Merge pull request #54877 from markuskowa/upd-openmpi4

openmpi: 3.1.3 -> 4.0.0
This commit is contained in:
markuskowa 2019-02-22 09:31:23 +01:00 committed by GitHub
commit 5c8c258727
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GPG key ID: 4AEE18F83AFDEB23
9 changed files with 375 additions and 17 deletions

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@ -618,7 +618,7 @@
The kubernetes module does no longer add the kubernetes package to
<varname>environment.systemPackages</varname> implicitly.
</para>
</listitem>
</listitem>
<listitem>
<para>
The <literal>intel</literal> driver has been removed from the default list of
@ -634,6 +634,13 @@
details in an existing one)
</para>
</listitem>
<listitem>
<para>
Openmpi has been updated to version 4.0.0, which removes some deprecated MPI-1 symbols.
This may break some older applications that still rely on those symbols.
An upgrade guide can be found <link xlink:href="https://www.open-mpi.org/faq/?category=mpi-removed">here</link>.
</para>
</listitem>
</itemizedlist>
</section>
</section>

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@ -1,4 +1,4 @@
{ stdenv, pkgs, fetchFromGitHub, automake, autoconf, libtool
{ stdenv, fetchpatch, fetchFromGitHub, autoreconfHook
, openblas, gfortran, openssh, openmpi
} :
@ -15,11 +15,22 @@ in stdenv.mkDerivation {
sha256 = "07i2idaas7pq3in5mdqq5ndvxln5q87nyfgk3vzw85r72c4fq5jh";
};
nativeBuildInputs = [ automake autoconf libtool ];
# upstream patches for openmpi-4 compatibility
patches = [ (fetchpatch {
name = "MPI_Type_struct-was-deprecated-in-MPI-2";
url = "https://github.com/GlobalArrays/ga/commit/36e6458993b1df745f43b7db86dc17087758e0d2.patch";
sha256 = "058qi8x0ananqx980p03yxpyn41cnmm0ifwsl50qp6sc0bnbnclh";
})
(fetchpatch {
name = "MPI_Errhandler_set-was-deprecated-in-MPI-2";
url = "https://github.com/GlobalArrays/ga/commit/f1ea5203d2672c1a1d0275a012fb7c2fb3d033d8.patch";
sha256 = "06n7ds9alk5xa6hd7waw3wrg88yx2azhdkn3cjs2k189iw8a7fqk";
})];
nativeBuildInputs = [ autoreconfHook ];
buildInputs = [ openmpi openblas gfortran openssh ];
preConfigure = ''
autoreconf -ivf
configureFlagsArray+=( "--enable-i8" \
"--with-mpi" \
"--with-mpi3" \

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@ -1,5 +1,5 @@
{ stdenv, fetchurl, gfortran, perl, libnl, rdma-core, zlib
, numactl
{ stdenv, fetchurl, fetchpatch, gfortran, perl, libnl
, rdma-core, zlib, numactl, libevent, hwloc
# Enable the Sun Grid Engine bindings
, enableSGE ? false
@ -9,22 +9,30 @@
}:
let
version = "3.1.3";
version = "4.0.0";
in stdenv.mkDerivation rec {
name = "openmpi-${version}";
src = with stdenv.lib.versions; fetchurl {
url = "http://www.open-mpi.org/software/ompi/v${major version}.${minor version}/downloads/${name}.tar.bz2";
sha256 = "1dks11scivgaskjs5955y9wprsl12wr3gn5r7wfl0l8gq03l7q4b";
sha256 = "0srnjwzsmyhka9hhnmqm86qck4w3xwjm8g6sbns58wzbrwv8l2rg";
};
patches = [ (fetchpatch {
# Fix a bug that ignores OMPI_MCA_rmaps_base_oversubscribe (upstream patch).
# This bug breaks the test from libs, such as scalapack,
# on machines with less than 4 cores.
url = https://github.com/open-mpi/ompi/commit/98c8492057e6222af6404b352430d0dd7553d253.patch;
sha256 = "1mpd8sxxprgfws96qqlzvqf58pn2vv2d0qa8g8cpv773sgw3b3gj";
}) ];
postPatch = ''
patchShebangs ./
'';
buildInputs = with stdenv; [ gfortran zlib ]
++ lib.optionals isLinux [ libnl numactl ]
++ lib.optionals isLinux [ libnl numactl libevent hwloc ]
++ lib.optional (isLinux || isFreeBSD) rdma-core;
nativeBuildInputs = [ perl ];

View file

@ -12,6 +12,9 @@ stdenv.mkDerivation rec {
sha256 = "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c";
};
# patch to rename outdated MPI functions
patches = [ ./openmpi4.patch ];
nativeBuildInputs = [ cmake openssh ];
buildInputs = [ mpi gfortran openblasCompat ];
@ -41,8 +44,8 @@ stdenv.mkDerivation rec {
homepage = http://www.netlib.org/scalapack/;
description = "Library of high-performance linear algebra routines for parallel distributed memory machines";
license = licenses.bsd3;
platforms = platforms.linux;
maintainers = [ maintainers.costrouc ];
platforms = [ "x86_64-linux" ];
maintainers = with maintainers; [ costrouc markuskowa ];
};
}

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@ -0,0 +1,143 @@
diff --git a/BLACS/SRC/blacs_get_.c b/BLACS/SRC/blacs_get_.c
index e979767..d4b04cf 100644
--- a/BLACS/SRC/blacs_get_.c
+++ b/BLACS/SRC/blacs_get_.c
@@ -23,7 +23,7 @@ F_VOID_FUNC blacs_get_(int *ConTxt, int *what, int *val)
case SGET_MSGIDS:
if (BI_COMM_WORLD == NULL) Cblacs_pinfo(val, &val[1]);
iptr = &val[1];
- ierr=MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, (BVOID **) &iptr,val);
+ ierr=MPI_Comm_get_attr(MPI_COMM_WORLD, MPI_TAG_UB, (BVOID **) &iptr,val);
val[0] = 0;
val[1] = *iptr;
break;
diff --git a/BLACS/SRC/cgamn2d_.c b/BLACS/SRC/cgamn2d_.c
index 2db6ccb..6958f32 100644
--- a/BLACS/SRC/cgamn2d_.c
+++ b/BLACS/SRC/cgamn2d_.c
@@ -221,7 +221,7 @@ F_VOID_FUNC cgamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/cgamx2d_.c b/BLACS/SRC/cgamx2d_.c
index 707c0b6..f802d01 100644
--- a/BLACS/SRC/cgamx2d_.c
+++ b/BLACS/SRC/cgamx2d_.c
@@ -221,7 +221,7 @@ F_VOID_FUNC cgamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/dgamn2d_.c b/BLACS/SRC/dgamn2d_.c
index dff23b4..a2627ac 100644
--- a/BLACS/SRC/dgamn2d_.c
+++ b/BLACS/SRC/dgamn2d_.c
@@ -221,7 +221,7 @@ F_VOID_FUNC dgamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/dgamx2d_.c b/BLACS/SRC/dgamx2d_.c
index a51f731..2a644d0 100644
--- a/BLACS/SRC/dgamx2d_.c
+++ b/BLACS/SRC/dgamx2d_.c
@@ -221,7 +221,7 @@ F_VOID_FUNC dgamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/igamn2d_.c b/BLACS/SRC/igamn2d_.c
index 16bc003..f6a7859 100644
--- a/BLACS/SRC/igamn2d_.c
+++ b/BLACS/SRC/igamn2d_.c
@@ -218,7 +218,7 @@ F_VOID_FUNC igamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/igamx2d_.c b/BLACS/SRC/igamx2d_.c
index 8165cbe..a7cfcc6 100644
--- a/BLACS/SRC/igamx2d_.c
+++ b/BLACS/SRC/igamx2d_.c
@@ -218,7 +218,7 @@ F_VOID_FUNC igamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/sgamn2d_.c b/BLACS/SRC/sgamn2d_.c
index d6c95e5..569c797 100644
--- a/BLACS/SRC/sgamn2d_.c
+++ b/BLACS/SRC/sgamn2d_.c
@@ -221,7 +221,7 @@ F_VOID_FUNC sgamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/sgamx2d_.c b/BLACS/SRC/sgamx2d_.c
index 4b0af6f..8897ece 100644
--- a/BLACS/SRC/sgamx2d_.c
+++ b/BLACS/SRC/sgamx2d_.c
@@ -221,7 +221,7 @@ F_VOID_FUNC sgamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/zgamn2d_.c b/BLACS/SRC/zgamn2d_.c
index 9de2b23..37897df 100644
--- a/BLACS/SRC/zgamn2d_.c
+++ b/BLACS/SRC/zgamn2d_.c
@@ -221,7 +221,7 @@ F_VOID_FUNC zgamn2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;
diff --git a/BLACS/SRC/zgamx2d_.c b/BLACS/SRC/zgamx2d_.c
index 414c381..0e9d474 100644
--- a/BLACS/SRC/zgamx2d_.c
+++ b/BLACS/SRC/zgamx2d_.c
@@ -221,7 +221,7 @@ F_VOID_FUNC zgamx2d_(int *ConTxt, F_CHAR scope, F_CHAR top, int *m, int *n,
{
#endif
i = 2;
- ierr=MPI_Type_struct(i, len, disp, dtypes, &MyType);
+ ierr=MPI_Type_create_struct(i, len, disp, dtypes, &MyType);
ierr=MPI_Type_commit(&MyType);
bp->N = bp2->N = 1;
bp->dtype = bp2->dtype = MyType;

View file

@ -13,11 +13,18 @@ buildPythonPackage rec {
inherit mpi;
};
patches = [ (fetchpatch {
# Disable tests failing with 3.1.x and MPI_THREAD_MULTIPLE
url = "https://bitbucket.org/mpi4py/mpi4py/commits/c2b6b7e642a182f9b00a2b8e9db363214470548a/raw";
sha256 = "0n6bz3kj4vcqb6q7d0mlj5vl6apn7i2bvfc9mpg59vh3wy47119q";
patches = [
(fetchpatch {
# Disable tests failing with 3.1.x and MPI_THREAD_MULTIPLE (upstream patch)
url = "https://bitbucket.org/mpi4py/mpi4py/commits/c2b6b7e642a182f9b00a2b8e9db363214470548a/raw";
sha256 = "0n6bz3kj4vcqb6q7d0mlj5vl6apn7i2bvfc9mpg59vh3wy47119q";
})
(fetchpatch {
# Open MPI: Workaround removal of MPI_{LB|UB} (upstream patch)
url = "https://bitbucket.org/mpi4py/mpi4py/commits/39ca784226460f9e519507269ebb29635dc8bd90/raw";
sha256 = "02kxikdlsrlq8yr5hca42536mxbrq4k4j8nqv7p1p2r0q21a919q";
})
];
postPatch = ''

View file

@ -0,0 +1,58 @@
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

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@ -0,0 +1,115 @@
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

View file

@ -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} '{}' +