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gnu: hdf5: Remove use of deprecated MPI1 symbols.
* gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch, gnu/packages/patches/hdf5-mpi-deprecations.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/maths.scm (hdf5, hdf5-1.10)[source]: Use them.
This commit is contained in:
Eric Bavier
parent
2bdf26f1c8
commit
7fedc3fdfb
4 changed files with 236 additions and 2 deletions
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@ -873,6 +873,8 @@ dist_patch_DATA = \
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%D%/packages/patches/hdf4-reproducibility.patch \
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%D%/packages/patches/hdf4-reproducibility.patch \
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%D%/packages/patches/hdf4-shared-fortran.patch \
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%D%/packages/patches/hdf4-shared-fortran.patch \
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%D%/packages/patches/hdf5-config-date.patch \
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%D%/packages/patches/hdf5-config-date.patch \
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%D%/packages/patches/hdf5-mpi-deprecations.patch \
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%D%/packages/patches/hdf5-1.8-mpi-deprecations.patch \
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%D%/packages/patches/hdf-eos2-build-shared.patch \
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%D%/packages/patches/hdf-eos2-build-shared.patch \
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%D%/packages/patches/hdf-eos2-remove-gctp.patch \
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%D%/packages/patches/hdf-eos2-remove-gctp.patch \
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%D%/packages/patches/hdf-eos2-fortrantests.patch \
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%D%/packages/patches/hdf-eos2-fortrantests.patch \
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@ -764,7 +764,8 @@ (define-public hdf5
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"/src/hdf5-" version ".tar.bz2")))
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"/src/hdf5-" version ".tar.bz2")))
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(sha256
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(sha256
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(base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
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(base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
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(patches (list (search-patch "hdf5-config-date.patch")))))
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(patches (search-patches "hdf5-config-date.patch"
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"hdf5-1.8-mpi-deprecations.patch"))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(inputs
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(inputs
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`(("zlib" ,zlib)))
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`(("zlib" ,zlib)))
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@ -877,7 +878,8 @@ (define-public hdf5-1.10
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"/src/hdf5-" version ".tar.bz2")))
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"/src/hdf5-" version ".tar.bz2")))
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(sha256
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(sha256
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(base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
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(base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
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(patches (list (search-patch "hdf5-config-date.patch")))))))
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(patches (search-patches "hdf5-config-date.patch"
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"hdf5-mpi-deprecations.patch"))))))
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(define-public hdf-java
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(define-public hdf-java
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(package
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(package
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169
gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch
Normal file
169
gnu/packages/patches/hdf5-1.8-mpi-deprecations.patch
Normal file
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@ -0,0 +1,169 @@
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--- a/src/H5.c
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+++ b/src/H5.c
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@@ -138,7 +138,7 @@
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if (mpi_initialized && !mpi_finalized) {
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int key_val;
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- if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN,
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+ if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN,
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(MPI_Comm_delete_attr_function *)H5_mpi_delete_cb,
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&key_val, NULL)))
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HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code)
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--- hdf5-1.8.19/testpar/t_cache.c
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+++ hdf5-1.8.19/testpar/t_cache.c
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@@ -1187,20 +1187,20 @@
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struct mssg_t sample; /* used to compute displacements */
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/* setup the displacements array */
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- if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) {
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+ if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) {
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nerrors++;
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success = FALSE;
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if ( verbose ) {
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- HDfprintf(stdout, "%d:%s: MPI_Address() call failed.\n",
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+ HDfprintf(stdout, "%d:%s: MPI_Get_address() call failed.\n",
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world_mpi_rank, fcn_name);
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}
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@@ -1215,14 +1215,14 @@
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if ( success ) {
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- result = MPI_Type_struct(9, block_len, displs, mpi_types, &mpi_mssg_t);
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+ result = MPI_Type_create_struct(9, block_len, displs, mpi_types, &mpi_mssg_t);
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if ( result != MPI_SUCCESS ) {
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nerrors++;
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success = FALSE;
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if ( verbose ) {
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- HDfprintf(stdout, "%d:%s: MPI_Type_struct() call failed.\n",
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+ HDfprintf(stdout, "%d:%s: MPI_Type_create_struct() call failed.\n",
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world_mpi_rank, fcn_name);
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}
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}
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--- hdf5-1.8.19/testpar/t_mpi.c
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+++ hdf5-1.8.19/testpar/t_mpi.c
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@@ -279,7 +279,7 @@
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printf("Skipped GB file range test "
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"because MPI_Offset cannot support it\n");
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}else{
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- buf = HDmalloc(MB);
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+ buf = (char *)HDmalloc(MB);
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VRFY((buf!=NULL), "malloc succeed");
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/* open a new file. Remove it first in case it exists. */
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@@ -624,7 +624,7 @@
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and this platform.
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1. Details for the test:
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-1) Create two derived datatypes with MPI_Type_hindexed:
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+1) Create two derived datatypes with MPI_Type_create_hindexed:
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datatype1:
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count = 1, blocklens = 1, offsets = 0,
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base type = MPI_BYTE(essentially a char)
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@@ -633,7 +633,7 @@
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base type = MPI_BYTE
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2) Using these two derived datatypes,
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- Build another derived datatype with MPI_Type_struct:
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+ Build another derived datatype with MPI_Type_create_struct:
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advtype: derived from datatype1 and datatype2
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advtype:
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count = 2, blocklens[0] = 1, blocklens[1]=1,
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@@ -676,10 +676,9 @@
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int mpi_err_strlen;
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int mpi_err;
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int i;
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- int nerrors = 0; /* number of errors */
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MPI_Datatype etype,filetype;
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MPI_Datatype adv_filetype,bas_filetype[2];
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- MPI_Datatype etypenew, filetypenew;
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+ MPI_Datatype filetypenew;
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MPI_Offset disp;
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MPI_Status Status;
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MPI_Aint adv_disp[2];
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@@ -715,7 +714,7 @@
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blocklens[0] = 1;
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offsets[0] = 0;
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- if((mpi_err= MPI_Type_hindexed(count,blocklens,offsets,MPI_BYTE,&filetype))
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+ if((mpi_err= MPI_Type_create_hindexed(count,blocklens,offsets,MPI_BYTE,&filetype))
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!= MPI_SUCCESS){
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MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
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printf("MPI_Type_contiguous failed (%s)\n", mpi_err_str);
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@@ -731,7 +730,7 @@
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count = 1;
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blocklens[0]=1;
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offsets[0] = 1;
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- if((mpi_err= MPI_Type_hindexed(count,blocklens,offsets,MPI_BYTE,&filetypenew))
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+ if((mpi_err= MPI_Type_create_hindexed(count,blocklens,offsets,MPI_BYTE,&filetypenew))
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!= MPI_SUCCESS){
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MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
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printf("MPI_Type_contiguous failed (%s)\n", mpi_err_str);
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@@ -752,10 +751,10 @@
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bas_filetype[0] = filetype;
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bas_filetype[1] = filetypenew;
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- if((mpi_err= MPI_Type_struct(outcount,adv_blocklens,adv_disp,bas_filetype,&adv_filetype))
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+ if((mpi_err= MPI_Type_create_struct(outcount,adv_blocklens,adv_disp,bas_filetype,&adv_filetype))
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!= MPI_SUCCESS){
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MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
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- printf("MPI_Type_struct failed (%s)\n", mpi_err_str);
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+ printf("MPI_Type_create_struct failed (%s)\n", mpi_err_str);
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return 1;
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}
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if((mpi_err=MPI_Type_commit(&adv_filetype))!=MPI_SUCCESS){
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@@ -842,7 +841,7 @@
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processes are needed.
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1. Details for the test:
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-1) Create one derived datatype with MPI_Type_hindexed:
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+1) Create one derived datatype with MPI_Type_create_hindexed:
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2) Choosing at least two processes to contribute none for IO with
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the buf size inside MPI_Write_at_all to 0.
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@@ -898,7 +897,7 @@
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offsets[1] = (mpi_size+mpi_rank)*count;
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if(count !=0) {
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- if((mpi_err = MPI_Type_hindexed(2,
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+ if((mpi_err = MPI_Type_create_hindexed(2,
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blocklens,
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offsets,
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etype,
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@@ -914,7 +913,7 @@
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return 1;
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} /* end if */
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- if((mpi_err = MPI_Type_hindexed(2,
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+ if((mpi_err = MPI_Type_create_hindexed(2,
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blocklens,
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offsets,
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etype,
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@@ -1098,7 +1097,7 @@
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* calls. By then, MPI calls may not work.
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*/
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if (H5dont_atexit() < 0){
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- printf("Failed to turn off atexit processing. Continue.\n", mpi_rank);
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+ printf("Failed to turn off atexit processing. Continue.\n");
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};
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H5open();
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if (parse_options(argc, argv) != 0){
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61
gnu/packages/patches/hdf5-mpi-deprecations.patch
Normal file
61
gnu/packages/patches/hdf5-mpi-deprecations.patch
Normal file
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@ -0,0 +1,61 @@
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--- a/src/H5.c
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+++ b/src/H5.c
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@@ -138,7 +138,7 @@
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if (mpi_initialized && !mpi_finalized) {
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int key_val;
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- if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN,
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+ if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN,
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(MPI_Comm_delete_attr_function *)H5_mpi_delete_cb,
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&key_val, NULL)))
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HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code)
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--- hdf5-1.10.4/testpar/t_cache.c
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+++ hdf5-1.10.4/testpar/t_cache.c
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@@ -1217,20 +1217,20 @@
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struct mssg_t sample; /* used to compute displacements */
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/* setup the displacements array */
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- if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) ||
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- ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) {
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+ if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) ||
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+ ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) {
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nerrors++;
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success = FALSE;
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if ( verbose ) {
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- HDfprintf(stdout, "%d:%s: MPI_Address() call failed.\n",
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+ HDfprintf(stdout, "%d:%s: MPI_Get_address() call failed.\n",
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world_mpi_rank, FUNC);
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}
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@@ -1245,14 +1245,14 @@
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if ( success ) {
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- result = MPI_Type_struct(9, block_len, displs, mpi_types, &mpi_mssg_t);
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+ result = MPI_Type_create_struct(9, block_len, displs, mpi_types, &mpi_mssg_t);
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if ( result != MPI_SUCCESS ) {
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nerrors++;
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success = FALSE;
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if ( verbose ) {
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- HDfprintf(stdout, "%d:%s: MPI_Type_struct() call failed.\n",
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+ HDfprintf(stdout, "%d:%s: MPI_Type_create_struct() call failed.\n",
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world_mpi_rank, FUNC);
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}
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}
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