From 1e54515e4be64b8e12d77c6df82cf1dd2eb2418c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Thu, 1 Feb 2018 11:20:47 +0100
Subject: [PATCH] 	new file:  
 g/GROMACS/GROMACS-5.1.4-foss-2016a-hybrid-single-PLUMED-v2.eb 	new file:  
 l/LAMMPS/LAMMPS-17Jan2018-intel-2017a-MIC.eb 	new file:  
 l/LAMMPS/LAMMPS-Makefile.intel_coprocessor.patch

---
 ....1.4-foss-2016a-hybrid-single-PLUMED-v2.eb | 33 ++++++++++
 l/LAMMPS/LAMMPS-17Jan2018-intel-2017a-MIC.eb  | 60 +++++++++++++++++++
 .../LAMMPS-Makefile.intel_coprocessor.patch   | 21 +++++++
 3 files changed, 114 insertions(+)
 create mode 100644 g/GROMACS/GROMACS-5.1.4-foss-2016a-hybrid-single-PLUMED-v2.eb
 create mode 100644 l/LAMMPS/LAMMPS-17Jan2018-intel-2017a-MIC.eb
 create mode 100644 l/LAMMPS/LAMMPS-Makefile.intel_coprocessor.patch

diff --git a/g/GROMACS/GROMACS-5.1.4-foss-2016a-hybrid-single-PLUMED-v2.eb b/g/GROMACS/GROMACS-5.1.4-foss-2016a-hybrid-single-PLUMED-v2.eb
new file mode 100644
index 00000000..3ec78aff
--- /dev/null
+++ b/g/GROMACS/GROMACS-5.1.4-foss-2016a-hybrid-single-PLUMED-v2.eb
@@ -0,0 +1,33 @@
+name = 'GROMACS'
+version = '5.1.4'
+versionsuffix = '-hybrid-single-PLUMED-v2'
+
+homepage = 'http://www.gromacs.org'
+description = """GROMACS is a versatile package to perform molecular dynamics,
+ i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles."""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/']
+sources = [SOURCELOWER_TAR_GZ]
+
+preconfigopts = 'plumed patch -p -e gromacs-5.1.4 &&'
+
+configopts = ' -DGMX_GPU=OFF  -DBUILD_SHARED_LIBS=OFF  -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=OFF  -DGMX_SIMD=AVX2_256  -DGMX_BUILD_OWN_FFTW=ON  -DGMX_MPI=ON'
+
+builddependencies = [
+    ('CMake', '3.5.2'),
+]
+
+dependencies = [
+    ('Boost', '1.61.0', '-serial'),
+    ('PLUMED', '2.3.0')
+]
+
+sanity_check_paths = {
+    'files': ['bin/gmx_mpi'],
+    'dirs': [''],
+}
+
+moduleclass = 'bio'
diff --git a/l/LAMMPS/LAMMPS-17Jan2018-intel-2017a-MIC.eb b/l/LAMMPS/LAMMPS-17Jan2018-intel-2017a-MIC.eb
new file mode 100644
index 00000000..76096066
--- /dev/null
+++ b/l/LAMMPS/LAMMPS-17Jan2018-intel-2017a-MIC.eb
@@ -0,0 +1,60 @@
+# IT4Innovations 2017
+
+easyblock = 'CmdCp'
+
+name = 'LAMMPS'
+version = '17Jan2018'
+versionsuffix = '-MIC'
+
+
+homepage = 'http://lammps.sandia.gov'
+description = """LAMMPS is a classical molecular dynamics code,
+and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
+Has potentials for solid-state materials (metals, semiconductors) and soft
+matter (biomolecules, polymers) and coarse-grained or mesoscopic systems.
+It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic,
+meso, or continuum scale.
+"""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = ['https://github.com/lammps/lammps/archive']
+sources = ['patch_17Jan2018.tar.gz']
+
+patches = [
+   'LAMMPS-Makefile.intel_coprocessor.patch',
+]
+
+dependencies = [
+    ('tbb', '2017.6.196', '', True),
+]
+
+builddependencies = [
+    ('Python', '2.7.13', '-base', True),
+    ('CMake', '3.5.2', '', True)
+]
+
+maxparallel = 1
+
+commands =  "cd src && "
+commands += "make lib-reax args='-m ifort' && make yes-reax && "
+commands += "make yes-kspace && make yes-manybody && make yes-molecule && "
+commands += "make yes-qeq && make yes-rigid && make yes-user-misc && "
+commands += "make yes-user-reaxc && make yes-user-omp && make yes-user-intel && "
+commands += "make yes-user-phonon && make yes-kokkos && "
+commands += "make -j 16 intel_coprocessor && mv lmp_intel_coprocessor lammps"
+
+cmds_map = [('.*', commands)]
+
+files_to_copy = [
+        (['src/lammps'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/lammps'],
+    'dirs': [''],
+}
+
+modluafooter = 'add_property("arch","mic-offload")'
+
+moduleclass = 'chem'
diff --git a/l/LAMMPS/LAMMPS-Makefile.intel_coprocessor.patch b/l/LAMMPS/LAMMPS-Makefile.intel_coprocessor.patch
new file mode 100644
index 00000000..c26333f6
--- /dev/null
+++ b/l/LAMMPS/LAMMPS-Makefile.intel_coprocessor.patch
@@ -0,0 +1,21 @@
+--- src/MAKE/OPTIONS/Makefile.intel_coprocessor.orig	2018-01-17 21:00:48.000000000 +0100
++++ src/MAKE/OPTIONS/Makefile.intel_coprocessor	2018-01-26 13:16:05.178751386 +0100
+@@ -15,7 +15,7 @@
+ DEPFLAGS =	-M
+ 
+ LINK =		mpiicpc
+-LINKFLAGS =	-g -O3 -xHost -qopenmp -qoffload
++LINKFLAGS =	-g -O3 –xMIC-AVX512 -qopenmp -qoffload
+ LIB =           -ltbbmalloc
+ SIZE =		size
+ 
+@@ -23,6 +23,9 @@
+ ARFLAGS =	-rc
+ SHLIBFLAGS =	-shared
+ 
++KOKKOS_DEVICES = OpenMP
++KOKKOS_ARCH = KNC
++KOKKOS_USE_TPLS=librt
+ # ---------------------------------------------------------------------
+ # LAMMPS-specific settings, all OPTIONAL
+ # specify settings for LAMMPS features you will use