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authorDavid Seifert <soap@gentoo.org>2022-01-29 01:00:14 +0100
committerDavid Seifert <soap@gentoo.org>2022-01-29 01:00:14 +0100
commit8fe21c3fd5b5e7be60a75a09ba4b3ec4bad417bd (patch)
treefef74cfda4902e035189d70cbab40f0109bc6d44 /sci-biology
parentdev-python/pebble: Keyword 4.6.3 for ~m68k (diff)
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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>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch362
-rw-r--r--sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild25
2 files changed, 375 insertions, 12 deletions
diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
new file mode 100644
index 000000000000..66e3e6482338
--- /dev/null
+++ b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
@@ -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);
diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
index 8e2a07f8183e..06fc28376ff5 100644
--- a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
@@ -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