mirror of
https://github.com/gentoo-mirror/gentoo.git
synced 2026-09-24 04:59:14 -07:00
sci-biology/tree-puzzle: fix build system and MPI
Closes: https://bugs.gentoo.org/690900 Closes: https://bugs.gentoo.org/810502 Closes: https://bugs.gentoo.org/814185 Signed-off-by: David Seifert <soap@gentoo.org>
This commit is contained in:
David Seifert
362
sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
Normal file
362
sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
Normal file
@@ -0,0 +1,362 @@
|
||||
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);
|
||||
@@ -1,7 +1,7 @@
|
||||
# Copyright 1999-2019 Gentoo Authors
|
||||
# Copyright 1999-2022 Gentoo Authors
|
||||
# Distributed under the terms of the GNU General Public License v2
|
||||
|
||||
EAPI=7
|
||||
EAPI=8
|
||||
|
||||
inherit toolchain-funcs
|
||||
|
||||
@@ -18,14 +18,10 @@ RESTRICT="test"
|
||||
DEPEND="mpi? ( virtual/mpi )"
|
||||
RDEPEND="${DEPEND}"
|
||||
|
||||
PATCHES=( "${FILESDIR}"/${PN}-impl-dec.patch )
|
||||
|
||||
pkg_setup() {
|
||||
use mpi && [[ $(tc-getCC) == icc* ]] &&
|
||||
die "The parallelized version of tree-puzzle cannot be compiled using icc.
|
||||
Either disable the \"mpi\" USE flag to compile only the non-parallelized
|
||||
version of the program, or use gcc as your compiler (CC=\"gcc\")."
|
||||
}
|
||||
PATCHES=(
|
||||
"${FILESDIR}"/${PN}-impl-dec.patch
|
||||
"${FILESDIR}"/${P}-MPI-3.0.patch
|
||||
)
|
||||
|
||||
src_configure() {
|
||||
default
|
||||
@@ -38,9 +34,14 @@ src_configure() {
|
||||
fi
|
||||
}
|
||||
|
||||
src_compile() {
|
||||
# hopelessly terrible build system, abuses Automake
|
||||
emake -j1
|
||||
}
|
||||
|
||||
src_install() {
|
||||
dobin src/puzzle
|
||||
use mpi && dobin src/ppuzzle
|
||||
dobin src/puzzle $(usev mpi src/ppuzzle)
|
||||
|
||||
einstalldocs
|
||||
|
||||
# User manual
|
||||
|
||||
Reference in New Issue
Block a user