/* mpisupport.c * Optional support for MPI parallelization in Infernal. * * EPN, Mon Aug 27 12:38:13 2007 * SVN $Id$ */ #include "esl_config.h" #include "p7_config.h" #include "config.h" #ifdef HAVE_MPI #include #include #include #include #include "mpi.h" #include "easel.h" #include "esl_mpi.h" #include "hmmer.h" #include "infernal.h" static int expinfo_MPIPackSize(ExpInfo_t *exp, MPI_Comm comm, int *ret_n); static int expinfo_MPIPack(ExpInfo_t *exp, char *buf, int n, int *position, MPI_Comm comm); static int expinfo_MPIUnpack(char *buf, int n, int *pos, MPI_Comm comm, ExpInfo_t **ret_exp); static int cm_hit_MPISend(CM_HIT *hit, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc); static int cm_hit_MPIPackSize(CM_HIT *hit, MPI_Comm comm, int *ret_n); static int cm_hit_MPIPack(CM_HIT *hit, char *buf, int n, int *pos, MPI_Comm comm); static int cm_hit_MPIUnpack(char *buf, int n, int *pos, MPI_Comm comm, CM_HIT *hit); static int cm_hit_MPIRecv(int source, int tag, MPI_Comm comm, char **buf, int *nalloc, CM_HIT *hit); /***************************************************************** * 1. Communicating a CM. *****************************************************************/ /* Function: cm_master_MPIBcast() * Incept: EPN, Wed May 9 17:24:53 2007 * * Purpose: Broadcasts CM from a master. * * If is NULL, broadcasts a end-of-data signal, to * tell workers to shut down. * */ int cm_master_MPIBcast(CM_t *cm, char *errbuf, int tag, MPI_Comm comm, char **buf, int *nalloc) { int status; int code; int sz, n, pos; /* Figure out size */ if (MPI_Pack_size(1, MPI_INT, comm, &n) != 0) ESL_XEXCEPTION(eslESYS, "mpi pack size failed"); if (cm != NULL) { if ((status = cm_nonconfigured_MPIPackSize(cm, comm, &sz)) != eslOK) return status; n += sz; } /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } /* Pack the status code and CM into the buffer */ pos = 0; code = (cm == NULL) ? eslEOD : eslOK; if (MPI_Pack(&code, 1, MPI_INT, *buf, n, &pos, comm) != 0) ESL_EXCEPTION(eslESYS, "mpi pack failed"); if (cm != NULL) { if ((status = cm_nonconfigured_MPIPack(cm, errbuf, *buf, n, &pos, comm)) != eslOK) return status; } /* Broadcast the size of the packed CM */ if (MPI_Bcast(&n, 1, MPI_INT, 0, MPI_COMM_WORLD) != 0) ESL_EXCEPTION(eslESYS, "mpi broadcast failed"); /* Broadcast the packed CM */ if (MPI_Bcast (*buf, n, MPI_PACKED, 0, MPI_COMM_WORLD) != 0) ESL_EXCEPTION(eslESYS, "mpi broadcast failed"); return eslOK; ERROR: return status; } /* Function: cm_worker_MPIBcast() * Incept: EPN, Mon Aug 27 14:44:11 2007 * * Purpose: Receives a broadcasted buffer size and then a * broadcasted work unit of that size that consists * of a single CM tagged as from * communicator (usually 0, a master). * * Work units are prefixed by a status code. If the unit's * code is and no errors are encountered, this * routine will return and a non- <*ret_cm>. * If the unit's code is (a shutdown signal), * this routine returns and <*ret_cm> is . * * If the packed CM is an end-of-data signal, return * , and <*ret_cm> is . * * Returns: on success. <*ret_cm> contains the new CM; it * is allocated here, and the caller is responsible for * free'ing it. <*buf> may have been reallocated to a * larger size, and <*nalloc> may have been increased. * * * Throws: if an MPI call fails; if an allocation fails. * In either case, <*ret_msa> is NULL, and the and its size * <*nalloc> remain valid. * Xref: J1/72. * */ int cm_worker_MPIBcast(char *errbuf, int tag, MPI_Comm comm, char **buf, int *nalloc, ESL_ALPHABET **abc, CM_t **ret_cm) { int status, code; int n; int pos; /* Receive the buffer size broadcast */ if (MPI_Bcast(&n, 1, MPI_INT, 0, MPI_COMM_WORLD) != 0) ESL_EXCEPTION(eslESYS, "mpi broadcast failed."); /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } /* Receive the CM broadcast */ if (MPI_Bcast (*buf, n, MPI_PACKED, 0, MPI_COMM_WORLD) != 0) ESL_EXCEPTION(eslESYS, "mpi broadcast failed."); /* Unpack it - where the first integer is a status code, OK or EOD */ pos = 0; if (MPI_Unpack (*buf, n, &pos, &code, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (code == eslEOD) { status = eslEOD; goto ERROR; } return cm_nonconfigured_MPIUnpack(abc, errbuf, *buf, *nalloc, &pos, comm, ret_cm); ERROR: *ret_cm = NULL; return status; } /* Function: cm_nonconfigured_MPIUnpack() * Synopsis: Unpacks a CM (packed by cm_nonconfigured_MPIPack()) from an MPI buffer. * Incept: EPN, Mon Aug 27 14:44:11 2007 * * Purpose: Unpack a newly allocated CM from MPI packed buffer * , starting from position <*pos>, where the total length * of the buffer in bytes is . Note that * the full CM data structure was not packed, only * the parts that could have been changed from their initial * (default) values in CMFileRead() are packed. In this * case it's safe to 'fill-in' the 'rest' of the CM with a ConfigCM() * call, which saves us from broadcasting the 'rest' of the CM. * * Returns: on success. <*pos> is updated to the position of * the next element in to unpack (if any). <*ret_cm> * contains a newly allocated CM, which the caller is * responsible for free'ing. * * Throws: on an MPI call failure. on allocation failure. * In either case, <*ret_cm> is , and the state of * and <*pos> is undefined and should be considered to be corrupted. */ int cm_nonconfigured_MPIUnpack(ESL_ALPHABET **abc, char *errbuf, char *buf, int n, int *pos, MPI_Comm comm, CM_t **ret_cm) { int status; CM_t *cm = NULL; P7_HMM *hmm = NULL; ESL_ALPHABET *aabc = NULL; int atype, i, K, M, nnodes; float tmp_fp7_gfmu; float tmp_fp7_gflambda; cm = CreateCMShell(); if (cm == NULL) { status = eslEMEM; goto ERROR; } if (MPI_Unpack(buf, n, pos, &(cm->M), 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->nodes), 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->clen), 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &atype, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->flags), 1, MPI_INT, comm) != 0) ESL_EXCEPTION(eslESYS, "mpi unpack failed"); /* note: it's important cm->flags is set prior to CreateCMBody() call below, to properly allocate * cm->rf, cm->consensus, cm->map, or not */ /* Set or verify the alphabet */ if (*abc == NULL) { /* still unknown: set it, pass control of it back to caller */ if ((*abc = esl_alphabet_Create(atype)) == NULL) { status = eslEMEM; goto ERROR; } } else { /* already known: check it */ if ((*abc)->type != atype) { status = eslEINCOMPAT; goto ERROR; } } CreateCMBody(cm, cm->nodes, cm->M, cm->clen, (*abc)); /* For convenience below */ K = cm->abc->K; M = cm->M; nnodes = cm->nodes; /* Unpack the rest of the CM */ /* note cm->flags is how it was immediately after CM is read from file, so the only flags that can possibly be raised are: * CMH_ACC, CMH_DESC, CM_RF, CMH_GA, CMH_TC, CMH_NC, CMH_CHKSUM, CMH_MAP, CMH_CONS, CMH_EXPTAIL_STATS, CMH_FILTER_STATS, * CMH_QDB, CMH_QDB_LOCAL, CMH_FP7, CM_IS_RSEARCH, CM_RSEARCHTRANS, CM_RSEARCH_EMIT */ if (MPI_Unpack(buf, n, pos, cm->e[0], M*K*K, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->t[0], M*MAXCONNECT, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->sttype, M+1, MPI_CHAR, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->stid, M+1, MPI_CHAR, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->ndidx, M, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->cfirst, M, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->cnum, M, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->plast, M, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->pnum, M, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->nodemap, nnodes, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->ndtype, nnodes, MPI_CHAR, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->nseq), 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->eff_nseq), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->el_selfsc), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->null2_omega), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->null3_omega), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->checksum), 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, cm->null, K, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->W), 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->beta_W), 1,MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->tau), 1,MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->maxtau), 1,MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->ga), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->nc), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &(cm->tc), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); /* name and all the optional stuff */ if ((status = esl_mpi_UnpackOpt(buf, n, pos, (void**)&(cm->name), NULL, MPI_CHAR, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if ((status = esl_mpi_UnpackOpt(buf, n, pos, (void**)&(cm->acc), NULL, MPI_CHAR, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if ((status = esl_mpi_UnpackOpt(buf, n, pos, (void**)&(cm->desc), NULL, MPI_CHAR, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if ((status = esl_mpi_UnpackOpt(buf, n, pos, (void**)&(cm->comlog), NULL, MPI_CHAR, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if ((status = esl_mpi_UnpackOpt(buf, n, pos, (void**)&(cm->ctime), NULL, MPI_CHAR, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (cm->flags & CMH_RF) { if (MPI_Unpack(buf, n, pos, cm->rf, cm->clen+2, MPI_CHAR, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); } if (cm->flags & CMH_CONS) { if (MPI_Unpack(buf, n, pos, cm->consensus, cm->clen+2, MPI_CHAR, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); } if (cm->flags & CMH_MAP) { if (MPI_Unpack(buf, n, pos, cm->map, cm->clen+1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); } /* the E-value stats */ if (cm->flags & CMH_EXPTAIL_STATS) { ESL_ALLOC(cm->expA, sizeof(ExpInfo_t *) * EXP_NMODES); for(i = 0; i < EXP_NMODES; i++) { if((status = expinfo_MPIUnpack(buf, n, pos, comm, &(cm->expA[i]))) != eslOK) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); } } /* Finally unpack any additional p7 filter stats, and the p7 models themselves */ if (cm->flags & CMH_FP7) { if (MPI_Unpack(buf, n, pos, &tmp_fp7_gfmu, 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &tmp_fp7_gflambda, 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if((status = p7_hmm_MPIUnpack(buf, n, pos, comm, &aabc, &hmm)) != eslOK) ESL_XEXCEPTION(status, "mpi unpack failed"); if((status = cm_SetFilterHMM(cm, hmm, tmp_fp7_gfmu, tmp_fp7_gflambda)) != eslOK) ESL_XEXCEPTION(eslESYS, "Unable to set filter HMM for CM"); } /* Verify we're not configured */ if((status = cm_nonconfigured_Verify(cm, errbuf)) != eslOK) ESL_XEXCEPTION(status, errbuf); *ret_cm = cm; return eslOK; ERROR: if(cm != NULL) FreeCM(cm); return status; } /* Function: cm_nonconfigured_MPIPack() * Incept: EPN, Mon Aug 27 14:24:57 2007 * * Purpose: Packs CM into an MPI packed message buffer * of length bytes, starting at byte position <*position>, * for MPI communicator . Note that * the full CM data structure is not packed, only * the parts that could have been changed from their initial * (default) values in CMFileRead() are packed. In this * case it's safe to 'fill-in' the 'rest' of the CM with a ConfigCM() * call, which saves us from broadcasting the 'rest' of the CM. * * The caller must know that 's allocation of * bytes is large enough to append the packed CM at * position <*pos>. This typically requires a call to * first, and reallocation if * needed. * * Returns: on success; now contains the * packed , and <*position> is set to the byte * immediately following the last byte of the CM * in . * * Throws: if is configured. * if an MPI call fails; or if the * buffer's length was overflowed in trying to pack * into . In either case, the state of * and <*position> is undefined, and both should * be considered to be corrupted. */ int cm_nonconfigured_MPIPack(CM_t *cm, char *errbuf, char *buf, int n, int *pos, MPI_Comm comm) { int status; int i; int K = cm->abc->K; int M = cm->M; int nnodes = cm->nodes; int clen = cm->clen; /* Verify we're not configured */ if((status = cm_nonconfigured_Verify(cm, errbuf)) != eslOK) ESL_XEXCEPTION(status, errbuf); if (MPI_Pack(&M, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&nnodes, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&clen, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack((void *) &(cm->abc->type), 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->flags), 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); /* note cm->flags is how it was immediately after CM is read from file, so the only flags that can possibly be raised are: * CMH_ACC, CMH_DESC, CM_RF, CMH_GA, CMH_TC, CMH_NC, CMH_CHKSUM, CMH_MAP, CMH_CONS, CMH_EXPTAIL_STATS, CMH_FILTER_STATS, * CMH_QDB, CMH_QDB_LOCAL, CMH_MLP7_STATS, CMH_AP7_STATS, CM_IS_RSEARCH, CM_RSEARCHTRANS, CM_RSEARCH_EMIT */ if (MPI_Pack(cm->e[0], M*K*K, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->t[0], M*MAXCONNECT, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->sttype, M+1, MPI_CHAR, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->stid, M+1, MPI_CHAR, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->ndidx, M, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->cfirst, M, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->cnum, M, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->plast, M, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->pnum, M, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->nodemap, nnodes, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->ndtype, nnodes, MPI_CHAR, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->nseq), 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->eff_nseq), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->el_selfsc), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->null2_omega), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->null3_omega), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->checksum), 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(cm->null, K, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->W), 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->beta_W), 1,MPI_DOUBLE, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->tau), 1,MPI_DOUBLE, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->maxtau), 1,MPI_DOUBLE, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->ga), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->nc), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->tc), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); /* name and all the optional stuff */ if ((status = esl_mpi_PackOpt(cm->name, -1, MPI_CHAR, buf, n, pos, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack failed"); if ((status = esl_mpi_PackOpt(cm->acc, -1, MPI_CHAR, buf, n, pos, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack failed"); if ((status = esl_mpi_PackOpt(cm->desc, -1, MPI_CHAR, buf, n, pos, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack failed"); if ((status = esl_mpi_PackOpt(cm->comlog, -1, MPI_CHAR, buf, n, pos, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack failed"); if ((status = esl_mpi_PackOpt(cm->ctime, -1, MPI_CHAR, buf, n, pos, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack failed"); if (cm->flags & CMH_RF) { if (MPI_Pack(cm->rf, cm->clen+2, MPI_CHAR, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); } if (cm->flags & CMH_CONS) { if (MPI_Pack(cm->consensus, cm->clen+2, MPI_CHAR, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); } if (cm->flags & CMH_MAP) { if (MPI_Pack(cm->map, cm->clen+1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); } /* the E-value stats */ if (cm->flags & CMH_EXPTAIL_STATS) { for(i = 0; i < EXP_NMODES; i++) { if ((status = expinfo_MPIPack(cm->expA[i], buf, n, pos, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack failed"); } } if ((cm->flags & CMH_FP7) && (cm->fp7 != NULL)) { if (MPI_Pack(&(cm->fp7_evparam[CM_p7_GFMU]), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(cm->fp7_evparam[CM_p7_GFLAMBDA]), 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if((status = p7_hmm_MPIPack(cm->fp7, buf, n, pos, comm)) != eslOK) ESL_XEXCEPTION(status, "pack failed"); } if (*pos > n) ESL_XEXCEPTION(eslEMEM, "buffer overflow"); return eslOK; ERROR: return status; } /* Function: cm_nonconfigured_MPIPackSize() * * Synopsis: Calculates size needed to pack a CM that has * just been read from a CM file by a CMFileRead() * call, we'll need to pack far less than a fully * configure CM in this case. * * Incept: EPN, Mon Aug 27 10:34:15 2007 * based on p7_hmm_MPIPackSize() from HMMER3. * * Purpose: Calculate an upper bound on the number of bytes * that will need to pack a CM * in a packed MPI message for MPI communicator * ; return that number of bytes in <*ret_n>. * * Returns: on success, and <*ret_n> contains the answer. * * Throws: if an MPI call fails, and <*ret_n> is 0. */ int cm_nonconfigured_MPIPackSize(CM_t *cm, MPI_Comm comm, int *ret_n) { int status; int i; int n = 0; int K = cm->abc->K; int M = cm->M; int nnodes = cm->nodes; int sz; if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += 5*sz; /* M, nodes, clen, abc->type, flags */ if (MPI_Pack_size(M*K*K, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* e */ if (MPI_Pack_size(M*MAXCONNECT, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* t */ if (MPI_Pack_size(M+1, MPI_CHAR, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += 2*sz; /* sttype, stid */ if (MPI_Pack_size(M, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += 5*sz; /* ndidx, cfirst, cnum, plast, pnum */ if (MPI_Pack_size(nnodes, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nodemap */ if (MPI_Pack_size(nnodes, MPI_CHAR, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* ndtype */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nseq */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += 4*sz; /* eff_nseq, el_selfsc, null2_omega, null3_omega */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* checksum */ if (MPI_Pack_size(K, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* null */ if (MPI_Pack_size(M, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += 2*sz; /* dmin/dmax */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* W */ if (MPI_Pack_size(1, MPI_DOUBLE, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += 4*sz; /* beta_W, beta_qdb, tau, maxtau */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += 3*sz; /* ga, tc, nc */ if ((status = esl_mpi_PackOptSize(cm->name, -1, MPI_CHAR, comm, &sz)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* name */ if ((status = esl_mpi_PackOptSize(cm->acc, -1, MPI_CHAR, comm, &sz)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* acc */ if ((status = esl_mpi_PackOptSize(cm->desc, -1, MPI_CHAR, comm, &sz)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* desc */ if ((status = esl_mpi_PackOptSize(cm->comlog, -1, MPI_CHAR, comm, &sz)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* comlog */ if ((status = esl_mpi_PackOptSize(cm->ctime, -1, MPI_CHAR, comm, &sz)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* ctime */ if (cm->flags & CMH_RF) if (MPI_Pack_size(cm->clen+2, MPI_CHAR, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* rf */ if (cm->flags & CMH_CONS) if (MPI_Pack_size(cm->clen+2, MPI_CHAR, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* consensus */ if (cm->flags & CMH_MAP) if (MPI_Pack_size(cm->clen+1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* map */ if (cm->flags & CMH_EXPTAIL_STATS) { for(i = 0; i < EXP_NMODES; i++) { if ((status = expinfo_MPIPackSize(cm->expA[i], comm, &sz)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; } } /* Finally, compute size for additional p7 filters */ if((cm->flags & CMH_FP7) && (cm->fp7 != NULL)) { if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += 2*sz; /* tmp_fp7_gfmu and tmp_fp7_gflambda */ if ((status = p7_hmm_MPIPackSize(cm->fp7, comm, &sz)) != eslOK) ESL_XEXCEPTION(status, "p7_hmm_MPIPackSize() failed"); n += sz; /* cm->ap7A[i] p7 HMM */ } *ret_n = n; return eslOK; ERROR: *ret_n = 0; return status; } /* Function: expinfo_MPIPackSize() * Synopsis: Calculates number of bytes needed to pack a * ExpInfo_t object. Follows 'Purpose' * of other *_MPIPackSize() functions above. * * Incept: EPN, Wed Dec 12 05:00:01 2007 * * Returns: on success, and <*ret_n> contains the answer. * * Throws: if an MPI call fails, and <*ret_n> is set to 0. * * Note: The sizing calls here need to stay matched up with * the calls in . */ int expinfo_MPIPackSize(ExpInfo_t *exp, MPI_Comm comm, int *ret_n) { int status; int sz; int n = 0; status = MPI_Pack_size(1, MPI_INT, comm, &sz); n += 2*sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* nrandhits, is_valid */ status = MPI_Pack_size(1, MPI_DOUBLE, comm, &sz); n += 6*sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* mu_orig, mu_extrap, lambda, tailp, cur_eff_dbsize, dbsize */ *ret_n = n; return eslOK; ERROR: *ret_n = 0; return status; } /* Function: expinfo_MPIPack() * Synopsis: Packs ExpInfo_t into MPI buffer. * See 'Purpose','Returns' and 'Throws' * of other *_MPIPack()'s for more info. * * Incept: EPN, Wed Dec 12 05:03:40 2007 */ int expinfo_MPIPack(ExpInfo_t *exp, char *buf, int n, int *position, MPI_Comm comm) { int status; ESL_DPRINTF2(("expinfo_MPIPack(): ready.\n")); status = MPI_Pack((double *) &(exp->cur_eff_dbsize), 1, MPI_DOUBLE, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack((double *) &(exp->lambda), 1, MPI_DOUBLE, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack((double *) &(exp->mu_extrap), 1, MPI_DOUBLE, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack((double *) &(exp->mu_orig), 1, MPI_DOUBLE, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack((double *) &(exp->dbsize), 1, MPI_DOUBLE, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack((int *) &(exp->nrandhits), 1, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack((double *) &(exp->tailp), 1, MPI_DOUBLE, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack((int *) &(exp->is_valid), 1, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); ESL_DPRINTF2(("expinfo_results_MPIPack(): done. Packed %d bytes into buffer of size %d\n", *position, n)); if (*position > n) ESL_EXCEPTION(eslEMEM, "buffer overflow"); return eslOK; } /* Function: expinfo_MPIUnpack() * Synopsis: Unpacks ExpInfo_t from an MPI buffer. * Follows 'Purpose', 'Returns', 'Throws' of other * *_MPIUnpack() functions above. * * Incept: EPN, Wed Dec 12 05:29:19 2007 */ int expinfo_MPIUnpack(char *buf, int n, int *pos, MPI_Comm comm, ExpInfo_t **ret_exp) { int status; ExpInfo_t *exp; ESL_ALLOC(exp, sizeof(ExpInfo_t)); status = MPI_Unpack (buf, n, pos, &(exp->cur_eff_dbsize), 1, MPI_DOUBLE, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &(exp->lambda), 1, MPI_DOUBLE, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &(exp->mu_extrap), 1, MPI_DOUBLE, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &(exp->mu_orig), 1, MPI_DOUBLE, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &(exp->dbsize), 1, MPI_DOUBLE, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &(exp->nrandhits), 1, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &(exp->tailp), 1, MPI_DOUBLE, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &(exp->is_valid), 1, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); *ret_exp = exp; return eslOK; ERROR: if(exp != NULL) free(exp); *ret_exp = NULL; return status; } /* Function: cm_dsq_MPISend() * * Incept: EPN, Tue Aug 28 15:20:16 2007 * EPN, Fri Jan 13 05:25:13 2012 [updated] * * Purpose: Sends a digitized sequence, its length and a sequence index * as a work unit to MPI process ( ranges from <0..nproc-1>), * tagging the message with MPI tag for MPI communicator * . The receiver uses to receive the dsq. * * Work units are prefixed by a status code. If is * , the work unit is an code followed by * the packed MSA. If is NULL, the work unit is an * code, which knows how * to interpret; this is typically used for an end-of-data * signal to cleanly shut down worker processes. * * In order to minimize alloc/free cycles, caller passes a * pointer to a working buffer <*buf> of size <*nalloc> * characters. If necessary (i.e. if is too big to * fit), <*dsq> will be reallocated and <*nalloc> increased * to the new size. As a special case, if <*dsq> is * and <*nalloc> is 0, the buffer will be allocated * appropriately, but the caller is still responsible for * free'ing it. * * Args: dsq - digitized seq to send * L - length of dsq we're sending (dsq could extend further) * idx - sequence index (serves as unique id) for the dsq we're sending * dest - MPI destination (0..nproc-1) * tag - MPI tag * buf - pointer to a working buffer * nalloc - current allocated size of <*buf>, in characters * * Returns: on success; <*buf> may have been reallocated and * <*nalloc> may have been increased. * * Throws: if an MPI call fails; if a malloc/realloc * fails. In either case, <*buf> and <*nalloc> remain valid and useful * memory (though the contents of <*buf> are undefined). */ int cm_dsq_MPISend(ESL_DSQ *dsq, int64_t L, int64_t idx, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc) { int status; int code; int sz, n, pos; /* First, figure out the size of the work unit */ if (MPI_Pack_size(1, MPI_INT, comm, &n) != 0) ESL_EXCEPTION(eslESYS, "mpi pack size failed"); /* status code */ if (dsq != NULL) { if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_EXCEPTION(eslESYS, "mpi pack size failed"); /* L */ n += sz; if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_EXCEPTION(eslESYS, "mpi pack size failed"); /* idx */ n += sz; if (MPI_Pack_size(L+2, MPI_BYTE, comm, &sz) != 0) ESL_EXCEPTION(eslESYS, "mpi pack size failed"); /* dsq */ n += sz; } ESL_DPRINTF2(("cm_dsq_MPISend(): dsq has size %d\n", n)); /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { ESL_REALLOC(*buf, sizeof(char) * n); *nalloc = n; } ESL_DPRINTF2(("cm_dsq_MPISend(): buffer is ready\n")); /* Pack the status code, L, idx, and dsq into the buffer */ pos = 0; code = (dsq == NULL) ? eslEOD : eslOK; if (MPI_Pack(&code, 1, MPI_INT, *buf, n, &pos, comm) != 0) ESL_EXCEPTION(eslESYS, "mpi pack failed"); if (dsq != NULL) { if (MPI_Pack(&L, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_EXCEPTION(eslESYS, "mpi pack failed"); if (MPI_Pack(&idx, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_EXCEPTION(eslESYS, "mpi pack failed"); if (MPI_Pack(dsq, L+2, MPI_BYTE, *buf, n, &pos, comm) != 0) ESL_EXCEPTION(eslESYS, "mpi pack failed"); } ESL_DPRINTF2(("cm_dsq_MPISend(): dsq is packed into %d bytes\n", pos)); /* Send the packed profile to destination */ if (MPI_Send(*buf, n, MPI_PACKED, dest, tag, comm) != 0) ESL_EXCEPTION(eslESYS, "mpi send failed"); ESL_DPRINTF2(("cm_dsq_MPISend(): dsq is sent.\n")); return eslOK; ERROR: return status; } /* Function: cm_dsq_MPIRecv() * * Incept: EPN, Tue Aug 28 15:29:34 2007 * EPN, Fri Jan 13 05:25:29 2012 [updated] * * Purpose: Receives a work unit that consists of a digitized sequence * its length and an index from (<0..nproc-1>, or * ) tagged as from communicator . * * Work units are prefixed by a status code. If the unit's * code is and no errors are encountered, this * routine will return a non- <*ret_dsq> and * a valid <*ret_L> and <*ret_idx> (equal to whatever was * received (could be -1)). If the unit's code is * (a shutdown signal), this routine returns , * <*ret_dsq> is and <*ret_L> and <*ret_idx> are -1. * * To minimize alloc/free cycles in this routine, caller * passes a pointer to a buffer <*buf> of size <*nalloc> * characters. These are passed by reference, because when * necessary, <*buf> will be reallocated and <*nalloc> * increased to the new size. As a special case, if <*buf> * is and <*nalloc> is 0, the buffer will be * allocated appropriately, but the caller is still * responsible for free'ing it. * * If the packed dsq is an end-of-data signal, return * , and <*ret_dsq> is . * * Returns: on success. <*ret_dsq> contains the new dsq; it * is allocated here, and the caller is responsible for * free'ing it. <*buf> may have been reallocated to a * larger size, and <*nalloc> may have been increased. * * * Throws: if an MPI call fails; if an allocation fails. * In either case, <*ret_dsq> is NULL, and the and its size * <*nalloc> remain valid. */ int cm_dsq_MPIRecv(int source, int tag, MPI_Comm comm, char **buf, int *nalloc, ESL_DSQ **ret_dsq, int64_t *ret_L, int64_t *ret_idx) { int status, code; ESL_DSQ *dsq = NULL; int64_t L = -1; int64_t idx = -1; int n; int pos; MPI_Status mpistatus; /* Probe first, because we need to know if our buffer is big enough. */ if (MPI_Probe(source, tag, comm, &mpistatus) != 0) ESL_XEXCEPTION(eslESYS, "mpi probe failed"); if (MPI_Get_count(&mpistatus, MPI_PACKED, &n) != 0) ESL_XEXCEPTION(eslESYS, "mpi get count failed"); /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } /* Receive the packed work unit */ ESL_DPRINTF2(("cm_dsq_MPIRecv(): about to receive dsq.\n")); if (MPI_Recv(*buf, n, MPI_PACKED, source, tag, comm, &mpistatus) != 0) ESL_XEXCEPTION(eslESYS, "mpi recv failed"); ESL_DPRINTF2(("cm_dsq_MPIRecv(): dsq has been received.\n")); /* Unpack it - where the first integer is a status code, OK or EOD */ ESL_DPRINTF2(("cm_dsq_MPIRecv(): about to unpack dsq.\n")); pos = 0; if (MPI_Unpack (*buf, n, &pos, &code, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (code == eslEOD) { status = eslEOD; goto ERROR; } if (MPI_Unpack (*buf, n, &pos, &L, 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack (*buf, n, &pos, &idx, 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); ESL_ALLOC(dsq, sizeof(ESL_DSQ) * (L+2)); if (MPI_Unpack (*buf, n, &pos, dsq, L+2, MPI_BYTE, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); dsq[0] = dsq[(L+1)] = eslDSQ_SENTINEL; /* overwrite */ ESL_DPRINTF2(("cm_dsq_MPIRecv(): dsq has been unpacked.\n")); *ret_L = L; *ret_idx = idx; *ret_dsq = dsq; return eslOK; ERROR: if (dsq != NULL) free(dsq); *ret_dsq = NULL; *ret_L = -1; *ret_idx = -1; return status; } /* Function: cm_parsetree_MPIPackSize() * Synopsis: Calculates number of bytes needed to pack a * parsetree. * Incept: EPN, Wed Aug 29 05:44:28 2007 * * Purpose: Calculate an upper bound on the number of bytes * that will need to pack * a parsetree in a packed MPI message in * communicator ; return that number of bytes * in <*ret_n>. * * Caller will generally use this result to determine how * to allocate a buffer before starting to pack into it. * * Returns: on success, and <*ret_n> contains the answer. * * Throws: if an MPI call fails, and <*ret_n> is set to 0. * * Note: The sizing calls here need to stay matched up with * the calls in . */ int cm_parsetree_MPIPackSize(Parsetree_t *tr, MPI_Comm comm, int *ret_n) { int status; int sz; int n = 0; status = MPI_Pack_size(1, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->n */ /* don't send tr->nalloc, it'll be set is as tr->n when this is unpacked */ status = MPI_Pack_size(1, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->memblock */ status = MPI_Pack_size(1, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->is_std */ status = MPI_Pack_size(1, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->pass_idx */ status = MPI_Pack_size(1, MPI_FLOAT,comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->trpenalty */ status = MPI_Pack_size(tr->n, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->emitl[] */ status = MPI_Pack_size(tr->n, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->emitr[] */ status = MPI_Pack_size(tr->n, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->state[] */ status = MPI_Pack_size(tr->n, MPI_CHAR, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->mode[] */ status = MPI_Pack_size(tr->n, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->nxtl[] */ status = MPI_Pack_size(tr->n, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->nxtr[] */ status = MPI_Pack_size(tr->n, MPI_INT, comm, &sz); n += sz; if (status != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); /* tr->prv[] */ *ret_n = n; return eslOK; ERROR: *ret_n = 0; return status; } /* Function: cm_parsetree_MPIPack() * Synopsis: Packs parsetree into MPI buffer. * Incept: EPN, Wed Aug 29 05:22:32 2007 * * Purpose: Packs parsetree into an * MPI packed message buffer of length bytes, * starting at byte position * <*position>, for MPI communicator . * * Returns: on success; now contains the * packed , and <*position> is set to the byte * immediately following the last byte of the results * in . * * Throws: if an MPI call fails; or if the * buffer's length is overflowed by trying to pack * into . In either case, the state of * and <*position> is undefined, and both should * be considered to be corrupted. * */ int cm_parsetree_MPIPack(Parsetree_t *tr, char *buf, int n, int *position, MPI_Comm comm) { int status; ESL_DPRINTF2(("cm_parsetree_MPIPack(): ready.\n")); status = MPI_Pack(&tr->n, 1, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(&tr->memblock, 1, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(&tr->is_std, 1, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(&tr->pass_idx, 1, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(&tr->trpenalty, 1, MPI_FLOAT,buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(tr->emitl, tr->n, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(tr->emitr, tr->n, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(tr->state, tr->n, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(tr->mode, tr->n, MPI_CHAR, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(tr->nxtl, tr->n, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(tr->nxtr, tr->n, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); status = MPI_Pack(tr->prv, tr->n, MPI_INT, buf, n, position, comm); if (status != 0) ESL_EXCEPTION(eslESYS, "pack failed"); ESL_DPRINTF2(("cm_parsetree_MPIPack(): done. Packed %d bytes into buffer of size %d\n", *position, n)); if (*position > n) ESL_EXCEPTION(eslEMEM, "buffer overflow"); return eslOK; } /* Function: cm_parsetree_MPIUnpack() * Synopsis: Unpacks parsetree from an MPI buffer. * Incept: EPN, Wed Aug 29 05:10:20 2007 * * Purpose: Unpack a newly allocated parsetree node from MPI packed buffer * , starting from position <*pos>, where the total length * of the buffer in bytes is . * * Returns: on success. <*pos> is updated to the position of * the next element in to unpack (if any). <*ret_tr> * contains a newly allocated parsetree, which the caller is * responsible for free'ing. * * Throws: on an MPI call failure. on allocation failure. * In either case, <*ret_tr> is , and the state of * and <*pos> is undefined and should be considered to be corrupted. */ int cm_parsetree_MPIUnpack(char *buf, int n, int *pos, MPI_Comm comm, Parsetree_t **ret_tr) { int status; Parsetree_t *tr = NULL; int tr_n; status = MPI_Unpack (buf, n, pos, &tr_n, 1, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); tr = CreateParsetree(tr_n); tr->n = tr_n; tr->nalloc = tr_n; status = MPI_Unpack (buf, n, pos, &tr->memblock, 1, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &tr->is_std, 1, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &tr->pass_idx, 1, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, &tr->trpenalty, 1, MPI_FLOAT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, tr->emitl, tr_n, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, tr->emitr, tr_n, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, tr->state, tr_n, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, tr->mode, tr_n, MPI_CHAR, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, tr->nxtl, tr_n, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, tr->nxtr, tr_n, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); status = MPI_Unpack (buf, n, pos, tr->prv, tr_n, MPI_INT, comm); if (status != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); *ret_tr = tr; return eslOK; ERROR: if (tr != NULL) FreeParsetree(tr); *ret_tr = NULL; return status; } /***************************************************************** * Communicating CM_PIPELINE *****************************************************************/ /* Function: cm_pipeline_MPISend() * Synopsis: Send pipeline data as an MPI message. * Incept: EPN, Thu Jun 2 14:36:01 2011 * MSF, Wed Sep 09 09:09:47 2009 [Janelia] (p7_pipeline_MPISend()) * * Purpose: Sends pipeline statistics to MPI process * (where ranges from 0..), with MPI tag * for MPI communicator . * * In order to minimize alloc/free cycles in this routine, * caller passes a pointer to a working buffer <*buf> of * size <*nalloc> characters. If necessary (i.e. if is * too big to fit), <*buf> will be reallocated and <*nalloc> * increased to the new size. As a special case, if <*buf> * is and <*nalloc> is 0, the buffer will be * allocated appropriately, but the caller is still * responsible for free'ing it. * * If is NULL, the pipeline statistics are initialized * to zeros. * * Returns: on success. */ int cm_pipeline_MPISend(CM_PIPELINE *pli, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc) { int status; int sz, n, pos; int pass_idx; CM_PIPELINE bogus; /* This will look wasteful, but the MPI spec doesn't guarantee that * MPI_Pack_size(x, ...) + MPI_Pack_size(x, ... ) == MPI_Pack_size(2x, ...). * Indeed there are some hints in the spec that that's *not* true. * So we assume we must match our Pack_size calls exactly to our Pack calls. */ n = 0; if (MPI_Pack_size(1, MPI_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* mode */ if (MPI_Pack_size(1, MPI_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* Z_setby */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nseqs */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nmodels */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nnodes */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nmodels_hmmonly */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nnodes_hmmonly */ if (MPI_Pack_size(1, MPI_DOUBLE, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* Z */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* cur_cm_idx */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* cur_seq_idx */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* cur_pass_idx */ for(pass_idx = 0; pass_idx < NPLI_PASSES; pass_idx++) { if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* npli_top */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* npli_bot */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nres_top */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* nres_bot */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_msv */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_vit */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_fwd */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_gfwd */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_edef */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_cyk */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_ins */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_output */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_msvbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_vitbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_fwdbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_gfwdbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_past_edefbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_msv */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_vit */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_fwd */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_gfwd */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_edef */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_cyk */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_ins */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_output */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_msvbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_vitbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_fwdbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_gfwdbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pos_past_edefbias */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_overflow_fcyk */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_overflow_final */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_aln_hb */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* n_aln_dccyk */ } /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } /* if no pipeline was defined, return zeros for the stats */ if (pli == NULL) { bogus.mode = CM_SEARCH_SEQS; /* that's 0. (some compilers complain if you set 0 directly. */ bogus.Z_setby = CM_ZSETBY_SSIINFO; /* ditto. */ bogus.nseqs = 0; bogus.nmodels = 0; bogus.nnodes = 0; bogus.nmodels_hmmonly = 0; bogus.nnodes_hmmonly = 0; bogus.Z = 0.0; bogus.cur_cm_idx = -1; bogus.cur_seq_idx = -1; bogus.cur_pass_idx = -1; for(pass_idx = 0; pass_idx < NPLI_PASSES; pass_idx++) { cm_pli_ZeroAccounting(&(bogus.acct[pass_idx])); } pli = &bogus; } /* Pack the pipeline into the buffer */ pos = 0; if (MPI_Pack(&pli->mode, 1, MPI_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->Z_setby, 1, MPI_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->nseqs, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->nmodels, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->nnodes, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->nmodels_hmmonly, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->nnodes_hmmonly, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->Z, 1, MPI_DOUBLE, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->cur_cm_idx, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->cur_seq_idx, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&pli->cur_pass_idx, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); for(pass_idx = 0; pass_idx < NPLI_PASSES; pass_idx++) { if (MPI_Pack(&(pli->acct[pass_idx].npli_top), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].npli_bot), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].nres_top), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].nres_bot), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_msv), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_vit), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_fwd), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_gfwd), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_edef), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_cyk), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_ins), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_output), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_msvbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_vitbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_fwdbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_gfwdbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_past_edefbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_msv), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_vit), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_fwd), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_gfwd), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_edef), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_cyk), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_ins), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_output), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_msvbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_vitbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_fwdbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_gfwdbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].pos_past_edefbias), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_overflow_fcyk), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_overflow_final), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_aln_hb), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&(pli->acct[pass_idx].n_aln_dccyk), 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); } /* Send the packed pipeline to destination */ MPI_Send(*buf, n, MPI_PACKED, dest, tag, comm); return eslOK; ERROR: return status; } /* Function: cm_pipeline_MPIRecv() * Synopsis: Receive pipeline data as an MPI message. * Incept: EPN, Thu Jun 2 14:41:46 2011 * MSF, Wed Sep 09 09:09:47 2009 [Janelia] (p7_pipeline_MPIRecv() * * Purpose: Receive a pipeline from (where is usually * process 0, the master) with tag from communicator , * and return it in <*ret_pli>. * * To minimize alloc/free cycles in this routine, caller * passes a pointer to a buffer <*buf> of size <*nalloc> * characters. These are passed by reference because if * necessary, will be reallocated and * increased to the new size. As a special case, if * is and is 0, the buffer will be * allocated appropriately, but the caller is still * responsible for free'ing it. * * Returns: on success. <*ret_pli> contains the new pipeline; * it is allocated here, and the caller is responsible for * free'ing it. <*buf> may have been reallocated to a * larger size, and <*nalloc> may have been increased. * */ int cm_pipeline_MPIRecv(int source, int tag, MPI_Comm comm, char **buf, int *nalloc, ESL_GETOPTS *go, CM_PIPELINE **ret_pli) { int status; CM_PIPELINE *pli = NULL; int n; int pos; int pass_idx; MPI_Status mpistatus; /* Probe first, because we need to know if our buffer is big enough. */ MPI_Probe(source, tag, comm, &mpistatus); MPI_Get_count(&mpistatus, MPI_PACKED, &n); /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } /* Receive the packed pipeline */ MPI_Recv(*buf, n, MPI_PACKED, source, tag, comm, &mpistatus); /* Unpack it - watching out for the EOD signal of M = -1. */ pos = 0; /* irrelevant, these are overwritten below */ if ((pli = cm_pipeline_Create(go, NULL, 1, 1, 0, CM_ZSETBY_SSIINFO, CM_SEARCH_SEQS)) == NULL) { status = eslEMEM; goto ERROR; } /* mode will be immediately overwritten */ if (MPI_Unpack(*buf, n, &pos, &(pli->mode), 1, MPI_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->Z_setby), 1, MPI_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->nseqs), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->nmodels), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->nnodes), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->nmodels_hmmonly), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->nnodes_hmmonly), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->Z), 1, MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->cur_cm_idx), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->cur_seq_idx), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->cur_pass_idx), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); for(pass_idx = 0; pass_idx < NPLI_PASSES; pass_idx++) { if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].npli_top), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].npli_bot), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].nres_top), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].nres_bot), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_msv), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_vit), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_fwd), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_gfwd), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_edef), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_cyk), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_ins), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_output), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_msvbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_vitbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_fwdbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_gfwdbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_past_edefbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_msv), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_vit), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_fwd), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_gfwd), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_edef), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_cyk), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_ins), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_output), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_msvbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_vitbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_fwdbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_gfwdbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].pos_past_edefbias), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_overflow_fcyk), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_overflow_final), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_aln_hb), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &(pli->acct[pass_idx].n_aln_dccyk), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); } *ret_pli = pli; return eslOK; ERROR: if (pli != NULL) cm_pipeline_Destroy(pli, NULL); *ret_pli = NULL; return status; } /***************************************************************** * Communicating CM_TOPHITS *****************************************************************/ /* Function: cm_tophits_MPISend() * Synopsis: Send the TOPHITS as an MPI work unit. * Incept: EPN, Thu Jun 2 08:45:05 2011 * MSF, Mon Sep 21 22:22:00 2009 [Janelia] (p7_tophits_MPISend() * * Purpose: Sends the TOPHITS as a work unit to MPI process * (where ranges from 0..), tagged * with MPI tag , for MPI communicator , as * the sole workunit or result. * * After the TOPHITS information has been sent, send * the each hit as an indepentant message. * * Returns: on success; <*buf> may have been reallocated and * <*nalloc> may have been increased. * * Throws: if an MPI call fails; if a malloc/realloc * fails. In either case, <*buf> and <*nalloc> remain valid and useful * memory (though the contents of <*buf> are undefined). */ int cm_tophits_MPISend(CM_TOPHITS *th, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc) { int status; int sz, n, pos; int i; CM_HIT *hit = NULL; sz = 0; n = 0; /* calculate the buffer size needed to hold the largest hit */ hit = th->unsrt; for (i = 0; i < th->N; i++) { if ((status = cm_hit_MPIPackSize(hit, comm, &sz)) != eslOK) goto ERROR; n = ESL_MAX(n, sz); hit++; } if (MPI_Pack_size(3, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n = ESL_MAX(n, sz); /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } pos = 0; if (MPI_Pack(&th->N, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&th->nreported, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&th->nincluded, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); /* Send the packed tophits information */ if (MPI_Send(*buf, n, MPI_PACKED, dest, tag, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi send failed"); if (th->N == 0) return eslOK; /* loop through the hit list sending to dest */ hit = th->unsrt; for (i = 0; i < th->N; i++) { if ((status = cm_hit_MPISend(hit, dest, tag, comm, buf, nalloc)) != eslOK) goto ERROR; hit++; } return eslOK; ERROR: return status; } /* Function: cm_tophits_MPIRecv() * Synopsis: Receives an TOPHITS as a work unit from an MPI sender. * Incept: EPN, Thu Jun 2 14:07:19 2011 * MSF, Mon Sep 21 22:22:00 2009 [Janelia] (p7_tophits_MPIRecv()) * * Purpose: Sends the TOPHITS as a work unit to MPI process * (where ranges from 0..), tagged * with MPI tag , for MPI communicator , as * the sole workunit or result. * * After the TOPHITS information has been sent, send * the each hit as an indepentant message. * * Returns: on success; <*buf> may have been reallocated and * <*nalloc> may have been increased. * * Throws: if an MPI call fails; if a malloc/realloc * fails. In either case, <*buf> and <*nalloc> remain valid and useful * memory (though the contents of <*buf> are undefined). */ int cm_tophits_MPIRecv(int source, int tag, MPI_Comm comm, char **buf, int *nalloc, CM_TOPHITS **ret_th) { int n; int status; int pos; CM_TOPHITS *th = NULL; CM_HIT *hit = NULL; MPI_Status mpistatus; uint64_t nhits; uint64_t inx; /* Probe first, because we need to know if our buffer is big enough. */ MPI_Probe(source, tag, comm, &mpistatus); MPI_Get_count(&mpistatus, MPI_PACKED, &n); /* make sure we are getting the tag we expect and from whom we expect if from */ if (tag != MPI_ANY_TAG && mpistatus.MPI_TAG != tag) { status = eslFAIL; goto ERROR; } if (source != MPI_ANY_SOURCE && mpistatus.MPI_SOURCE != source) { status = eslFAIL; goto ERROR; } /* set the source and tag */ tag = mpistatus.MPI_TAG; source = mpistatus.MPI_SOURCE; /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } /* Receive the packed top hits */ MPI_Recv(*buf, n, MPI_PACKED, source, tag, comm, &mpistatus); /* Unpack it - watching out for the EOD signal of M = -1. */ pos = 0; if ((th = cm_tophits_Create()) == NULL) { status = eslEMEM; goto ERROR; } if (MPI_Unpack(*buf, n, &pos, &nhits, 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &th->nreported, 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(*buf, n, &pos, &th->nincluded, 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); /* loop through all of the hits sent */ for (inx = 0; inx < nhits; inx++) { if ((status = cm_tophits_CreateNextHit(th, &hit)) != eslOK) goto ERROR; if ((status = cm_hit_MPIRecv(source, tag, comm, buf, nalloc, hit)) != eslOK) goto ERROR; } *ret_th = th; return eslOK; ERROR: if (th != NULL) cm_tophits_Destroy(th); *ret_th = NULL; return status; } /* Function: cm_hit_MPISend() */ int cm_hit_MPISend(CM_HIT *hit, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc) { int status; int pos; int n = *nalloc; /* Pack the HIT into the buffer */ pos = 0; if ((status = cm_hit_MPIPack(hit, *buf, n, &pos, comm)) != eslOK) goto ERROR; /* Send the packed HIT to the destination. */ if (MPI_Send(*buf, n, MPI_PACKED, dest, tag, comm) != 0) ESL_EXCEPTION(eslESYS, "mpi send failed"); return eslOK; ERROR: return status; } /* Function: cm_hit_MPIRecv() */ int cm_hit_MPIRecv(int source, int tag, MPI_Comm comm, char **buf, int *nalloc, CM_HIT *hit) { int n; int status; int pos; MPI_Status mpistatus; /* Probe first, because we need to know if our buffer is big enough. */ MPI_Probe(source, tag, comm, &mpistatus); MPI_Get_count(&mpistatus, MPI_PACKED, &n); /* make sure we are getting the tag we expect and from whom we expect if from */ if (tag != MPI_ANY_TAG && mpistatus.MPI_TAG != tag) { status = eslFAIL; goto ERROR; } if (source != MPI_ANY_SOURCE && mpistatus.MPI_SOURCE != source) { status = eslFAIL; goto ERROR; } /* set the source and tag */ tag = mpistatus.MPI_TAG; source = mpistatus.MPI_SOURCE; /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } /* Receive the packed top hits */ MPI_Recv(*buf, n, MPI_PACKED, source, tag, comm, &mpistatus); /* Unpack it - watching out for the EOD signal of M = -1. */ pos = 0; if ((status = cm_hit_MPIUnpack(*buf, n, &pos, comm, hit)) != eslOK) goto ERROR; return eslOK; ERROR: return status; } /* Function: cm_hit_MPIPackSize() * Synopsis: Calculates size needed to pack a HIT. * Incept: MSF, Mon Sep 21 22:22:00 2009 [Janelia] * * Purpose: Calculate an upper bound on the number of bytes * that will need to pack an CM_HIT * in a packed MPI message for MPI communicator * ; return that number of bytes in <*ret_n>. * * Returns: on success, and <*ret_n> contains the answer. * * Throws: if an MPI call fails, and <*ret_n> is 0. */ int cm_hit_MPIPackSize(CM_HIT *hit, MPI_Comm comm, int *ret_n) { int status; int n = 0; int sz; CM_ALIDISPLAY *ad = hit->ad; /* CM_HIT data */ if (MPI_Pack_size(5, MPI_LONG, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* start, stop, seq_idx, cm_idx, srcL */ if (MPI_Pack_size(6, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* in_rc, root, mode, pass_idx, hmmonly, glocal */ if (MPI_Pack_size(2, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* score, bias */ if (MPI_Pack_size(2, MPI_DOUBLE, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pvalue, evalue */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* flags */ if ((status = esl_mpi_PackOptSize(hit->name, -1, MPI_CHAR, comm, &sz)) != eslOK) goto ERROR; n += sz; if ((status = esl_mpi_PackOptSize(hit->acc, -1, MPI_CHAR, comm, &sz)) != eslOK) goto ERROR; n += sz; if ((status = esl_mpi_PackOptSize(hit->desc, -1, MPI_CHAR, comm, &sz)) != eslOK) goto ERROR; n += sz; /* CM_ALIDISPLAY data */ if (MPI_Pack_size(16, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* offset info */ if (MPI_Pack_size(7, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* N, N_el, cfrom_emit, cto_emit, cfrom_span, cto_span, clen */ if (MPI_Pack_size(2, MPI_LONG, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* sequence info */ if (MPI_Pack_size(1, MPI_DOUBLE, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* tau */ if (MPI_Pack_size(4, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* sc, avgpp, gc, matrix_Mb */ if (MPI_Pack_size(1, MPI_DOUBLE, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* elapsed_secs */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* hmmonly */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* memsize */ if (MPI_Pack_size(ad->memsize, MPI_CHAR, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* mem */ *ret_n = n; return eslOK; ERROR: *ret_n = 0; return status; } /* Function: cm_hit_MPIPack() * Synopsis: Packs the HIT into MPI buffer. * Incept: MSF, Mon Sep 21 22:22:00 2009 [Janelia] * * Purpose: Packs HIT into an MPI packed message buffer * of length bytes, starting at byte position <*position>, * for MPI communicator . * * The caller must know that 's allocation of * bytes is large enough to append the packed HIT at * position <*pos>. This typically requires a call to * first, and reallocation if * needed. * * Returns: on success; now contains the * packed , and <*position> is set to the byte * immediately following the last byte of the HIT * in . * * Throws: if an MPI call fails; or if the * buffer's length was overflowed in trying to pack * into . In either case, the state of * and <*position> is undefined, and both should * be considered to be corrupted. */ int cm_hit_MPIPack(CM_HIT *hit, char *buf, int n, int *pos, MPI_Comm comm) { int status; int offset; CM_ALIDISPLAY *ad = hit->ad; if (MPI_Pack(&hit->start, 1, MPI_LONG, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->stop, 1, MPI_LONG, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->in_rc, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->root, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->mode, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->cm_idx, 1, MPI_LONG, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->seq_idx, 1, MPI_LONG, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->pass_idx, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->score, 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->bias, 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->pvalue, 1, MPI_DOUBLE, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->evalue, 1, MPI_DOUBLE, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->flags, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->srcL, 1, MPI_LONG, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->hmmonly, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&hit->glocal, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if ((status = esl_mpi_PackOpt(hit->name, -1, MPI_CHAR, buf, n, pos, comm)) != eslOK) return status; if ((status = esl_mpi_PackOpt(hit->acc, -1, MPI_CHAR, buf, n, pos, comm)) != eslOK) return status; if ((status = esl_mpi_PackOpt(hit->desc, -1, MPI_CHAR, buf, n, pos, comm)) != eslOK) return status; offset = (ad->rfline == NULL) ? -1 : ad->rfline - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->ncline == NULL) ? -1 : ad->ncline - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->csline == NULL) ? -1 : ad->csline - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->model == NULL) ? -1 : ad->model - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->mline == NULL) ? -1 : ad->mline - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->aseq == NULL) ? -1 : ad->aseq - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->ppline == NULL) ? -1 : ad->ppline - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->aseq_el == NULL) ? -1 : ad->aseq_el - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->rfline_el == NULL) ? -1 : ad->rfline_el - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->ppline_el == NULL) ? -1 : ad->ppline_el - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->N, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->N_el, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->cmname == NULL) ? -1 : ad->cmname - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->cmacc == NULL) ? -1 : ad->cmacc - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->cmdesc == NULL) ? -1 : ad->cmdesc - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->cfrom_emit, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->cto_emit, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->cfrom_span, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->cto_span, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->clen, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->sqname == NULL) ? -1 : ad->sqname - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->sqacc == NULL) ? -1 : ad->sqacc - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); offset = (ad->sqdesc == NULL) ? -1 : ad->sqdesc - ad->mem; if (MPI_Pack(&offset, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->sqfrom, 1, MPI_LONG, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->sqto, 1, MPI_LONG, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->sc, 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->avgpp, 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->gc, 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->tau, 1, MPI_DOUBLE, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->matrix_Mb, 1, MPI_FLOAT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->elapsed_secs, 1, MPI_DOUBLE, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->hmmonly, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&ad->memsize, 1, MPI_INT, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack( ad->mem, ad->memsize, MPI_CHAR, buf, n, pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (*pos > n) ESL_EXCEPTION(eslEMEM, "buffer overflow"); return eslOK; ERROR: return status; } /* Function: cm_hit_MPIUnpack() * Synopsis: Unpacks an HIT from an MPI buffer. * Incept: EPN, Thu Jun 2 14:29:20 2011 * MSF, Mon Sep 21 22:22:00 2009 [Janelia] (p7_hit_MPIUnpack()) * * Purpose: Unpack a newly allocated HIT from MPI packed buffer * , starting from position <*pos>, where the total length * of the buffer in bytes is . * * Returns: on success. <*pos> is updated to the position of * the next element in to unpack (if any). <*ret_hit> * contains a newly allocated HIT, which the caller is * responsible for free'ing. * * Throws: on an MPI call failure. on allocation failure. * In either case, <*ret_hit> is , and the state of * and <*pos> is undefined and should be considered to be corrupted. */ int cm_hit_MPIUnpack(char *buf, int n, int *pos, MPI_Comm comm, CM_HIT *hit) { int status; int rfline, ncline, csline, model, mline, aseq, ppline, aseq_el, rfline_el, ppline_el; int cmname, cmacc, cmdesc; int sqname, sqacc, sqdesc; CM_ALIDISPLAY *ad; ESL_ALLOC(ad, sizeof(CM_ALIDISPLAY)); if (MPI_Unpack(buf, n, pos, &hit->start, 1, MPI_LONG, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->stop, 1, MPI_LONG, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->in_rc, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->root, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->mode, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->cm_idx, 1, MPI_LONG, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->seq_idx, 1, MPI_LONG, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->pass_idx, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->score, 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->bias, 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->pvalue, 1, MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->evalue, 1, MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->flags, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->srcL, 1, MPI_LONG, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->hmmonly, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &hit->glocal, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if ((status = esl_mpi_UnpackOpt(buf, n, pos, (void**)&(hit->name), NULL, MPI_CHAR, comm)) != eslOK) goto ERROR; if ((status = esl_mpi_UnpackOpt(buf, n, pos, (void**)&(hit->acc), NULL, MPI_CHAR, comm)) != eslOK) goto ERROR; if ((status = esl_mpi_UnpackOpt(buf, n, pos, (void**)&(hit->desc), NULL, MPI_CHAR, comm)) != eslOK) goto ERROR; if (MPI_Unpack(buf, n, pos, &rfline, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ncline, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &csline, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &model, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &mline, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &aseq, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ppline, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &aseq_el, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &rfline_el, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ppline_el, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->N, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->N_el, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &cmname, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &cmacc, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &cmdesc, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->cfrom_emit, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->cto_emit, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->cfrom_span, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->cto_span, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->clen, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &sqname, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &sqacc, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &sqdesc, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->sqfrom, 1, MPI_LONG, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->sqto, 1, MPI_LONG, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->sc, 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->avgpp, 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->gc, 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->tau, 1, MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->matrix_Mb, 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->elapsed_secs, 1, MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->hmmonly, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); if (MPI_Unpack(buf, n, pos, &ad->memsize, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); /* allocate the string pools for the alignments */ ESL_ALLOC(ad->mem, ad->memsize); if (MPI_Unpack(buf, n, pos, ad->mem, ad->memsize, MPI_CHAR, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed"); ad->rfline = (rfline == -1) ? NULL : ad->mem + rfline; ad->ncline = (ncline == -1) ? NULL : ad->mem + ncline; ad->csline = (csline == -1) ? NULL : ad->mem + csline; ad->model = (model == -1) ? NULL : ad->mem + model; ad->mline = (mline == -1) ? NULL : ad->mem + mline; ad->aseq = (aseq == -1) ? NULL : ad->mem + aseq; ad->ppline = (ppline == -1) ? NULL : ad->mem + ppline; ad->aseq_el = (aseq_el == -1) ? NULL : ad->mem + aseq_el; ad->rfline_el = (rfline_el == -1) ? NULL : ad->mem + rfline_el; ad->ppline_el = (ppline_el == -1) ? NULL : ad->mem + ppline_el; ad->cmname = (cmname == -1) ? NULL : ad->mem + cmname; ad->cmacc = (cmacc == -1) ? NULL : ad->mem + cmacc; ad->cmdesc = (cmdesc == -1) ? NULL : ad->mem + cmdesc; ad->sqname = (sqname == -1) ? NULL : ad->mem + sqname; ad->sqacc = (sqacc == -1) ? NULL : ad->mem + sqacc; ad->sqdesc = (sqdesc == -1) ? NULL : ad->mem + sqdesc; hit->ad = ad; return eslOK; ERROR: return status; } /* Function: cm_alndata_MPISend() * Synopsis: Send alignment data as an MPI message. * Incept: EPN, Fri Jan 13 09:19:54 2012 * * Purpose: Sends alignment data to MPI process * (where ranges from 0..), with MPI tag * for MPI communicator . * * In order to minimize alloc/free cycles in this routine, * caller passes a pointer to a working buffer <*buf> of * size <*nalloc> characters. If necessary (i.e. if is * too big to fit), <*buf> will be reallocated and <*nalloc> * increased to the new size. As a special case, if <*buf> * is and <*nalloc> is 0, the buffer will be * allocated appropriately, but the caller is still * responsible for free'ing it. * * If is TRUE, we pack up and include * sq>, else we don't. * * Returns: on success. * if data is NULL, errbuf is filled. * * Throws: on a MPI error, errbuf not filled. */ int cm_alndata_MPISend(CM_ALNDATA *data, int include_sq, char *errbuf, int dest, int tag, MPI_Comm comm, char **buf, int *nalloc) { int status; int sz, n, pos; int has_ppstr; int has_tr; int64_t pplen; /* length of ppstr */ if(data == NULL) ESL_FAIL(eslEINCOMPAT, errbuf, "cm_alndata_MPISend(), data is NULL"); has_ppstr = (data->ppstr == NULL) ? FALSE : TRUE; has_tr = (data->tr == NULL) ? FALSE : TRUE; pplen = has_ppstr? data->sq->L+1 : 0; /* This will look wasteful, but the MPI spec doesn't guarantee that * MPI_Pack_size(x, ...) + MPI_Pack_size(x, ... ) == MPI_Pack_size(2x, ...). * Indeed there are some hints in the spec that that's *not* true. * So we assume we must match our Pack_size calls exactly to our Pack calls. */ n = 0; /* first tally up size of everything that's mandatory */ if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* idx */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* sc */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pp */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* spos */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* epos */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* secs_band */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* secs_aln */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* secs_tot */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* mb_tot */ if (MPI_Pack_size(1, MPI_DOUBLE, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* tau */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* thresh1 */ if (MPI_Pack_size(1, MPI_FLOAT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* thresh2 */ /* now the optional info */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* include_sq */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* has_tr */ if (MPI_Pack_size(1, MPI_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* has_ppstr */ if (include_sq) { if ((status = esl_sq_MPIPackSize(data->sq, comm, &sz)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* sq */ } if (has_tr) { if ((status = cm_parsetree_MPIPackSize(data->tr, comm, &sz)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* tr */ } if (has_ppstr) { if (MPI_Pack_size(1, MPI_LONG_LONG_INT, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* pplen */ if (MPI_Pack_size(pplen, MPI_CHAR, comm, &sz) != 0) ESL_XEXCEPTION(eslESYS, "pack size failed"); n += sz; /* ppstr */ } /* Make sure the buffer is allocated appropriately */ if (*buf == NULL || n > *nalloc) { void *tmp; ESL_RALLOC(*buf, tmp, sizeof(char) * n); *nalloc = n; } /* Pack it, in same order as above */ pos = 0; /* mandatory values */ if (MPI_Pack(&data->idx, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->sc, 1, MPI_FLOAT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->pp, 1, MPI_FLOAT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->spos, 1, MPI_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->epos, 1, MPI_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->secs_bands, 1, MPI_FLOAT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->secs_aln, 1, MPI_FLOAT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->secs_tot, 1, MPI_FLOAT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->mb_tot, 1, MPI_FLOAT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->tau, 1, MPI_DOUBLE, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->thresh1, 1, MPI_FLOAT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&data->thresh2, 1, MPI_FLOAT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); /* optional info */ if (MPI_Pack(&include_sq, 1, MPI_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&has_tr, 1, MPI_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(&has_ppstr, 1, MPI_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (include_sq) { if ((status = esl_sq_MPIPack(data->sq, *buf, n, &pos, comm)) != eslOK) ESL_XEXCEPTION(eslESYS, "pack failed"); } if (has_tr) { if ((status = cm_parsetree_MPIPack(data->tr, *buf, n, &pos, comm) != eslOK)) ESL_XEXCEPTION(eslESYS, "pack failed"); } if (has_ppstr) { if (MPI_Pack(&pplen, 1, MPI_LONG_LONG_INT, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); if (MPI_Pack(data->ppstr, pplen, MPI_CHAR, *buf, n, &pos, comm) != 0) ESL_XEXCEPTION(eslESYS, "pack failed"); } /* Send the packed data to destination */ MPI_Send(*buf, n, MPI_PACKED, dest, tag, comm); return eslOK; ERROR: return status; } /* Function: cm_alndata_MPIUnpack() * Synopsis: Unpacks a CM_ALNDATA from an MPI buffer. * Incept: EPN, Fri Jan 13 10:30:05 2012 * * Purpose: Allocate for and fill a new CM_ALNDATA object * from MPI packed buffer , starting from * position <*pos>, where the total length of the * buffer in bytes is . Return it in * <*ret_data>. Caller is responsible for free'ing * it. * * Returns: on success. <*pos> is updated to the position of * the next element in to unpack (if any). <*ret_alndata> * contains a newly allocated HIT, which the caller is * responsible for free'ing. * * Throws: on an MPI call failure. on allocation failure. * In either case, <*ret_data> is , and the state of * and <*pos> is undefined and should be considered to be corrupted. */ int cm_alndata_MPIUnpack(char *buf, int n, int *pos, MPI_Comm comm, ESL_ALPHABET *abc, CM_ALNDATA **ret_data) { int status; CM_ALNDATA *data = NULL; int has_sq; int has_tr; int has_ppstr; int64_t pplen; /* length of ppstr */ if ((data = cm_alndata_Create()) == NULL) { status = eslEMEM; goto ERROR; } /* mandatory stuff */ if (MPI_Unpack(buf, n, pos, &(data->idx), 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->sc), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->pp), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->spos), 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->epos), 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->secs_bands), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->secs_aln), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->secs_tot), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->mb_tot), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->tau), 1, MPI_DOUBLE, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->thresh1), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &(data->thresh2), 1, MPI_FLOAT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); /* optional stuff */ if (MPI_Unpack(buf, n, pos, &has_sq, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &has_tr, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (MPI_Unpack(buf, n, pos, &has_ppstr, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); if (has_sq) { if ((status = esl_sq_MPIUnpack(abc, buf, n, pos, comm, &(data->sq))) != eslOK) ESL_XEXCEPTION(eslESYS, "unpack failed"); } if (has_tr) { if ((status = cm_parsetree_MPIUnpack(buf, n, pos, comm, &(data->tr))) != eslOK) ESL_XEXCEPTION(eslESYS, "unpack failed"); } if (has_ppstr) { if (MPI_Unpack(buf, n, pos, &pplen, 1, MPI_LONG_LONG_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); ESL_ALLOC(data->ppstr, sizeof(char) * pplen); if (MPI_Unpack(buf, n, pos, data->ppstr, pplen, MPI_CHAR, comm) != 0) ESL_XEXCEPTION(eslESYS, "unpack failed"); } *ret_data = data; return eslOK; ERROR: if (data != NULL) cm_alndata_Destroy(data, TRUE); *ret_data = NULL; return status; } #endif