From d69daf6bb62f62db4aad764e1d9a4da565f08aca Mon Sep 17 00:00:00 2001
From: Stian Soiland-Reyes <stain@apache.org>
Date: Fri, 15 Feb 2019 14:55:19 +0000
Subject: [PATCH] Update to Gromacs 2019 (#13523)

* Update to Gromacs 2019 and 2018.5
http://manual.gromacs.org/documentation/2019/download.html
---
 recipes/gromacs/{ => 2018}/build.sh  |  0
 recipes/gromacs/{ => 2018}/meta.yaml | 10 +++---
 recipes/gromacs/2019/build.sh        | 21 ++++++++++++
 recipes/gromacs/2019/meta.yaml       | 50 ++++++++++++++++++++++++++++
 recipes/gromacs/README.md            | 19 +++++++++++
 5 files changed, 95 insertions(+), 5 deletions(-)
 rename recipes/gromacs/{ => 2018}/build.sh (100%)
 rename recipes/gromacs/{ => 2018}/meta.yaml (77%)
 create mode 100644 recipes/gromacs/2019/build.sh
 create mode 100644 recipes/gromacs/2019/meta.yaml
 create mode 100644 recipes/gromacs/README.md

diff --git a/recipes/gromacs/build.sh b/recipes/gromacs/2018/build.sh
similarity index 100%
rename from recipes/gromacs/build.sh
rename to recipes/gromacs/2018/build.sh
diff --git a/recipes/gromacs/meta.yaml b/recipes/gromacs/2018/meta.yaml
similarity index 77%
rename from recipes/gromacs/meta.yaml
rename to recipes/gromacs/2018/meta.yaml
index ce0dd2473e76b..ce13d2171818f 100644
--- a/recipes/gromacs/meta.yaml
+++ b/recipes/gromacs/2018/meta.yaml
@@ -5,7 +5,7 @@ about:
 
 package:
   name: gromacs
-  version: 2018.4
+  version: 2018.5
 
 build:
   number: 0
@@ -15,13 +15,13 @@ build:
 # for latest release. Note that version scheme changed from
 # 5.1 to 2016.x and 2018.x
 source:
-  url: http://ftp.gromacs.org/pub/gromacs/gromacs-2018.4.tar.gz
-  md5: 7bede4c1a656531fc43b95805e9a5a94
-  sha256: 6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891
+  url: http://ftp.gromacs.org/pub/gromacs/gromacs-2018.5.tar.gz
+  md5: 1484e421721b7787becf6f88d23292e6
+  sha256: 32261df6f7ec4149fc0508f9af416953d056e281590359838c1ed6644ba097b8
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - cmake
   host:
     - openmp # [linux]
diff --git a/recipes/gromacs/2019/build.sh b/recipes/gromacs/2019/build.sh
new file mode 100644
index 0000000000000..105ef902b2811
--- /dev/null
+++ b/recipes/gromacs/2019/build.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+mkdir build
+cd build
+## See INSTALL of gromacs distro
+cmake .. \
+  -DSHARED_LIBS_DEFAULT=OFF \
+  -DBUILD_SHARED_LIBS=OFF \
+  -DGMX_PREFER_STATIC_LIBS=YES \
+  -DGMX_BUILD_OWN_FFTW=OFF \
+  -DGMX_DEFAULT_SUFFIX=ON \
+  -DREGRESSIONTEST_DOWNLOAD=ON \
+  -DGMX_MPI=OFF \
+  -DGMX_GPU=ON \
+  -DGMX_SIMD=SSE2 \
+  -DGMX_USE_OPENCL=ON \
+  -DCMAKE_PREFIX_PATH=$PREFIX \
+  -DGMX_INSTALL_PREFIX=$PREFIX \
+  -DCMAKE_INSTALL_PREFIX=$PREFIX
+make -j 8
+make check
+make install
diff --git a/recipes/gromacs/2019/meta.yaml b/recipes/gromacs/2019/meta.yaml
new file mode 100644
index 0000000000000..ab954a14d06f6
--- /dev/null
+++ b/recipes/gromacs/2019/meta.yaml
@@ -0,0 +1,50 @@
+about:
+  home: http://www.gromacs.org/
+  license: GNU Lesser General Public License (LGPL)
+  summary: GROMACS is a versatile package to perform molecular dynamics.
+
+package:
+  name: gromacs
+  version: 2019
+
+build:
+  number: 0
+#  skip: True  # [osx]
+
+# See http://manual.gromacs.org/documentation/
+# for latest release. Note that version scheme changed from
+# 5.1 to 2016.x and 2018.x
+source:
+  url: http://ftp.gromacs.org/pub/gromacs/gromacs-2019.tar.gz
+  md5: fcd283dd0fe5ceb54dd9d735d75cbc65
+  sha256: c5b281a5f0b5b4eeb1f4c7d4dc72f96985b566561ca28acc9c7c16f6ee110d0b
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+  host:
+    - openmp # [linux]
+    - ocl-icd  # [linux]
+    - libhwloc 2.*
+    - fftw
+    - perl
+    - python >=2.7,<3
+  run:
+    - ocl-icd # [linux]
+    - openmp # [linux]
+    - fftw
+    - libhwloc 2.*
+
+test:
+  commands:
+    - gmx -version
+
+
+extra:
+  identifiers:
+    - biotools:gromacs
+    - doi:10.5281/zenodo.2424363
+    - doi:10.5281/zenodo.2424486
+    - doi:10.1016/j.softx.2015.06.001
+    - rrid:RRID:SCR_014565
diff --git a/recipes/gromacs/README.md b/recipes/gromacs/README.md
new file mode 100644
index 0000000000000..4756c1d825d2e
--- /dev/null
+++ b/recipes/gromacs/README.md
@@ -0,0 +1,19 @@
+GROMACS versions are released in series, so we maintain one
+recipe folder for each major version.
+
+Be careful with the CI build time if updating multiple 
+recipes, a single build takes about 1h12.
+
+From http://manual.gromacs.org/documentation/2019/release-notes/index.html#gromacs-2019-series
+
+> Major releases contain changes to the functionality supported, whereas patch releases contain only fixes for issues identified in the corresponding major releases.
+
+> Two versions of GROMACS are under active maintenance, the 2019 series and the
+> 2018 series. In the latter, only highly conservative fixes will be made, and
+> only to address issues that affect scientific correctness. 
+
+> Naturally, some of those releases will be made after the year 2018 ends, but
+> we keep 2018 in the name so users understand how up to date their version is.
+> Such fixes will also be incorporated into the 2019 release series, as
+> appropriate. Around the time the 2020 release is made, the 2018 series will no
+> longer be maintained.