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gentoo-full-overlay/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch

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https://bugs.gentoo.org/690900
rename MPI 1.0 to 3.0+ functions:
- MPI_Address -> MPI_Get_address
- MPI_Type_struct -> MPI_Type_create_struct
--- a/src/ppuzzle.c
+++ b/src/ppuzzle.c
@@ -297,13 +297,13 @@
else MPI_Recv(&dummy, 0, MPI_INT, PP_MyMaster, PP_UPDATEEEI, PP_Comm, &stat);
Dtypes[0] = MPI_DOUBLE; Dtypelens[0] = tpmradix;
- MPI_Address(&(Eval[0]), &(Dtypeaddr[0]));
+ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[0]));
Dtypes[1] = MPI_DOUBLE; Dtypelens[1] = tpmradix * tpmradix;
- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[1]));
+ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[1]));
Dtypes[2] = MPI_DOUBLE; Dtypelens[2] = tpmradix * tpmradix;
- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[2]));
+ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[2]));
- MPI_Type_struct(3, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
+ MPI_Type_create_struct(3, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
MPI_Type_commit(&PP_Data);
MPI_Bcast (MPI_BOTTOM, 1, PP_Data, PP_MyMaster, PP_Comm);
@@ -341,19 +341,19 @@
double* DMVector = new_dvector(jobs);
Dtypes[0] = MPI_DOUBLE; Dtypelens[0] = jobs;
- MPI_Address(&(DMVector[0]), &(Dtypeaddr[0]));
+ MPI_Get_address(&(DMVector[0]), &(Dtypeaddr[0]));
Dtypes[1] = MPI_DOUBLE; Dtypelens[1] = numcats;
- MPI_Address(&(Rates[0]), &(Dtypeaddr[1]));
+ MPI_Get_address(&(Rates[0]), &(Dtypeaddr[1]));
Dtypes[2] = MPI_DOUBLE; Dtypelens[2] = 1;
- MPI_Address(&(fracinv), &(Dtypeaddr[2]));
+ MPI_Get_address(&(fracinv), &(Dtypeaddr[2]));
Dtypes[3] = MPI_DOUBLE; Dtypelens[3] = tpmradix;
- MPI_Address(&(Eval[0]), &(Dtypeaddr[3]));
+ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[3]));
Dtypes[4] = MPI_DOUBLE; Dtypelens[4] = tpmradix * tpmradix;
- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[4]));
+ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[4]));
Dtypes[5] = MPI_DOUBLE; Dtypelens[5] = tpmradix * tpmradix;
- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[5]));
+ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[5]));
- MPI_Type_struct(6, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
+ MPI_Type_create_struct(6, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
MPI_Type_commit(&PP_Data);
if (PP_IamMaster) {
@@ -719,10 +719,10 @@
#endif
doubles[0] = frconst;
- MPI_Address(ints, Dtypeaddr);
- MPI_Address(doubles, (Dtypeaddr+1));
+ MPI_Get_address(ints, Dtypeaddr);
+ MPI_Get_address(doubles, (Dtypeaddr+1));
- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes);
+ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes);
MPI_Type_commit(&PP_Sizes);
for (dest=1; dest<PP_NumProcs; dest++) {
@@ -797,10 +797,10 @@
fprintf(STDOUT, "(%2d) Receiving Sizes ...\n", PP_Myid);
# endif /* PVERBOSE3 */
- MPI_Address(ints, Dtypeaddr);
- MPI_Address(doubles, (Dtypeaddr+1));
+ MPI_Get_address(ints, Dtypeaddr);
+ MPI_Get_address(doubles, (Dtypeaddr+1));
- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes);
+ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes);
MPI_Type_commit(&PP_Sizes);
error = MPI_Probe(PP_MyMaster, MPI_ANY_TAG, PP_Comm, &stat);
@@ -889,31 +889,31 @@
# endif /* PVERBOSE2 */
Dtypes [0] = MPI_CHAR; Dtypelens [0] = Maxspc * Numptrn;
- MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
+ MPI_Get_address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
Dtypes [1] = MPI_INT; Dtypelens [1] = Maxsite ;
- MPI_Address(&(Alias[0]), &(Dtypeaddr[1]));
+ MPI_Get_address(&(Alias[0]), &(Dtypeaddr[1]));
Dtypes [2] = MPI_INT; Dtypelens [2] = Numptrn ;
- MPI_Address(&(Weight[0]), &(Dtypeaddr[2]));
+ MPI_Get_address(&(Weight[0]), &(Dtypeaddr[2]));
Dtypes [3] = MPI_INT; Dtypelens [3] = Numptrn ;
- MPI_Address(&(constpat[0]), &(Dtypeaddr[3]));
+ MPI_Get_address(&(constpat[0]), &(Dtypeaddr[3]));
Dtypes [4] = MPI_DOUBLE; Dtypelens [4] = numcats ;
- MPI_Address(&(Rates[0]), &(Dtypeaddr[4]));
+ MPI_Get_address(&(Rates[0]), &(Dtypeaddr[4]));
Dtypes [5] = MPI_DOUBLE; Dtypelens [5] = tpmradix ;
- MPI_Address(&(Eval[0]), &(Dtypeaddr[5]));
+ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[5]));
Dtypes [6] = MPI_DOUBLE; Dtypelens [6] = tpmradix ;
- MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6]));
+ MPI_Get_address(&(Freqtpm[0]), &(Dtypeaddr[6]));
Dtypes [7] = MPI_DOUBLE; Dtypelens [7] = tpmradix * tpmradix ;
- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7]));
+ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[7]));
Dtypes [8] = MPI_DOUBLE; Dtypelens [8] = tpmradix * tpmradix ;
- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8]));
+ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[8]));
Dtypes [9] = MPI_DOUBLE; Dtypelens [9] = tpmradix * tpmradix ;
- MPI_Address(&(iexp[0][0]), &(Dtypeaddr[9]));
+ MPI_Get_address(&(iexp[0][0]), &(Dtypeaddr[9]));
Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ;
- MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10]));
+ MPI_Get_address(&(Distanmat[0][0]), &(Dtypeaddr[10]));
Dtypes [11] = MPI_DOUBLE; Dtypelens [11] = numcats * tpmradix * tpmradix ;
- MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11]));
+ MPI_Get_address(&(ltprobr[0][0][0]), &(Dtypeaddr[11]));
- MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
+ MPI_Type_create_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
MPI_Type_commit(&PP_Data);
@@ -984,31 +984,31 @@
# endif /* PVERBOSE2 */
Dtypes [0] = MPI_CHAR; Dtypelens [0] = Maxspc * Numptrn;
- MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
+ MPI_Get_address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
Dtypes [1] = MPI_INT; Dtypelens [1] = Maxsite ;
- MPI_Address(&(Alias[0]), &(Dtypeaddr[1]));
+ MPI_Get_address(&(Alias[0]), &(Dtypeaddr[1]));
Dtypes [2] = MPI_INT; Dtypelens [2] = Numptrn ;
- MPI_Address(&(Weight[0]), &(Dtypeaddr[2]));
+ MPI_Get_address(&(Weight[0]), &(Dtypeaddr[2]));
Dtypes [3] = MPI_INT; Dtypelens [3] = Numptrn ;
- MPI_Address(&(constpat[0]), &(Dtypeaddr[3]));
+ MPI_Get_address(&(constpat[0]), &(Dtypeaddr[3]));
Dtypes [4] = MPI_DOUBLE; Dtypelens [4] = numcats ;
- MPI_Address(&(Rates[0]), &(Dtypeaddr[4]));
+ MPI_Get_address(&(Rates[0]), &(Dtypeaddr[4]));
Dtypes [5] = MPI_DOUBLE; Dtypelens [5] = tpmradix ;
- MPI_Address(&(Eval[0]), &(Dtypeaddr[5]));
+ MPI_Get_address(&(Eval[0]), &(Dtypeaddr[5]));
Dtypes [6] = MPI_DOUBLE; Dtypelens [6] = tpmradix ;
- MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6]));
+ MPI_Get_address(&(Freqtpm[0]), &(Dtypeaddr[6]));
Dtypes [7] = MPI_DOUBLE; Dtypelens [7] = tpmradix * tpmradix ;
- MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7]));
+ MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[7]));
Dtypes [8] = MPI_DOUBLE; Dtypelens [8] = tpmradix * tpmradix ;
- MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8]));
+ MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[8]));
Dtypes [9] = MPI_DOUBLE; Dtypelens [9] = tpmradix * tpmradix ;
- MPI_Address(&(iexp[0][0]), &(Dtypeaddr [9]));
+ MPI_Get_address(&(iexp[0][0]), &(Dtypeaddr [9]));
Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ;
- MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10]));
+ MPI_Get_address(&(Distanmat[0][0]), &(Dtypeaddr[10]));
Dtypes [11] = MPI_DOUBLE; Dtypelens [11] = numcats * tpmradix * tpmradix ;
- MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11]));
+ MPI_Get_address(&(ltprobr[0][0][0]), &(Dtypeaddr[11]));
- MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
+ MPI_Type_create_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
MPI_Type_commit(&PP_Data);
for (dest=1; dest<PP_NumProcs; dest++) {
@@ -1150,10 +1150,10 @@
ints[4] = usebestq;
ints[5] = approx;
- MPI_Address(ints, Dtypeaddr);
- MPI_Address(doubles, (Dtypeaddr+1));
+ MPI_Get_address(ints, Dtypeaddr);
+ MPI_Get_address(doubles, (Dtypeaddr+1));
- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart);
+ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart);
MPI_Type_commit(&PP_Quart);
# ifdef PVERBOSE2
@@ -1201,10 +1201,10 @@
PP_quartrecved++;
PP_quartrecvedn++;
- MPI_Address(ints, Dtypeaddr);
- MPI_Address(doubles, (Dtypeaddr+1));
+ MPI_Get_address(ints, Dtypeaddr);
+ MPI_Get_address(doubles, (Dtypeaddr+1));
- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart);
+ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart);
MPI_Type_commit(&PP_Quart);
error = MPI_Recv(MPI_BOTTOM, 1, PP_Quart, MPI_ANY_SOURCE, PP_QUART, PP_Comm, &stat);
@@ -1368,10 +1368,10 @@
ulis[5] = fullresqs; /* number of fully resolved quartets */
ulis[6] = missingqs; /* number of missing quartets */
- MPI_Address(ulis, Dtypeaddr);
- MPI_Address(ints, (Dtypeaddr+1));
+ MPI_Get_address(ulis, Dtypeaddr);
+ MPI_Get_address(ints, (Dtypeaddr+1));
- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs);
+ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs);
MPI_Type_commit(&PP_QBlockSpecs);
# ifdef PVERBOSE2
@@ -1384,12 +1384,12 @@
fprintf(STDOUT, "(%2d) ... Sent QuartBlockSpecs (%ld, %ld, %ld, %d)\n", PP_Myid, ulis[0], ulis[1], ulis[2], ints[0]);
# endif /* PVERBOSE3 */
- MPI_Address(trueaddr, DtypeaddrRes);
+ MPI_Get_address(trueaddr, DtypeaddrRes);
DtypelensRes[0] = truenum;
- MPI_Address(bq, (DtypeaddrRes + 1));
+ MPI_Get_address(bq, (DtypeaddrRes + 1));
DtypelensRes[1] = numofbq;
- MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes);
+ MPI_Type_create_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes);
MPI_Type_commit(&PP_QBlockRes);
error = MPI_Ssend(MPI_BOTTOM, 1, PP_QBlockRes, PP_MyMaster, PP_QUARTBLOCK, PP_Comm);
@@ -1455,10 +1455,10 @@
# ifdef PVERBOSE3
fprintf(STDOUT, "(%2d) Receiving QuartBlock ...\n", PP_Myid);
# endif /* PVERBOSE3 */
- MPI_Address(ulis, Dtypeaddr);
- MPI_Address(ints, (Dtypeaddr+1));
+ MPI_Get_address(ulis, Dtypeaddr);
+ MPI_Get_address(ints, (Dtypeaddr+1));
- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs);
+ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs);
MPI_Type_commit(&PP_QBlockSpecs);
MPI_Probe(MPI_ANY_SOURCE, PP_QUARTBLOCKSPECS, PP_Comm, &stat);
@@ -1486,13 +1486,13 @@
# endif /* PVERBOSE3 */
DtypelensRes[0] = truenum;
- MPI_Address(trueaddr, DtypeaddrRes);
+ MPI_Get_address(trueaddr, DtypeaddrRes);
bq = calloc((size_t) *numofbq, sizeof(uli));
DtypelensRes[1] = *numofbq;
- MPI_Address(bq, (DtypeaddrRes+1));
- MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes);
+ MPI_Get_address(bq, (DtypeaddrRes+1));
+ MPI_Type_create_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes);
MPI_Type_commit(&PP_QBlockRes);
error = MPI_Recv(MPI_BOTTOM, 1, PP_QBlockRes, dest, PP_QUARTBLOCK, PP_Comm, &stat);
@@ -1637,8 +1637,8 @@
Dtypelens[0] = (Numquartets + 1)/2;
}
- MPI_Address(&(quartetinfo[0]), Dtypeaddr);
- MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts);
+ MPI_Get_address(&(quartetinfo[0]), Dtypeaddr);
+ MPI_Type_create_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts);
MPI_Type_commit(&PP_AllQuarts);
for (dest=1; dest<PP_NumProcs; dest++) {
@@ -1686,8 +1686,8 @@
Dtypelens[0] = (*Numquartets + 1)/2;
}
- MPI_Address(&(quartetinfo[0]), Dtypeaddr);
- MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts);
+ MPI_Get_address(&(quartetinfo[0]), Dtypeaddr);
+ MPI_Type_create_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts);
MPI_Type_commit(&PP_AllQuarts);
error = MPI_Recv(MPI_BOTTOM, 1, PP_AllQuarts, PP_MyMaster, PP_ALLQUARTS, PP_Comm, &stat);
@@ -1748,13 +1748,13 @@
for (n=0; n<(int)blocksize; n++) {
Dtypes[n] = MPI_CHAR;
Dtypelens[n] = (taxa - 3) * taxa;
- MPI_Address(&(biparts[n][0][0]), &(Dtypeaddr[n]));
+ MPI_Get_address(&(biparts[n][0][0]), &(Dtypeaddr[n]));
}
pstptr = pstlist;
for (n=0; n<pstnum; n++) {
Dtypes[(int)blocksize + n] = MPI_CHAR;
Dtypelens[(int)blocksize + n] = psteptreestrlen;
- MPI_Address((*pstptr).tree, &(Dtypeaddr[(int)blocksize + n]));
+ MPI_Get_address((*pstptr).tree, &(Dtypeaddr[(int)blocksize + n]));
pstnumarr[n] = (*pstptr).count;
# ifdef PVERBOSE3
fprintf(STDOUT, "(%2d) Sent tree item ->%d: [%d/%d] #=%d \"%s\"\n",
@@ -1764,9 +1764,9 @@
}
Dtypes[((int)blocksize + pstnum)] = MPI_INT;
Dtypelens[((int)blocksize + pstnum)] = pstnum;
- MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)]));
+ MPI_Get_address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)]));
- MPI_Type_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts);
+ MPI_Type_create_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts);
MPI_Type_commit(&PP_Biparts);
error = MPI_Ssend(MPI_BOTTOM, 1, PP_Biparts, PP_MyMaster, PP_PUZZLEBLOCK, PP_Comm);
@@ -1843,20 +1843,20 @@
(*bip)[n] = new_cmatrix(*taxa - 3, *taxa);
Dtypes[n] = MPI_CHAR;
Dtypelens[n] = (*taxa - 3) * *taxa;
- MPI_Address(&((*bip)[n][0][0]), &(Dtypeaddr[n]));
+ MPI_Get_address(&((*bip)[n][0][0]), &(Dtypeaddr[n]));
}
for (n=0; n<pstlistnum; n++) {
pstarr[n] = (char *)calloc((size_t) psteptreestrlen, sizeof(char));
Dtypes[(int)*blocksize + n] = MPI_CHAR;
Dtypelens[(int)*blocksize + n] = psteptreestrlen;
- MPI_Address(&(pstarr[n][0]), &(Dtypeaddr[(int)*blocksize + n]));
+ MPI_Get_address(&(pstarr[n][0]), &(Dtypeaddr[(int)*blocksize + n]));
}
Dtypes[(int)*blocksize + pstlistnum] = MPI_INT;
Dtypelens[(int)*blocksize + pstlistnum] = pstlistnum;
- MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[(int)*blocksize + pstlistnum]));
+ MPI_Get_address(&(pstnumarr[0]), &(Dtypeaddr[(int)*blocksize + pstlistnum]));
- MPI_Type_struct(((int)*blocksize + pstlistnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts);
+ MPI_Type_create_struct(((int)*blocksize + pstlistnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts);
MPI_Type_commit(&PP_Biparts);
error = MPI_Recv(MPI_BOTTOM, 1, PP_Biparts, dest, PP_PUZZLEBLOCK, PP_Comm, &stat);
@@ -2053,10 +2053,10 @@
fprintf(STDOUT, "(%2d) ... Sent DONE Signal\n", PP_Myid);
# endif /* PVERBOSE3 */
- MPI_Address(ints, Dtypeaddr);
- MPI_Address(doubles, (Dtypeaddr+1));
+ MPI_Get_address(ints, Dtypeaddr);
+ MPI_Get_address(doubles, (Dtypeaddr+1));
- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats);
+ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats);
MPI_Type_commit(&PP_Stats);
doquartrecved[0] = 0;
@@ -2173,10 +2173,10 @@
doubles[4] = tarr.cpu;
doubles[5] = tarr.time;
- MPI_Address(ints, Dtypeaddr);
- MPI_Address(doubles, (Dtypeaddr+1));
+ MPI_Get_address(ints, Dtypeaddr);
+ MPI_Get_address(doubles, (Dtypeaddr+1));
- MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats);
+ MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats);
MPI_Type_commit(&PP_Stats);
error = MPI_Ssend(MPI_BOTTOM, 1, PP_Stats, PP_MyMaster, PP_STATS, PP_Comm);
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