern int esl_sq_MPIRecv(int source, int tag, MPI_Comm comm, const ESL_ALPHABET *abc,
char **buf, int *nalloc, ESL_SQ **ret_sq);
/* 3. Communicating ESL_MSA (multiple sequence alignments) */
extern int esl_msa_MPISend(const ESL_MSA *msa, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc);
extern int esl_msa_MPIPackSize(const ESL_MSA *msa, MPI_Comm comm, int *ret_n);
extern int esl_msa_MPIPack(const ESL_MSA *msa, char *buf, int n, int *position, MPI_Comm comm);
extern int esl_msa_MPIUnpack(const ESL_ALPHABET *abc, char *buf, int n, int *pos, MPI_Comm comm, ESL_MSA **ret_msa);
extern int esl_msa_MPIRecv(int source, int tag, MPI_Comm comm, const ESL_ALPHABET *abc, char **buf, int *nalloc, ESL_MSA **ret_msa);
/* 4. Communicating ESL_STOPWATCH (process timing) */
extern int esl_stopwatch_MPIReduce(ESL_STOPWATCH *w, int root, MPI_Comm comm);
#endif /*HAVE_MPI*/
#endif /*eslMPI_INCLUDED*/
|
