Add/conveyorlc (#5)

* store state of adding conveylorlc
Signed-off-by: Vanessasaurus <814322+vsoch@users.noreply.github.com>

.devcontainer/Dockerfile

@@ -2,8 +2,8 @@ FROM ubuntu:22.04
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 ENV EDITOR=vim
 
-RUN apt-get update && apt-get upgrade
-RUN apt-get install --yes \
+RUN apt-get update && \
+    apt-get install --yes \
         ca-certificates \
         bash-completion \
         build-essential \

default.nix

@@ -18,11 +18,15 @@ rec {
   adiak = pkgs.callPackage ./pkgs/hpc/adiak {
     inherit maintainers;
   };
+  caliper = pkgs.callPackage ./pkgs/hpc/caliper {
+    inherit adiak;
+    inherit maintainers;
+  };
   conduit = pkgs.callPackage ./pkgs/hpc/conduit {
     inherit maintainers;
   };
-  caliper = pkgs.callPackage ./pkgs/hpc/caliper {
-    inherit adiak;
+  conveyorlc = pkgs.callPackage ./pkgs/hpc/conveyorlc {
+    inherit conduit;
     inherit maintainers;
   };
 }

pkgs/hpc/conduit/default.nix

@@ -4,7 +4,6 @@
 , withFortran? false
 , pythonSupport ? true
 , zfpSupport ? true
-, hdf5Support ? true
 , shared ? !stdenv.hostPlatform.isStatic,
 ...
 }:
@@ -60,12 +59,11 @@ stdenv.mkDerivation rec {
   # depends_on("hdf5", when="+hdf5")
   # depends_on("hdf5~shared", when="+hdf5~shared")
 
-  nativeBuildInputs = [cmake pkgs.bash pkgs.extra-cmake-modules pkgs.tree];
+  nativeBuildInputs = [cmake pkgs.bash pkgs.extra-cmake-modules pkgs.tree pkgs.hdf5];
   buildInputs =
     lib.optional pythonSupport pkgs.python39 ++
     lib.optional pythonSupport pkgs.python39Packages.numpy ++
     lib.optional pythonSupport pkgs.python39Packages.mpi4py ++
-    lib.optional hdf5Support pkgs.hdf5 ++
     lib.optional zfpSupport pkgs.zfp ++
 
     # These shouldn't be both provided
@@ -83,8 +81,9 @@ stdenv.mkDerivation rec {
     "-DBUILD_SHARED_LIBS=${onOffBool shared}"
     "-DENABLE_FORTRAN=${onOffBool withFortran}"
     "-DENABLE_PYTHON=${onOffBool pythonSupport}"
-    "-DENABLE_UTILS=OFF"
-    "-DENABLE_EXAMPLES=OFF"
+    "-DHDF5_DIR=${lib.getDev pkgs.hdf5}"
+    "-DENABLE_UTILS=ON"
+    "-DENABLE_EXAMPLES=ON"
     "-DBUILD_TESTS=OFF"
     "-DBUILD_DOCS=OFF"
   ];

pkgs/hpc/conveyorlc/default.nix

@@ -0,0 +1,62 @@
+{ lib, stdenv, pkgs, fetchurl, fetchFromGitHub, cmake, maintainers, conduit
+, shared ? !stdenv.hostPlatform.isStatic,
+...
+}:
+
+let
+   onOffBool = b: if b then "ON" else "OFF";
+   boost = pkgs.boost172.override { useMpi = true; };
+in
+
+
+stdenv.mkDerivation rec {
+  pname = "conveyorlc";
+  version = "1.1.0";
+
+  src = fetchFromGitHub {
+    owner = "XiaohuaZhangLLNL";
+    repo = "conveyorlc";
+    rev = "efb98b021edd5ef230eaff257ce2534ea01ab1ba";
+    sha256 = "sha256-L/pWqKFM1/68X9HPHKMBYODlDI3Jh4IVqffDGjVNCrc=";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [cmake pkgs.extra-cmake-modules];
+  buildInputs = [
+      boost
+      pkgs.openmpi
+      pkgs.openbabel2
+      pkgs.zlib
+      pkgs.hdf5-cpp
+      pkgs.sqlite
+      conduit
+  ];
+
+  # We set the conduit paths from Nix instead
+  preConfigure = ''
+   rm cmake/FindConduit.cmake
+  '';
+
+  cmakeFlags = [
+    "-DCONDUIT_DIR=${lib.getDev conduit}"
+    "-DCONDUIT_FOUND=TRUE"
+    "-DCONDUIT_INCLUDE_DIRS=${lib.getDev conduit}/include/conduit"
+    "-DCONDUIT_CMAKE_CONFIG_DIR=${lib.getDev conduit}/lib/cmake/conduit"
+    "-DCMAKE_CXX_FLAGS=-lhdf5"
+    "-DHDF5_ROOT=${lib.getDev pkgs.hdf5-cpp}"
+    "-DOPENBABEL3_INCLUDE_DIRS=${lib.getDev pkgs.openbabel2}/include/openbabel-2.0"
+  ];
+
+  meta = with lib; {
+    description = "A Parallel Virtual Screening Pipeline for Docking and MM/GSBA";
+    longDescription = ''
+      An open source project from Lawrence Livermore National
+      Laboratory that provides a parallel virtual screening pipeline
+      for docking and MM/GSBA
+    '';
+    homepage = "https://github.com/XiaohuaZhangLLNL/conveyorlc";
+    license = licenses.gpl3;
+    maintainers = [ maintainers.vsoch ];
+    platforms = platforms.linux;
+  };
+}