From 99ca454f2366c1468a7d400cb1ccc5294fd19529 Mon Sep 17 00:00:00 2001 From: Markus Kowalewski Date: Thu, 21 Feb 2019 14:04:05 +0100 Subject: hdf5: add openmpi-4 compatibility patches --- ...-to-use-the-MPI-2-function-MPI_Type_get_e.patch | 58 +++++++++++ .../misc/hdf5/0001-Yanked-all-MPI-1-calls.patch | 115 +++++++++++++++++++++ pkgs/tools/misc/hdf5/default.nix | 10 +- 3 files changed, 181 insertions(+), 2 deletions(-) create mode 100644 pkgs/tools/misc/hdf5/0001-Updated-H5S-to-use-the-MPI-2-function-MPI_Type_get_e.patch create mode 100644 pkgs/tools/misc/hdf5/0001-Yanked-all-MPI-1-calls.patch (limited to 'pkgs/tools') diff --git a/pkgs/tools/misc/hdf5/0001-Updated-H5S-to-use-the-MPI-2-function-MPI_Type_get_e.patch b/pkgs/tools/misc/hdf5/0001-Updated-H5S-to-use-the-MPI-2-function-MPI_Type_get_e.patch new file mode 100644 index 000000000000..8b32ea4bab1c --- /dev/null +++ b/pkgs/tools/misc/hdf5/0001-Updated-H5S-to-use-the-MPI-2-function-MPI_Type_get_e.patch @@ -0,0 +1,58 @@ +From 38c202df4db8eddd5e6f6f7d6506ce97912a3111 Mon Sep 17 00:00:00 2001 +From: Dana Robinson +Date: Mon, 26 Nov 2018 22:10:06 -0800 +Subject: [PATCH] Updated H5S to use the MPI-2 function MPI_Type_get_exten() + where available. OpenMPI 4.0 removed the deprecated MPI-1 MPI_type_extent() + call by default, so this avoids needing a special OpenMPI build. + +--- + src/H5Smpio.c | 26 ++++++++++++++++++++++++-- + 1 file changed, 24 insertions(+), 2 deletions(-) + +diff --git a/src/H5Smpio.c b/src/H5Smpio.c +index 2bd275a729..e71e2cb858 100644 +--- a/src/H5Smpio.c ++++ b/src/H5Smpio.c +@@ -879,7 +879,18 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, + HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) + } + +- MPI_Type_extent (inner_type, &inner_extent); ++#if MPI_VERSION >= 2 ++{ ++ /* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default, ++ * so we're using the MPI-2 version even though we don't need the lb ++ * value. ++ */ ++ MPI_Aint unused_lb_arg; ++ MPI_Type_get_extent(inner_type, &unused_lb_arg, &inner_extent); ++} ++#else ++ MPI_Type_extent(inner_type, &inner_extent); ++#endif + stride_in_bytes = inner_extent * (MPI_Aint)d[i].strid; + + /* If the element count is larger than what a 32 bit integer can hold, +@@ -1500,7 +1511,18 @@ static herr_t H5S_mpio_create_large_type (hsize_t num_elements, + } + } + +- MPI_Type_extent (old_type, &old_extent); ++#if MPI_VERSION >= 2 ++{ ++ /* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default, ++ * so we're using the MPI-2 version even though we don't need the lb ++ * value. ++ */ ++ MPI_Aint unused_lb_arg; ++ MPI_Type_get_extent(old_type, &unused_lb_arg, &old_extent); ++} ++#else ++ MPI_Type_extent(old_type, &old_extent); ++#endif + + /* Set up the arguments for MPI_Type_struct constructor */ + type[0] = outer_type; +-- +2.18.1 + diff --git a/pkgs/tools/misc/hdf5/0001-Yanked-all-MPI-1-calls.patch b/pkgs/tools/misc/hdf5/0001-Yanked-all-MPI-1-calls.patch new file mode 100644 index 000000000000..8dc831dbba12 --- /dev/null +++ b/pkgs/tools/misc/hdf5/0001-Yanked-all-MPI-1-calls.patch @@ -0,0 +1,115 @@ +From 8cf3bfb14bd2a80f13d269a9e84cd99f86f19254 Mon Sep 17 00:00:00 2001 +From: Dana Robinson +Date: Tue, 27 Nov 2018 10:31:54 -0800 +Subject: [PATCH] Yanked all MPI-1 calls + +--- + src/H5.c | 2 +- + src/H5Smpio.c | 24 ++++++++---------------- + testpar/t_cache.c | 20 ++++++++++---------- + 3 files changed, 19 insertions(+), 27 deletions(-) + +diff --git a/src/H5.c b/src/H5.c +index d1967e611b..bf4643ca59 100644 +--- a/src/H5.c ++++ b/src/H5.c +@@ -138,7 +138,7 @@ H5_init_library(void) + 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) +diff --git a/src/H5Smpio.c b/src/H5Smpio.c +index e71e2cb858..935d27972e 100644 +--- a/src/H5Smpio.c ++++ b/src/H5Smpio.c +@@ -879,18 +879,14 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, + HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) + } + +-#if MPI_VERSION >= 2 +-{ + /* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default, + * so we're using the MPI-2 version even though we don't need the lb + * value. + */ +- MPI_Aint unused_lb_arg; +- MPI_Type_get_extent(inner_type, &unused_lb_arg, &inner_extent); +-} +-#else +- MPI_Type_extent(inner_type, &inner_extent); +-#endif ++ { ++ MPI_Aint unused_lb_arg; ++ MPI_Type_get_extent(inner_type, &unused_lb_arg, &inner_extent); ++ } + stride_in_bytes = inner_extent * (MPI_Aint)d[i].strid; + + /* If the element count is larger than what a 32 bit integer can hold, +@@ -1511,18 +1507,14 @@ static herr_t H5S_mpio_create_large_type (hsize_t num_elements, + } + } + +-#if MPI_VERSION >= 2 +-{ + /* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default, + * so we're using the MPI-2 version even though we don't need the lb + * value. + */ +- MPI_Aint unused_lb_arg; +- MPI_Type_get_extent(old_type, &unused_lb_arg, &old_extent); +-} +-#else +- MPI_Type_extent(old_type, &old_extent); +-#endif ++ { ++ MPI_Aint unused_lb_arg; ++ MPI_Type_get_extent(old_type, &unused_lb_arg, &old_extent); ++ } + + /* Set up the arguments for MPI_Type_struct constructor */ + type[0] = outer_type; +diff --git a/testpar/t_cache.c b/testpar/t_cache.c +index 5e15ec274c..ca5ded9ecf 100644 +--- a/testpar/t_cache.c ++++ b/testpar/t_cache.c +@@ -1217,15 +1217,15 @@ setup_derived_types(void) + 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; +@@ -1245,7 +1245,7 @@ setup_derived_types(void) + + 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 ) { + +-- +2.18.1 + diff --git a/pkgs/tools/misc/hdf5/default.nix b/pkgs/tools/misc/hdf5/default.nix index 3d50b068cc49..ae34cfd32358 100644 --- a/pkgs/tools/misc/hdf5/default.nix +++ b/pkgs/tools/misc/hdf5/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${name}/src/${name}.tar.bz2"; sha256 = "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"; - }; + }; passthru = { mpiSupport = (mpi != null); @@ -45,7 +45,13 @@ stdenv.mkDerivation rec { ++ optionals (mpi != null) ["--enable-parallel" "CC=${mpi}/bin/mpicc"] ++ optional enableShared "--enable-shared"; - patches = [./bin-mv.patch]; + patches = [ + ./bin-mv.patch + # upstream patches for openmpi-4 compatiblity + # To be removed with the upgrade to 1.10.5 + ./0001-Updated-H5S-to-use-the-MPI-2-function-MPI_Type_get_e.patch + ./0001-Yanked-all-MPI-1-calls.patch + ]; postInstall = '' find "$out" -type f -exec remove-references-to -t ${stdenv.cc} '{}' + -- cgit 1.4.1