Merge https://github.com/NixOS/nixpkgs

3 files changed, 16 insertions, 12 deletions

diff --git a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix
index 5defaafa3cd0..29b983cde536 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix
@@ -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 = ''
diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
index e4ffb94eeba7..1b77cef6b809 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
@@ -25,14 +25,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "16.1.33";
+  version = "16.1.35";
   pname = "jmol";
 
   src = let
     baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
   in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    hash = "sha256-vOFGmLsCQNYRBMuDRVrdjWE6/MxY7IucB1OpV4cdZrs=";
+    hash = "sha256-r1ydAwAdXl5RRj64W0j8L7XbgnC7VOYjFNE019BcbpY=";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix b/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix
index 82daf5f85e74..2a17be9f8a92 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/nwchem/default.nix
@@ -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; };