per GaMD update 20160104 from author

.gitignore

@@ -0,0 +1,25 @@
+# build directory
+RPMS/
+SOURCES/
+BUILD/
+SPECS/
+disk*/
+*.iso
+
+_os
+_arch
+_distribution
+.rpmmacros
+
+# ignore version, rules  files
+Rules-*.mk
+Rules.mk
+Rolls.mk
+roll*.mk
+rocks-*.mk
+
+# ignore protected src files
+src/amber/*bz2
+src/amber/*tgz
+src/amber/amber14_GaMD_patch*
+

DESCRIPTION

@@ -0,0 +1 @@
+GaMD patched AMBER Molecular Dynamics Package

Makefile

@@ -0,0 +1,100 @@
+#
+# Makefile
+#
+# @Copyright@
+# 
+# 				Rocks(r)
+# 		         www.rocksclusters.org
+# 		         version 6.2 (SideWinder)
+# 
+# Copyright (c) 2000 - 2014 The Regents of the University of California.
+# All rights reserved.	
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+# 
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# 
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice unmodified and in its entirety, this list of conditions and the
+# following disclaimer in the documentation and/or other materials provided 
+# with the distribution.
+# 
+# 3. All advertising and press materials, printed or electronic, mentioning
+# features or use of this software must display the following acknowledgement: 
+# 
+# 	"This product includes software developed by the Rocks(r)
+# 	Cluster Group at the San Diego Supercomputer Center at the
+# 	University of California, San Diego and its contributors."
+# 
+# 4. Except as permitted for the purposes of acknowledgment in paragraph 3,
+# neither the name or logo of this software nor the names of its
+# authors may be used to endorse or promote products derived from this
+# software without specific prior written permission.  The name of the
+# software includes the following terms, and any derivatives thereof:
+# "Rocks", "Rocks Clusters", and "Avalanche Installer".  For licensing of 
+# the associated name, interested parties should contact Technology 
+# Transfer & Intellectual Property Services, University of California, 
+# San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, 
+# Ph: (858) 534-5815, FAX: (858) 534-7345, E-MAIL:invent@ucsd.edu
+# 
+# THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS''
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS
+# BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+# IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# 
+# @Copyright@
+#
+
+ifndef ROLLCOMPILER
+  ROLLCOMPILER = gnu
+endif
+ifndef ROLLMPI
+  ROLLMPI = openmpi
+endif
+ifndef ROLLNETWORK
+  ROLLNETWORK = eth
+endif
+
+-include $(ROLLSROOT)/etc/Rolls.mk
+
+preroll::
+	# Copy and substitute lines of nodes/*.xml.in that reference 
+	# ROLLCOMPILER, ROLLNETWORK, and ROLLMPI, making one line copy for each variable value
+	for i in `ls nodes/*.in`; do \
+	  export o=`echo $$i | sed 's/\.in//'`; \
+	  cp $$i $$o; \
+	  for c in $(ROLLCOMPILER); do \
+	    perl -pi -e 'print and s/ROLLCOMPILER/'$${c}'/g if m/ROLLCOMPILER/' $$o; \
+	  done; \
+	  for n in $(ROLLNETWORK); do \
+	    perl -pi -e 'print and s/ROLLNETWORK/'$${n}'/g if m/ROLLNETWORK/' $$o; \
+	  done; \
+	  for m in $(ROLLMPI); do \
+	    perl -pi -e 'print and s/ROLLMPI/'$${m}'/g if m/ROLLMPI/' $$o; \
+	  done; \
+	  perl -pi -e '$$_ = "" if m/ROLL(COMPILER|NETWORK|MPI)/' $$o; \
+	done
+
+default:
+	$(MAKE) ROLLCOMPILER="$(ROLLCOMPILER)" ROLLNETWORK="$(ROLLNETWORK)" ROLLMPI="$(ROLLMPI)" roll
+
+clean::
+	rm -f _arch bootstrap.py
+
+cvsclean: clean
+	for i in `ls nodes/*.in`; do \
+	  export o=`echo $$i | sed 's/\.in//'`; \
+	  rm -f $$o; \
+	done
+	rm -rf RPMS SRPMS
+	rm -rf build.log 

README.rst

@@ -0,0 +1,91 @@
+.. hightlight:: rst
+
+AMBER Roll
+================
+AMBER Molecular Dynamics
+
+.. contents::
+
+Introduction
+--------------
+This roll installs AMBER tools. 
+There are 4 flavors compiled for each compiler (gnu, intel): ::
+
+    serial,
+    mpi
+    cuda
+    cuda mpi
+
+Downloads
+-----------
+Amber is a licensed software. Get licensed files for AMBAER and AmberTools from 
+amber roll and  put source files in ``src/amber``.
+Download GaMD patches (provided by developer Yinglong Miao): :: 
+
+     amber14_GaMD_patch_confidential.txt  
+     amber14-gamd-updates-20160104.tgz  
+
+Building the roll
+------------------
+**Dependencies**
+
+- The ``mpi`` roll must be installed on the build/install host. 
+  depends on mpi libraries. 
+- The ``cuda`` roll must be installed on build/install host . In the absence of cuda, edit 
+  ``src/amber/Makefile``  targets to remove cuda-specific compilation.
+- The roll sources assumes that modulefiles provided by ``intel``, ``cuda`` and ``mpi``
+  rolls are available.
+
+The roll uses ``openmpi`` compiled with ``gnu`` compiler for ``eth`` fabric. 
+To make a roll use the following command: ::
+
+    # make ROLLCOMPILER='gnu' ROLLMPI='openmpi'  ROLLNETWORK='eth' 2>&1 | tee build.log
+
+or simply ::
+
+    # make  2>&1 | tee build.log
+
+A successful build will create the file ``amberGaMD-*.disk1.iso``.  
+
+Installing
+-------------
+
+To install, execute these instructions on a Rocks frontend: ::
+
+    # rocks add roll amberGaMD*.iso
+    # rocks enable roll amberGaMD
+    # (cd /export/rocks/install; rocks create distro)
+    # rocks run roll amberGaMD > add-amberGaMD.sh
+    # bash add-amberGaMD.sh
+    
+Rebuild the compute nodes or :: 
+
+    # rocks run host compute "yum clean all; yum install amberGaMD-gnu-eth amberGaMD-module-gnu-eth"
+
+
+What is installed
+-------------------
+
+The roll installs GaMD patched amber14 (AmberTools15)  and environment module files in: ::
+
+    /opt/amberGaMD/gnu - compiled with GNU
+    /opt/modulefiles/applications/amberGaMD<VERSION> - environment modules
+
+
+Building GaMD version of roll
+-----------------------------
+
+For Sep 2015 workshop  buid `amberGaMD` roll based on a received patch for amber14 source 
+Create the following changes to the amber roll source: ::
+
+       modified:   src/amber-modules/amber.module.in
+       modified:   src/amber-modules/version.mk
+       modified:   src/amber/Makefile
+       modified:   src/amber/version.mk
+       modified:   version.mk
+
+       replace in graphs/default: amber.xml with amberGaMD.xml
+       replace in nodes: amber-common.xml.in with amberGaMD-common.xml.in
+
+       add a GaMD patch/distro to src/amber/ (patch received via email from author, source )
+

graphs/default/amberGaMD.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0" standalone="no"?>
+
+<graph>
+
+	<description>
+	AMBER Molecular Dynamics Package
+	http://ambermd.org
+	</description>
+
+	<copyright>
+	Copyright (c) 2000 - 2014 The Regents of the University of California.
+	All rights reserved. Rocks(r) 6.2 www.rocksclusters.org
+	</copyright>
+
+	<changelog>
+	</changelog>
+
+	<edge from="base" to="amberGaMD-common"/>
+	<order head="base">
+		<tail>amberGaMD-common</tail>
+	</order>
+
+</graph>

nodes/amberGaMD-common.xml.in

@@ -0,0 +1,24 @@
+<?xml version="1.0" standalone="no"?>
+
+<kickstart>
+
+	<description>
+	AMBER Molecular Dynamics 
+	http://ambermd.org
+	</description>
+
+	<copyright>
+	Copyright (c) 2000 - 2014 The Regents of the University of California.
+	All rights reserved. Rocks(r) 6.2 www.rocksclusters.org
+	</copyright>
+
+	<changelog>
+	</changelog>
+
+	<package>amberGaMD-ROLLCOMPILER-ROLLNETWORK</package>
+	<package>amberGaMD-module-ROLLCOMPILER-ROLLNETWORK</package>
+
+<post>
+</post>
+
+</kickstart>

src/Makefile

@@ -0,0 +1,87 @@
+# $Id$
+#
+# @Copyright@
+# 
+# 				Rocks(r)
+# 		         www.rocksclusters.org
+# 		         version 6.2 (SideWinder)
+# 
+# Copyright (c) 2000 - 2014 The Regents of the University of California.
+# All rights reserved.	
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+# 
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# 
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice unmodified and in its entirety, this list of conditions and the
+# following disclaimer in the documentation and/or other materials provided 
+# with the distribution.
+# 
+# 3. All advertising and press materials, printed or electronic, mentioning
+# features or use of this software must display the following acknowledgement: 
+# 
+# 	"This product includes software developed by the Rocks(r)
+# 	Cluster Group at the San Diego Supercomputer Center at the
+# 	University of California, San Diego and its contributors."
+# 
+# 4. Except as permitted for the purposes of acknowledgment in paragraph 3,
+# neither the name or logo of this software nor the names of its
+# authors may be used to endorse or promote products derived from this
+# software without specific prior written permission.  The name of the
+# software includes the following terms, and any derivatives thereof:
+# "Rocks", "Rocks Clusters", and "Avalanche Installer".  For licensing of 
+# the associated name, interested parties should contact Technology 
+# Transfer & Intellectual Property Services, University of California, 
+# San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, 
+# Ph: (858) 534-5815, FAX: (858) 534-7345, E-MAIL:invent@ucsd.edu
+# 
+# THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS''
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS
+# BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+# IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# 
+# @Copyright@
+#
+
+-include $(shell ${ROCKSROOT}/bin/arch).mk
+-include $(shell ${ROCKSROOT}/bin/os).mk
+
+MPI_FLAVORS = openmpi
+
+default:
+	@echo "copyright|rpm|pkg|clean"
+
+copyright rpm pkg clean::
+	for i in $(SRCDIRS); do \
+	  i=`echo $$i | sed 's/^\.\///'`; \
+	  flavor=`echo $$i | sed 's/-modules//'`; \
+	  echo $(MPI_FLAVORS) | grep -q "\<$$flavor\>"; \
+	  if test $$? -eq 0; then \
+	    echo $(ROLLMPI) | grep -q "\<$$flavor\>"; \
+	    if test $$? -ne 0; then \
+	      continue; \
+	    fi; \
+	  fi; \
+	  grep -q ROLLCOMPILER $$i/version.mk; \
+	  if test $$? -eq 0; then \
+	    for c in $(ROLLCOMPILER); do \
+	      for n in $(ROLLNETWORK); do \
+	        echo make $@ in $$i with ROLLCOMPILER=$$c ROLLNETWORK=$$n; \
+	        (cd $$i && $(MAKE) ROLLCOMPILER=$$c ROLLNETWORK=$$n $@) || exit 2; \
+	      done; \
+	    done; \
+	  else \
+	    (cd $$i && $(MAKE) ROLLCOMPILER="$(ROLLCOMPILER)" ROLLNETWORK="$(ROLLNETWORK)" $@) || exit 2; \
+	  fi; \
+	done