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hdf5: 1.10.4 -> 1.10.5

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This commit is contained in:
Markus Kowalewski 2019-04-02 16:26:05 +02:00 committed by Frederik Rietdijk
parent 7bd2c5a604
commit 015888ce7f
3 changed files with 2 additions and 179 deletions
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58
pkgs/tools/misc/hdf5/0001-Updated-H5S-to-use-the-MPI-2-function-MPI_Type_get_e.patch
View File

@ -1,58 +0,0 @@
From 38c202df4db8eddd5e6f6f7d6506ce97912a3111 Mon Sep 17 00:00:00 2001
From: Dana Robinson <derobins@hdfgroup.org>
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

115
pkgs/tools/misc/hdf5/0001-Yanked-all-MPI-1-calls.patch
View File

@ -1,115 +0,0 @@
From 8cf3bfb14bd2a80f13d269a9e84cd99f86f19254 Mon Sep 17 00:00:00 2001
From: Dana Robinson <derobins@hdfgroup.org>
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

8
pkgs/tools/misc/hdf5/default.nix
View File

@ -16,11 +16,11 @@ assert !cpp || mpi == null;
let inherit (stdenv.lib) optional optionals; in
stdenv.mkDerivation rec {
version = "1.10.4";
version = "1.10.5";
name = "hdf5-${version}";
src = fetchurl {
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${name}/src/${name}.tar.bz2";
sha256 = "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj";
sha256 = "0i3g6v521vigzbx8wpd32ibsiiw92r65ca3qdbn0d8fj8f4fmmk8";
};
passthru = {
@ -47,10 +47,6 @@ stdenv.mkDerivation rec {
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 = ''