Amber20 release

6 files changed, 83 insertions, 91 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 0e98d811d98f..ce505d05d077 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,36 +1,39 @@
 pkgbase = pmemd
 	pkgdesc = PMEMD module of AMBER software package
-	pkgver = 18
-	pkgrel = 3
+	pkgver = 20
+	pkgrel = 1
 	url = http://ambermd.org/
 	arch = x86_64
 	license = custom
+	makedepends = cmake>=3.8.1
 	makedepends = make
 	makedepends = gcc8
-	makedepends = gcc8-fortran
+	makedepends = flex
+	makedepends = bison
+	makedepends = patch
 	makedepends = tcsh
 	makedepends = imake
-	makedepends = patch
-	depends = openmpi3-gcc8
-	depends = fakeroot
-	depends = zlib
-	depends = bzip2
-	depends = gcc8-libs
-	depends = flex
-	depends = python2
+	makedepends = openmpi-gcc8
+	makedepends = cuda>=7.5
+	depends = ambertools
+	optdepends = openmpi-gcc8: MPI support
+	optdepends = cuda: GPU acceleration support
 	optdepends = plumed: metadynamics support
 	optdepends = plumed-mpi: metadynamics support with MPI
 	options = staticlibs
 	options = !buildflags
-	options = !makeflags
-	source = local://AmberTools19.tar.bz2
-	source = local://Amber18.tar.bz2
+	source = local://AmberTools20.tar.bz2
+	source = local://Amber20.tar.bz2
 	source = pmemd
 	source = pmemd.MPI
-	md5sums = afffe8a5473a0bd143b98f0396f52f0f
-	md5sums = 6b38d9cfb6e33b719bdf7fe73b26e841
-	md5sums = ef2dc0fec7e716075c044a019d8f8f0c
-	md5sums = a4fe6129d03ad814744b85584d1aba9a
+	source = pmemd.cuda
+	source = pmemd.cuda.MPI
+	md5sums = 8c1fe81833796a9cb823019e02c522e0
+	md5sums = 559d5b7b872344c268a62ebd5d33f71d
+	md5sums = 9a4dab06ab1ba04f12950b26ec5285e5
+	md5sums = a9a440a1e0c1b1aee7f356869d03b18e
+	md5sums = 69c5d2bdc5e1f6e854c640db7ce1c2ff
+	md5sums = 451eec2b6fa7572f6b61104709588824
 
 pkgname = pmemd
 
diff --git a/PKGBUILD b/PKGBUILD
index 33acad4ec12d..2b03c731683b 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,97 +1,72 @@
 # Maintainer: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
 
 pkgname=pmemd
-pkgver=18
-_toolsver=19
-_gccver=8.3.0
-pkgrel=3
+pkgver=20
+_toolsver=20
+_gccver=8.4.0
+pkgrel=1
 pkgdesc="PMEMD module of AMBER software package"
 url="http://ambermd.org/"
-license=('custom')
-arch=('x86_64')
-depends=('openmpi3-gcc8' 'fakeroot' 'zlib' 'bzip2' 'gcc8-libs' 'flex' 'python2')
-makedepends=('make' 'gcc8' 'gcc8-fortran' 'tcsh' 'imake' 'patch')
-optdepends=('plumed: metadynamics support'
+license=(custom)
+arch=(x86_64)
+depends=(ambertools)
+makedepends=('cmake>=3.8.1' make gcc8 flex bison patch tcsh imake openmpi-gcc8 'cuda>=7.5')
+optdepends=('openmpi-gcc8: MPI support'
+            'cuda: GPU acceleration support'
+            'plumed: metadynamics support'
             'plumed-mpi: metadynamics support with MPI')
-md5sums=('afffe8a5473a0bd143b98f0396f52f0f'
-         '6b38d9cfb6e33b719bdf7fe73b26e841'
-         'ef2dc0fec7e716075c044a019d8f8f0c'
-         'a4fe6129d03ad814744b85584d1aba9a')
-options=(staticlibs !buildflags !makeflags)
+options=(staticlibs !buildflags)
 
 # Due to licensing issues you must register and download AmberTools package from AmberMD url and put it in directory with PKGBUILD.
 # Moreover, you MUST purchase Amber package from AmberMD group and also place it in directory with PKGBUILD.
 source=("local://AmberTools${_toolsver}.tar.bz2"
         "local://Amber${pkgver}.tar.bz2"
         "pmemd"
-        "pmemd.MPI")
+        "pmemd.MPI"
+        "pmemd.cuda"
+        "pmemd.cuda.MPI")
+md5sums=('8c1fe81833796a9cb823019e02c522e0'
+         '559d5b7b872344c268a62ebd5d33f71d'
+         '9a4dab06ab1ba04f12950b26ec5285e5'
+         'a9a440a1e0c1b1aee7f356869d03b18e'
+         '69c5d2bdc5e1f6e854c640db7ce1c2ff'
+         '451eec2b6fa7572f6b61104709588824')
 
 prepare() {
-  cd ${srcdir}/amber${pkgver}
+  cd ${srcdir}/amber${pkgver}_src
 
-  export AMBERHOME="${srcdir}/amber${pkgver}"
   ./update_amber --update
 }
 
 build() {
-  # set necessary variables
-  export LD_PRELOAD=/usr/lib/libstdc++.so
-  export AMBER_PREFIX="${srcdir}/amber${pkgver}"
-  export AMBERHOME="${srcdir}/amber${pkgver}"
-
-  if [ -z "${LD_LIBRARY_PATH}" ]; then
-     export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib"
-  else
-     export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib:${LD_LIBRARY_PATH}"
-  fi
-
-  export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:${LD_LIBRARY_PATH}"
-
-  # build serial version
-  cd ${srcdir}/amber${pkgver}
-  LANG=en_US.UTF-8 CC=gcc-8 CXX=g++-8 FC=gfortran-8 ./configure --with-python /usr/bin/python2 --no-updates gnu
-
-  # add support for PLUMED
-  if [ -e "/usr/bin/plumed-mpi-patch" -a -e "/usr/lib/plumed-mpi/patches/amber${pkgver}.diff" ]; then
-    msg2 "Adding support for PLUMED (with MPI)"
-    plumed-mpi-patch -p -e amber${pkgver}
-  elif [ -e "/usr/bin/plumed-patch" -a -e "/usr/lib/plumed/patches/amber${pkgver}.diff" ]; then
-    msg2 "Adding support for PLUMED"
-    plumed-patch -p -e amber${pkgver}
-  fi
-
-  # build internal libraries
-  cd ${srcdir}/amber${pkgver}/AmberTools/src/xblas
-  make lib-amb
-  mv libxblas-amb.a ../../../lib
-
-  cd ${srcdir}/amber${pkgver}/AmberTools/src/blas
-  make install
-
-  cd ${srcdir}/amber${pkgver}/AmberTools/src/lapack
-  make install
-
-  cd ${srcdir}/amber${pkgver}/AmberTools/src/arpack
-  make install
-
-  cd ${srcdir}/amber${pkgver}/src
-  make install
-
-  # build parallel version
-  cd ${srcdir}/amber${pkgver}
-  LANG=en_US.UTF-8 CC=gcc-8 CXX=g++-8 FC=gfortran-8 ./configure --with-python /usr/bin/python2 --no-updates -mpi gnu
-  cd ${srcdir}/amber${pkgver}/src
-  make install
+  cd ${srcdir}/amber${pkgver}_src/build
+
+  export AMBER_PREFIX="${srcdir}"
+
+  CC=gcc-8 CXX=g++-8 FC=gfortran-8 cmake $AMBER_PREFIX/amber${pkgver}_src \
+      -DCMAKE_INSTALL_PREFIX=/opt/amber \
+	  -DCOMPILER=MANUAL  \
+	  -DMPI=TRUE -DCUDA=TRUE \
+	  -DOPENMP=TRUE \
+	  -DINSTALL_TESTS=TRUE \
+	  -DDOWNLOAD_MINICONDA=FALSE \
+	  -DFORCE_DISABLE_LIBS="plumed" \
+	  -DFORCE_INTERNAL_LIBS="arpack;xblas;netcdf;netcdf-fortran;pnetcdf;fftw;boost;mpi4py" \
+	  2>&1 | tee cmake.log
+
+  cd src
+  make
 }
 
 package() {
-  cd ${srcdir}/amber${pkgver}/bin
+  mkdir -p ${pkgdir}/opt/amber
 
-  # install binaries
-  install -Dm755 pmemd ${pkgdir}/usr/lib/${pkgname}/bin/pmemd
-  install -Dm755 pmemd.MPI ${pkgdir}/usr/lib/${pkgname}/bin/pmemd.MPI
+  cd ${srcdir}/amber${pkgver}_src/build/src
+  make DESTDIR=${pkgdir} install
 
   # install wrappers
   install -Dm755 ${srcdir}/pmemd ${pkgdir}/usr/bin/pmemd
   install -Dm755 ${srcdir}/pmemd.MPI ${pkgdir}/usr/bin/pmemd.MPI
+  install -Dm755 ${srcdir}/pmemd.cuda ${pkgdir}/usr/bin/pmemd.cuda
+  install -Dm755 ${srcdir}/pmemd.cuda.MPI ${pkgdir}/usr/bin/pmemd.cuda.MPI
 }
diff --git a/pmemd b/pmemd
index 67d7c548a6de..d58d62da784f 100644..100755
--- a/pmemd
+++ b/pmemd
@@ -1,7 +1,7 @@
 #!/usr/bin/bash
 
-export _gccver=8.3.0
+export _gccver=8.4.0
 export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
-/usr/lib/pmemd/bin/pmemd "$@"
+/opt/amber/bin/pmemd "$@"
 
 exit 0
diff --git a/pmemd.MPI b/pmemd.MPI
index f1ed57611439..461a614e65c2 100644..100755
--- a/pmemd.MPI
+++ b/pmemd.MPI
@@ -1,7 +1,7 @@
 #!/usr/bin/bash
 
-export _gccver=8.3.0
+export _gccver=8.4.0
 export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
-/usr/lib/pmemd/bin/pmemd.MPI "$@"
+/opt/amber/bin/pmemd.MPI "$@"
 
 exit 0
diff --git a/pmemd.cuda b/pmemd.cuda
new file mode 100755
index 000000000000..42d9312d33e8
--- /dev/null
+++ b/pmemd.cuda
@@ -0,0 +1,7 @@
+#!/usr/bin/bash
+
+export _gccver=8.4.0
+export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
+/opt/amber/bin/pmemd.cuda_SPFP "$@"
+
+exit 0
diff --git a/pmemd.cuda.MPI b/pmemd.cuda.MPI
new file mode 100755
index 000000000000..27f9e3ce7206
--- /dev/null
+++ b/pmemd.cuda.MPI
@@ -0,0 +1,7 @@
+#!/usr/bin/bash
+
+export _gccver=8.4.0
+export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
+/opt/amber/bin/pmemd.cuda_SPFP.MPI "$@"
+
+exit 0