diff options
| -rw-r--r-- | gnu/local.mk | 2 | ||||
| -rw-r--r-- | gnu/packages/maths.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch | 169 | ||||
| -rw-r--r-- | gnu/packages/patches/hdf5-mpi-deprecations.patch | 61 |
4 files changed, 236 insertions, 2 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 785e49a774..f1bcef2a68 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -873,6 +873,8 @@ dist_patch_DATA = \ %D%/packages/patches/hdf4-reproducibility.patch \ %D%/packages/patches/hdf4-shared-fortran.patch \ %D%/packages/patches/hdf5-config-date.patch \ + %D%/packages/patches/hdf5-mpi-deprecations.patch \ + %D%/packages/patches/hdf5-1.8-mpi-deprecations.patch \ %D%/packages/patches/hdf-eos2-build-shared.patch \ %D%/packages/patches/hdf-eos2-remove-gctp.patch \ %D%/packages/patches/hdf-eos2-fortrantests.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 10b0978ba0..402b53ca0e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -764,7 +764,8 @@ incompatible with HDF5.") "/src/hdf5-" version ".tar.bz2"))) (sha256 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r")) - (patches (list (search-patch "hdf5-config-date.patch"))))) + (patches (search-patches "hdf5-config-date.patch" + "hdf5-1.8-mpi-deprecations.patch")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) @@ -877,7 +878,8 @@ extremely large and complex data collections.") "/src/hdf5-" version ".tar.bz2"))) (sha256 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj")) - (patches (list (search-patch "hdf5-config-date.patch"))))))) + (patches (search-patches "hdf5-config-date.patch" + "hdf5-mpi-deprecations.patch")))))) (define-public hdf-java (package diff --git a/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch b/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch new file mode 100644 index 0000000000..29242dc4e8 --- /dev/null +++ b/gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch @@ -0,0 +1,169 @@ +--- a/src/H5.c ++++ b/src/H5.c +@@ -138,7 +138,7 @@ + if (mpi_initialized && !mpi_finalized) { + int key_val; + +- if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN, ++ if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, + (MPI_Comm_delete_attr_function *)H5_mpi_delete_cb, + &key_val, NULL))) + HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code) +--- hdf5-1.8.19/testpar/t_cache.c ++++ hdf5-1.8.19/testpar/t_cache.c +@@ -1187,20 +1187,20 @@ + struct mssg_t sample; /* used to compute displacements */ + + /* setup the displacements array */ +- if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) { ++ if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) { + + nerrors++; + success = FALSE; + if ( verbose ) { +- HDfprintf(stdout, "%d:%s: MPI_Address() call failed.\n", ++ HDfprintf(stdout, "%d:%s: MPI_Get_address() call failed.\n", + world_mpi_rank, fcn_name); + } + +@@ -1215,14 +1215,14 @@ + + if ( success ) { + +- result = MPI_Type_struct(9, block_len, displs, mpi_types, &mpi_mssg_t); ++ result = MPI_Type_create_struct(9, block_len, displs, mpi_types, &mpi_mssg_t); + + if ( result != MPI_SUCCESS ) { + + nerrors++; + success = FALSE; + if ( verbose ) { +- HDfprintf(stdout, "%d:%s: MPI_Type_struct() call failed.\n", ++ HDfprintf(stdout, "%d:%s: MPI_Type_create_struct() call failed.\n", + world_mpi_rank, fcn_name); + } + } +--- hdf5-1.8.19/testpar/t_mpi.c ++++ hdf5-1.8.19/testpar/t_mpi.c +@@ -279,7 +279,7 @@ + printf("Skipped GB file range test " + "because MPI_Offset cannot support it\n"); + }else{ +- buf = HDmalloc(MB); ++ buf = (char *)HDmalloc(MB); + VRFY((buf!=NULL), "malloc succeed"); + + /* open a new file. Remove it first in case it exists. */ +@@ -624,7 +624,7 @@ + and this platform. + + 1. Details for the test: +-1) Create two derived datatypes with MPI_Type_hindexed: ++1) Create two derived datatypes with MPI_Type_create_hindexed: + datatype1: + count = 1, blocklens = 1, offsets = 0, + base type = MPI_BYTE(essentially a char) +@@ -633,7 +633,7 @@ + base type = MPI_BYTE + + 2) Using these two derived datatypes, +- Build another derived datatype with MPI_Type_struct: ++ Build another derived datatype with MPI_Type_create_struct: + advtype: derived from datatype1 and datatype2 + advtype: + count = 2, blocklens[0] = 1, blocklens[1]=1, +@@ -676,10 +676,9 @@ + int mpi_err_strlen; + int mpi_err; + int i; +- int nerrors = 0; /* number of errors */ + MPI_Datatype etype,filetype; + MPI_Datatype adv_filetype,bas_filetype[2]; +- MPI_Datatype etypenew, filetypenew; ++ MPI_Datatype filetypenew; + MPI_Offset disp; + MPI_Status Status; + MPI_Aint adv_disp[2]; +@@ -715,7 +714,7 @@ + blocklens[0] = 1; + offsets[0] = 0; + +- if((mpi_err= MPI_Type_hindexed(count,blocklens,offsets,MPI_BYTE,&filetype)) ++ if((mpi_err= MPI_Type_create_hindexed(count,blocklens,offsets,MPI_BYTE,&filetype)) + != MPI_SUCCESS){ + MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen); + printf("MPI_Type_contiguous failed (%s)\n", mpi_err_str); +@@ -731,7 +730,7 @@ + count = 1; + blocklens[0]=1; + offsets[0] = 1; +- if((mpi_err= MPI_Type_hindexed(count,blocklens,offsets,MPI_BYTE,&filetypenew)) ++ if((mpi_err= MPI_Type_create_hindexed(count,blocklens,offsets,MPI_BYTE,&filetypenew)) + != MPI_SUCCESS){ + MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen); + printf("MPI_Type_contiguous failed (%s)\n", mpi_err_str); +@@ -752,10 +751,10 @@ + bas_filetype[0] = filetype; + bas_filetype[1] = filetypenew; + +- if((mpi_err= MPI_Type_struct(outcount,adv_blocklens,adv_disp,bas_filetype,&adv_filetype)) ++ if((mpi_err= MPI_Type_create_struct(outcount,adv_blocklens,adv_disp,bas_filetype,&adv_filetype)) + != MPI_SUCCESS){ + MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen); +- printf("MPI_Type_struct failed (%s)\n", mpi_err_str); ++ printf("MPI_Type_create_struct failed (%s)\n", mpi_err_str); + return 1; + } + if((mpi_err=MPI_Type_commit(&adv_filetype))!=MPI_SUCCESS){ +@@ -842,7 +841,7 @@ + processes are needed. + + 1. Details for the test: +-1) Create one derived datatype with MPI_Type_hindexed: ++1) Create one derived datatype with MPI_Type_create_hindexed: + + 2) Choosing at least two processes to contribute none for IO with + the buf size inside MPI_Write_at_all to 0. +@@ -898,7 +897,7 @@ + offsets[1] = (mpi_size+mpi_rank)*count; + + if(count !=0) { +- if((mpi_err = MPI_Type_hindexed(2, ++ if((mpi_err = MPI_Type_create_hindexed(2, + blocklens, + offsets, + etype, +@@ -914,7 +913,7 @@ + return 1; + } /* end if */ + +- if((mpi_err = MPI_Type_hindexed(2, ++ if((mpi_err = MPI_Type_create_hindexed(2, + blocklens, + offsets, + etype, +@@ -1098,7 +1097,7 @@ + * calls. By then, MPI calls may not work. + */ + if (H5dont_atexit() < 0){ +- printf("Failed to turn off atexit processing. Continue.\n", mpi_rank); ++ printf("Failed to turn off atexit processing. Continue.\n"); + }; + H5open(); + if (parse_options(argc, argv) != 0){ diff --git a/gnu/packages/patches/hdf5-mpi-deprecations.patch b/gnu/packages/patches/hdf5-mpi-deprecations.patch new file mode 100644 index 0000000000..eb5d1cb681 --- /dev/null +++ b/gnu/packages/patches/hdf5-mpi-deprecations.patch @@ -0,0 +1,61 @@ +--- a/src/H5.c ++++ b/src/H5.c +@@ -138,7 +138,7 @@ + if (mpi_initialized && !mpi_finalized) { + int key_val; + +- if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN, ++ if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, + (MPI_Comm_delete_attr_function *)H5_mpi_delete_cb, + &key_val, NULL))) + HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code) +--- hdf5-1.10.4/testpar/t_cache.c ++++ hdf5-1.10.4/testpar/t_cache.c +@@ -1217,20 +1217,20 @@ + struct mssg_t sample; /* used to compute displacements */ + + /* setup the displacements array */ +- if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) || +- ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) { ++ if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) || ++ ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) { + + nerrors++; + success = FALSE; + if ( verbose ) { +- HDfprintf(stdout, "%d:%s: MPI_Address() call failed.\n", ++ HDfprintf(stdout, "%d:%s: MPI_Get_address() call failed.\n", + world_mpi_rank, FUNC); + } + +@@ -1245,14 +1245,14 @@ + + if ( success ) { + +- result = MPI_Type_struct(9, block_len, displs, mpi_types, &mpi_mssg_t); ++ result = MPI_Type_create_struct(9, block_len, displs, mpi_types, &mpi_mssg_t); + + if ( result != MPI_SUCCESS ) { + + nerrors++; + success = FALSE; + if ( verbose ) { +- HDfprintf(stdout, "%d:%s: MPI_Type_struct() call failed.\n", ++ HDfprintf(stdout, "%d:%s: MPI_Type_create_struct() call failed.\n", + world_mpi_rank, FUNC); + } + } |