forked from mirrors/nixpkgs
hdf5: add openmpi-4 compatibility patches
This commit is contained in:
Markus Kowalewski
parent
c6f039e59c
commit
99ca454f23
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@ -0,0 +1,58 @@
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From 38c202df4db8eddd5e6f6f7d6506ce97912a3111 Mon Sep 17 00:00:00 2001
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From: Dana Robinson <derobins@hdfgroup.org>
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Date: Mon, 26 Nov 2018 22:10:06 -0800
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Subject: [PATCH] Updated H5S to use the MPI-2 function MPI_Type_get_exten()
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where available. OpenMPI 4.0 removed the deprecated MPI-1 MPI_type_extent()
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call by default, so this avoids needing a special OpenMPI build.
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---
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src/H5Smpio.c | 26 ++++++++++++++++++++++++--
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1 file changed, 24 insertions(+), 2 deletions(-)
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diff --git a/src/H5Smpio.c b/src/H5Smpio.c
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index 2bd275a729..e71e2cb858 100644
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--- a/src/H5Smpio.c
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+++ b/src/H5Smpio.c
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@@ -879,7 +879,18 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size,
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
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}
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- MPI_Type_extent (inner_type, &inner_extent);
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+#if MPI_VERSION >= 2
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+{
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+ /* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default,
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+ * so we're using the MPI-2 version even though we don't need the lb
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+ * value.
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+ */
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+ MPI_Aint unused_lb_arg;
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+ MPI_Type_get_extent(inner_type, &unused_lb_arg, &inner_extent);
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+}
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+#else
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+ MPI_Type_extent(inner_type, &inner_extent);
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+#endif
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stride_in_bytes = inner_extent * (MPI_Aint)d[i].strid;
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/* If the element count is larger than what a 32 bit integer can hold,
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@@ -1500,7 +1511,18 @@ static herr_t H5S_mpio_create_large_type (hsize_t num_elements,
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}
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}
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- MPI_Type_extent (old_type, &old_extent);
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+#if MPI_VERSION >= 2
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+{
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+ /* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default,
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+ * so we're using the MPI-2 version even though we don't need the lb
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+ * value.
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+ */
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+ MPI_Aint unused_lb_arg;
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+ MPI_Type_get_extent(old_type, &unused_lb_arg, &old_extent);
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+}
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+#else
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+ MPI_Type_extent(old_type, &old_extent);
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+#endif
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/* Set up the arguments for MPI_Type_struct constructor */
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type[0] = outer_type;
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--
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2.18.1
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115
pkgs/tools/misc/hdf5/0001-Yanked-all-MPI-1-calls.patch
Normal file
115
pkgs/tools/misc/hdf5/0001-Yanked-all-MPI-1-calls.patch
Normal file
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@ -0,0 +1,115 @@
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From 8cf3bfb14bd2a80f13d269a9e84cd99f86f19254 Mon Sep 17 00:00:00 2001
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From: Dana Robinson <derobins@hdfgroup.org>
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Date: Tue, 27 Nov 2018 10:31:54 -0800
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Subject: [PATCH] Yanked all MPI-1 calls
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---
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src/H5.c | 2 +-
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src/H5Smpio.c | 24 ++++++++----------------
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testpar/t_cache.c | 20 ++++++++++----------
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3 files changed, 19 insertions(+), 27 deletions(-)
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diff --git a/src/H5.c b/src/H5.c
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index d1967e611b..bf4643ca59 100644
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--- a/src/H5.c
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+++ b/src/H5.c
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@@ -138,7 +138,7 @@ H5_init_library(void)
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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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diff --git a/src/H5Smpio.c b/src/H5Smpio.c
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index e71e2cb858..935d27972e 100644
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--- a/src/H5Smpio.c
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+++ b/src/H5Smpio.c
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@@ -879,18 +879,14 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size,
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
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}
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-#if MPI_VERSION >= 2
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-{
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/* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default,
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* so we're using the MPI-2 version even though we don't need the lb
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* value.
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*/
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- MPI_Aint unused_lb_arg;
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- MPI_Type_get_extent(inner_type, &unused_lb_arg, &inner_extent);
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-}
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-#else
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- MPI_Type_extent(inner_type, &inner_extent);
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-#endif
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+ {
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+ MPI_Aint unused_lb_arg;
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+ MPI_Type_get_extent(inner_type, &unused_lb_arg, &inner_extent);
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+ }
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stride_in_bytes = inner_extent * (MPI_Aint)d[i].strid;
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/* If the element count is larger than what a 32 bit integer can hold,
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@@ -1511,18 +1507,14 @@ static herr_t H5S_mpio_create_large_type (hsize_t num_elements,
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}
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}
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-#if MPI_VERSION >= 2
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-{
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/* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default,
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* so we're using the MPI-2 version even though we don't need the lb
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* value.
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*/
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- MPI_Aint unused_lb_arg;
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- MPI_Type_get_extent(old_type, &unused_lb_arg, &old_extent);
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-}
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-#else
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- MPI_Type_extent(old_type, &old_extent);
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-#endif
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+ {
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+ MPI_Aint unused_lb_arg;
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+ MPI_Type_get_extent(old_type, &unused_lb_arg, &old_extent);
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+ }
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/* Set up the arguments for MPI_Type_struct constructor */
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type[0] = outer_type;
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diff --git a/testpar/t_cache.c b/testpar/t_cache.c
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index 5e15ec274c..ca5ded9ecf 100644
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--- a/testpar/t_cache.c
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+++ b/testpar/t_cache.c
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@@ -1217,15 +1217,15 @@ setup_derived_types(void)
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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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@@ -1245,7 +1245,7 @@ setup_derived_types(void)
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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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--
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2.18.1
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@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
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src = fetchurl {
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src = fetchurl {
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url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${name}/src/${name}.tar.bz2";
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url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${name}/src/${name}.tar.bz2";
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sha256 = "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj";
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sha256 = "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj";
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};
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};
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passthru = {
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passthru = {
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mpiSupport = (mpi != null);
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mpiSupport = (mpi != null);
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@ -45,7 +45,13 @@ stdenv.mkDerivation rec {
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++ optionals (mpi != null) ["--enable-parallel" "CC=${mpi}/bin/mpicc"]
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++ optionals (mpi != null) ["--enable-parallel" "CC=${mpi}/bin/mpicc"]
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++ optional enableShared "--enable-shared";
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++ optional enableShared "--enable-shared";
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patches = [./bin-mv.patch];
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patches = [
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./bin-mv.patch
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# upstream patches for openmpi-4 compatiblity
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# To be removed with the upgrade to 1.10.5
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./0001-Updated-H5S-to-use-the-MPI-2-function-MPI_Type_get_e.patch
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./0001-Yanked-all-MPI-1-calls.patch
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];
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postInstall = ''
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postInstall = ''
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find "$out" -type f -exec remove-references-to -t ${stdenv.cc} '{}' +
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find "$out" -type f -exec remove-references-to -t ${stdenv.cc} '{}' +
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