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Merge pull request #246867 from markuskowa/add-mpi-hook

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add mpiCheckPhaseHook
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markuskowa 2023-08-26 11:54:56 +02:00 committed by GitHub
commit 212d454c2a
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GPG Key ID: 4AEE18F83AFDEB23
14 changed files with 127 additions and 57 deletions
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1
doc/hooks/index.md
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@ -17,6 +17,7 @@ installShellFiles.section.md
libiconv.section.md
libxml2.section.md
meson.section.md
mpi-check-hook.section.md
ninja.section.md
patch-rc-path-hooks.section.md
perl.section.md

24
doc/hooks/mpi-check-hook.section.md Normal file
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@ -0,0 +1,24 @@
# mpiCheckPhaseHook {#setup-hook-mpi-check}
This hook can be used to setup a check phase that
requires running a MPI application. It detects the
used present MPI implementaion type and exports
the neceesary environment variables to use
`mpirun` and `mpiexec` in a Nix sandbox.
Example:
```nix
{ mpiCheckPhaseHook, mpi, ... }:
...
nativeCheckInputs = [
openssh
mpiCheckPhaseHook
];
```

14
pkgs/applications/science/chemistry/cp2k/default.nix
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@ -1,4 +1,4 @@
{ lib, stdenv, fetchFromGitHub, python3, gfortran, blas, lapack
{ lib, stdenv, fetchFromGitHub, mpiCheckPhaseHook, python3, gfortran, blas, lapack
, fftw, libint, libvori, libxc, mpi, gsl, scalapack, openssh, makeWrapper
, libxsmm, spglib, which, pkg-config, plumed, zlib
, enableElpa ? false
@ -88,14 +88,18 @@ in stdenv.mkDerivation rec {
EOF
'';
nativeCheckInputs = [
mpiCheckPhaseHook
openssh
];
checkPhase = ''
export OMP_NUM_THREADS=1
runHook preCheck
export HYDRA_IFACE=lo # Fix to make mpich run in a sandbox
export OMPI_MCA_rmaps_base_oversubscribe=1
export CP2K_DATA_DIR=data
mpirun -np 2 exe/${arch}/libcp2k_unittest.${cp2kVersion}
runHook postCheck
'';
installPhase = ''

10
pkgs/applications/science/chemistry/nwchem/default.nix
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@ -3,6 +3,7 @@
, pkgs
, fetchFromGitHub
, fetchurl
, mpiCheckPhaseHook
, which
, openssh
, gcc
@ -190,16 +191,15 @@ stdenv.mkDerivation rec {
doCheck = false;
doInstallCheck = true;
nativeCheckInputs = [ mpiCheckPhaseHook ];
installCheckPhase = ''
export OMP_NUM_THREADS=1
# Fix to make mpich run in a sandbox
export HYDRA_IFACE=lo
export OMPI_MCA_rmaps_base_oversubscribe=1
runHook preInstallCheck
# run a simple water test
mpirun -np 2 $out/bin/nwchem $out/share/nwchem/QA/tests/h2o/h2o.nw > h2o.out
grep "Total SCF energy" h2o.out | grep 76.010538
runHook postInstallCheck
'';
passthru = { inherit mpi; };

5
pkgs/build-support/setup-hooks/mpi-check-hook/default.nix Normal file
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@ -0,0 +1,5 @@
{ callPackage, makeSetupHook }:
makeSetupHook {
name = "mpi-checkPhase-hook";
} ./mpi-check-hook.sh

54
pkgs/build-support/setup-hooks/mpi-check-hook/mpi-check-hook.sh Normal file
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@ -0,0 +1,54 @@
preCheckHooks+=('setupMpiCheck')
preInstallCheckHooks+=('setupMpiCheck')
setupMpiCheck() {
# Find out which MPI implementation we are using
# and set safe defaults that are guaranteed to run
# on any build machine
mpiType="NONE"
# OpenMPI signature
if command ompi_info &> /dev/null; then
mpiType="openmpi"
fi
# MPICH based implementations
if command mpichversion &> /dev/null; then
if [ "$mpiType" != "NONE" ]; then
echo "WARNING: found OpenMPI and MPICH/MVAPICH executables"
fi
version=$(mpichversion)
if [[ "$version" == *"MPICH"* ]]; then
mpiType="MPICH"
fi
if [[ "$version" == *"MVAPICH"* ]]; then
mpiType="MVAPICH"
fi
fi
echo "Found MPI implementation: $mpiType"
case $mpiType in
openmpi)
# make sure the test starts even if we have less than the requested amount of cores
export OMPI_MCA_rmaps_base_oversubscribe=1
# Disable CPU pinning
export OMPI_MCA_hwloc_base_binding_policy=none
;;
MPICH)
# Fix to make mpich run in a sandbox
export HYDRA_IFACE=lo
;;
MVAPICH)
# Disable CPU pinning
export MV2_ENABLE_AFFINITY=0
;;
esac
# Limit number of OpenMP threads. Default is "all cores".
export OMP_NUM_THREADS=1
}

13
pkgs/development/libraries/elpa/default.nix
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@ -1,5 +1,5 @@
{ lib, stdenv, fetchurl, autoreconfHook, gfortran, perl
, mpi, blas, lapack, scalapack, openssh
{ lib, stdenv, fetchurl, autoreconfHook, mpiCheckPhaseHook
, gfortran, perl, mpi, blas, lapack, scalapack, openssh
# CPU optimizations
, avxSupport ? stdenv.hostPlatform.avxSupport
, avx2Support ? stdenv.hostPlatform.avx2Support
@ -41,7 +41,7 @@ stdenv.mkDerivation rec {
substituteInPlace Makefile.am --replace '#!/bin/bash' '#!${stdenv.shell}'
'';
nativeBuildInputs = [ autoreconfHook perl openssh ];
nativeBuildInputs = [ autoreconfHook perl ];
buildInputs = [ mpi blas lapack scalapack ]
++ lib.optional enableCuda cudatoolkit;
@ -76,15 +76,10 @@ stdenv.mkDerivation rec {
doCheck = true;
nativeCheckInputs = [ mpiCheckPhaseHook openssh ];
preCheck = ''
#patchShebangs ./
# make sure the test starts even if we have less than 4 cores
export OMPI_MCA_rmaps_base_oversubscribe=1
# Fix to make mpich run in a sandbox
export HYDRA_IFACE=lo
# Run dual threaded
export OMP_NUM_THREADS=2

10
pkgs/development/libraries/science/math/dbcsr/default.nix
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@ -2,6 +2,7 @@
, lib
, fetchFromGitHub
, cmake
, mpiCheckPhaseHook
, pkg-config
, fypp
, gfortran
@ -64,13 +65,12 @@ stdenv.mkDerivation rec {
"-DUSE_MPI=ON"
];
checkInputs = [ openssh ];
checkInputs = [
openssh
mpiCheckPhaseHook
];
doCheck = true;
preCheck = ''
export HYDRA_IFACE=lo # Fix to make mpich run in a sandbox
export OMPI_MCA_rmaps_base_oversubscribe=1
'';
meta = with lib; {
description = "Distributed Block Compressed Sparse Row matrix library";

10
pkgs/development/libraries/science/math/p4est-sc/default.nix
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@ -1,4 +1,4 @@
{ lib, stdenv, fetchFromGitHub
{ lib, stdenv, fetchFromGitHub, mpiCheckPhaseHook
, autoreconfHook, pkg-config
, p4est-sc-debugEnable ? true, p4est-sc-mpiSupport ? true
, mpi, openssh, zlib
@ -47,10 +47,10 @@ stdenv.mkDerivation {
enableParallelBuilding = true;
makeFlags = [ "V=0" ];
preCheck = ''
export OMPI_MCA_rmaps_base_oversubscribe=1
export HYDRA_IFACE=lo
'';
nativeCheckInputs = lib.optionals mpiSupport [
mpiCheckPhaseHook
openssh
];
# disallow Darwin checks due to prototype incompatibility of qsort_r
# to be fixed in a future version of the source code

2
pkgs/development/libraries/science/math/p4est/default.nix
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@ -46,7 +46,7 @@ stdenv.mkDerivation {
++ lib.optional withMetis "--with-metis"
;
inherit (p4est-sc) makeFlags dontDisableStatic enableParallelBuilding preCheck doCheck;
inherit (p4est-sc) makeFlags dontDisableStatic enableParallelBuilding doCheck;
meta = {
branch = "prev3-develop";

17
pkgs/development/libraries/science/math/scalapack/default.nix
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@ -1,5 +1,5 @@
{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, openssh
, mpi, blas, lapack
{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake
, openssh, mpiCheckPhaseHook, mpi, blas, lapack
} :
assert blas.isILP64 == lapack.isILP64;
@ -35,7 +35,7 @@ stdenv.mkDerivation rec {
'';
nativeBuildInputs = [ cmake ];
nativeCheckInputs = [ openssh ];
nativeCheckInputs = [ openssh mpiCheckPhaseHook ];
buildInputs = [ blas lapack ];
propagatedBuildInputs = [ mpi ];
hardeningDisable = lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [ "stackprotector" ];
@ -61,17 +61,6 @@ stdenv.mkDerivation rec {
# sometimes fail due to this
checkFlagsArray = [ "ARGS=--timeout 10000" ];
preCheck = ''
# make sure the test starts even if we have less than 4 cores
export OMPI_MCA_rmaps_base_oversubscribe=1
# Fix to make mpich run in a sandbox
export HYDRA_IFACE=lo
# Run single threaded
export OMP_NUM_THREADS=1
'';
meta = with lib; {
homepage = "http://www.netlib.org/scalapack/";
description = "Library of high-performance linear algebra routines for parallel distributed memory machines";

13
pkgs/development/python-modules/meep/default.nix
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@ -4,6 +4,7 @@
, fetchFromGitHub
, autoreconfHook
, pkg-config
, mpiCheckPhaseHook
, gfortran
, mpi
, blas
@ -108,16 +109,12 @@ buildPythonPackage rec {
errors can be caught.
*/
doCheck = true;
nativeCheckInputs = [ mpiCheckPhaseHook openssh ];
checkPhase = ''
export PATH=$PATH:${openssh}/bin
runHook preCheck
export PYTHONPATH="$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
export OMP_NUM_THREADS=1
# Fix to make mpich run in a sandbox
export HYDRA_IFACE=lo
export OMPI_MCA_rmaps_base_oversubscribe=1
# Generate a python test script
cat > test.py << EOF
import meep as mp
@ -139,6 +136,8 @@ buildPythonPackage rec {
EOF
${mpi}/bin/mpiexec -np 2 python3 test.py
runHook postCheck
'';
meta = with lib; {

10
pkgs/development/python-modules/mpi4py/default.nix
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@ -1,4 +1,6 @@
{ lib, fetchPypi, fetchpatch, python, buildPythonPackage, mpi, openssh }:
{ lib, fetchPypi, fetchpatch, python, buildPythonPackage
, mpi, mpiCheckPhaseHook, openssh
}:
buildPythonPackage rec {
pname = "mpi4py";
@ -33,10 +35,6 @@ buildPythonPackage rec {
# sometimes packages specify where files should be installed outside the usual
# python lib prefix, we override that back so all infrastructure (setup hooks)
# work as expected
# Needed to run the tests reliably. See:
# https://bitbucket.org/mpi4py/mpi4py/issues/87/multiple-test-errors-with-openmpi-30
export OMPI_MCA_rmaps_base_oversubscribe=yes
'';
setupPyBuildFlags = ["--mpicc=${mpi}/bin/mpicc"];
@ -45,7 +43,7 @@ buildPythonPackage rec {
__darwinAllowLocalNetworking = true;
nativeCheckInputs = [ openssh ];
nativeCheckInputs = [ openssh mpiCheckPhaseHook ];
meta = with lib; {
description = "Python bindings for the Message Passing Interface standard";

1
pkgs/top-level/all-packages.nix
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@ -12323,6 +12323,7 @@ with pkgs;
outils = callPackage ../tools/misc/outils { };
mpi = openmpi; # this attribute should used to build MPI applications
mpiCheckPhaseHook = callPackage ../build-support/setup-hooks/mpi-check-hook { };
ucc = callPackage ../development/libraries/ucc { };