1 /* Support for MPI parallelization. 2 */ 3 #ifndef eslMPI_INCLUDED 4 #define eslMPI_INCLUDED 5 #include "esl_config.h" 6 #if defined(HAVE_MPI) 7 #include <mpi.h> 8 9 #include "esl_alphabet.h" 10 #include "esl_msa.h" 11 #include "esl_sq.h" 12 #include "esl_stopwatch.h" 13 14 /* Many MPI implementations are not MPI2.2 compliant, and do not 15 * support new MPI2.2 datatypes; work around that absence. [J10/152] 16 * This configuration is better here than esl_config.h.in, because 17 * we need to #include <mpi.h> first to see if the system MPI does 18 * the right thing, and esl_config.h.in is intended to be included 19 * BEFORE any system includes. 20 */ 21 #if MPI_VERSION < 2 || MPI_SUBVERSION < 2 22 #ifndef MPI_INT64_T 23 #define MPI_INT64_T MPI_LONG_LONG_INT 24 #endif 25 #ifndef MPI_UINT64_T 26 #define MPI_UINT64_T MPI_UNSIGNED_LONG_LONG 27 #endif 28 #ifndef MPI_UINT32_T 29 #define MPI_UINT32_T MPI_UNSIGNED 30 #endif 31 #ifndef MPI_INT16_T 32 #define MPI_INT16_T MPI_SHORT 33 #endif 34 #ifndef MPI_UINT8_T 35 #define MPI_UINT8_T MPI_UNSIGNED_CHAR 36 #endif 37 #endif /*MPI_VERSION,MPI_SUBVERSION*/ 38 39 /* 1. Communicating optional arrays */ 40 extern int esl_mpi_PackOpt(void *inbuf, int incount, MPI_Datatype type, void *pack_buf, 41 int pack_buf_size, int *position, MPI_Comm comm); 42 extern int esl_mpi_PackOptSize(void *inbuf, int incount, MPI_Datatype type, MPI_Comm comm, int *ret_n); 43 extern int esl_mpi_UnpackOpt(void *pack_buf, int pack_buf_size, int *pos, void **outbuf, 44 int *opt_n, MPI_Datatype type, MPI_Comm comm); 45 46 /* 2. Communicating ESL_SQ (single sequences) */ 47 extern int esl_sq_MPISend(ESL_SQ *sq, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc); 48 extern int esl_sq_MPIPackSize(ESL_SQ *sq, MPI_Comm comm, int *ret_n); 49 extern int esl_sq_MPIPack(ESL_SQ *sq, char *buf, int n, int *pos, MPI_Comm comm); 50 extern int esl_sq_MPIUnpack(const ESL_ALPHABET *abc, char *buf, int n, int *pos, MPI_Comm comm, ESL_SQ **ret_sq); 51 extern int esl_sq_MPIRecv(int source, int tag, MPI_Comm comm, const ESL_ALPHABET *abc, 52 char **buf, int *nalloc, ESL_SQ **ret_sq); 53 54 /* 3. Communicating ESL_MSA (multiple sequence alignments) */ 55 extern int esl_msa_MPISend(const ESL_MSA *msa, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc); 56 extern int esl_msa_MPIPackSize(const ESL_MSA *msa, MPI_Comm comm, int *ret_n); 57 extern int esl_msa_MPIPack(const ESL_MSA *msa, char *buf, int n, int *position, MPI_Comm comm); 58 extern int esl_msa_MPIUnpack(const ESL_ALPHABET *abc, char *buf, int n, int *pos, MPI_Comm comm, ESL_MSA **ret_msa); 59 extern int esl_msa_MPIRecv(int source, int tag, MPI_Comm comm, const ESL_ALPHABET *abc, char **buf, int *nalloc, ESL_MSA **ret_msa); 60 61 /* 4. Communicating ESL_STOPWATCH (process timing) */ 62 extern int esl_stopwatch_MPIReduce(ESL_STOPWATCH *w, int root, MPI_Comm comm); 63 64 65 #endif /*HAVE_MPI*/ 66 #endif /*eslMPI_INCLUDED*/ 67