From 6342930c01e8b0c1eb2d110a9aced969c2a9b95e Mon Sep 17 00:00:00 2001
From: nadyawilliams <nadya@sdsc.edu>
Date: Fri, 6 Nov 2015 13:32:13 -0800
Subject: [PATCH] add info about GaMD patch build

---
 GaMD-diffs | 117 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 README.rst |  20 +++++++++
 2 files changed, 137 insertions(+)
 create mode 100644 GaMD-diffs

diff --git a/GaMD-diffs b/GaMD-diffs
new file mode 100644
index 0000000..41edccb
--- /dev/null
+++ b/GaMD-diffs
@@ -0,0 +1,117 @@
+diff --git a/src/amber-modules/amber.module.in b/src/amber-modules/amber.module.in
+index 2d5a1ef..b6399b7 100644
+--- a/src/amber-modules/amber.module.in
++++ b/src/amber-modules/amber.module.in
+@@ -7,17 +7,17 @@
+ proc ModulesHelp { } {
+         global amberversion 
+ 
+-        puts stderr "\tAmber Tools from /opt/amber/@COMPILERNAME@/@ROLLNETWORK@"
++        puts stderr "\tGaMD patched Amber Tools from /opt/amberGaMD/@COMPILERNAME@/@ROLLNETWORK@"
+         puts stderr "\tAmber Toolkit Version $amberversion\n"
+ }
+ 
+-module-whatis   "Amber Toolkit Version @VERSION@"
++module-whatis   "GaMD patched Amber Toolkit Version @VERSION@"
+ module-whatis   "Compiled with @COMPILERNAME@ compiler"
+ 
+ # for Tcl script use only
+ set     amberversion @VERSION@
+ 
+-set amberHome /opt/amber/@COMPILERNAME@/@ROLLNETWORK@
++set amberHome /opt/amberGaMD/@COMPILERNAME@/@ROLLNETWORK@
+ setenv AMBERHOME $amberHome
+ prepend-path PATH $amberHome/bin
+ prepend-path LD_LIBRARY_PATH $amberHome/lib
+
+diff --git a/src/amber-modules/version.mk b/src/amber-modules/version.mk
+index aaa0f1c..2d416e1 100644
+--- a/src/amber-modules/version.mk
++++ b/src/amber-modules/version.mk
+@@ -23,9 +23,9 @@ VERSION.MK.MASTER.DIR = ../amber
+ VERSION.MK.INCLUDE = amber.version.mk
+ include $(VERSION.MK.INCLUDE) 
+ 
+-PACKAGE     = amber
++PACKAGE     = amberGaMD
+ CATEGORY    = applications
+-NAME        = amber-module-$(COMPILERNAME)-$(ROLLNETWORK)
++NAME        = amberGaMD-module-$(COMPILERNAME)-$(ROLLNETWORK)
+ RELEASE     = 0
+ PKGROOT     = /opt/modulefiles/$(CATEGORY)/$(PACKAGE)$(VERSION)
+ 
+diff --git a/src/amber/Makefile b/src/amber/Makefile
+index 6363d5a..fbeb2a9 100644
+--- a/src/amber/Makefile
++++ b/src/amber/Makefile
+@@ -42,6 +42,7 @@ build:
+ 	  export AMBERHOME=`pwd`/$(SOURCE_DIR); \
+ 	  cd $${AMBERHOME}; pwd ; \
+ 	  ./update_amber --update ; \
++	  patch -p0 < ../amber14_GaMD_patch_confidential.txt ; \
+ 	  ./configure $(ROLLCOMPILER); \
+ 	  make -j8 install;  make clean; \
+ 	  ./configure -mpi $(ROLLCOMPILER); \
+
+diff --git a/src/amber/version.mk b/src/amber/version.mk
+index e5177ba..fb8972c 100644
+--- a/src/amber/version.mk
++++ b/src/amber/version.mk
+@@ -8,7 +8,7 @@ ifndef ROLLNETWORK
+   ROLLNETWORK = eth
+ endif
+ 
+-NAME	    = amber-$(COMPILERNAME)-$(ROLLNETWORK)
++NAME	    = amberGaMD-$(COMPILERNAME)-$(ROLLNETWORK)
+ VERSION	    = 14
+ RELEASE	    = 0
+ SUFFIX      = tar.bz2
+@@ -22,7 +22,7 @@ TOOLSVERSION = 15
+ TOOLS_PKG   = $(TOOLS_NAME)$(TOOLSVERSION).$(SUFFIX)
+ TOOLS_DIR   = $(TOOLS_PKG:%.$(SUFFIX)=%)
+ 
+-PKGROOT     = /opt/amber/$(COMPILERNAME)/$(ROLLNETWORK)
++PKGROOT     = /opt/amberGaMD/$(COMPILERNAME)/$(ROLLNETWORK)
+ CUDAHOME    = /opt/cuda
+ 
+ RPM.EXTRAS = AutoReq:No
+
+diff --git a/version.mk b/version.mk
+index e940c46..f98e27a 100644
+--- a/version.mk
++++ b/version.mk
+@@ -1,4 +1,4 @@
+-ROLLNAME = amber
++ROLLNAME = amberGaMD
+ RELEASE  = 0
+ COLOR    = DarkTurquoise
+ 
+--- amber-common.xml.in	2015-11-06 13:10:46.860867993 -0800
++++ amberGaMD-common.xml.in	2015-09-16 09:13:49.198369090 -0700
+@@ -15,9 +15,8 @@
+ 	<changelog>
+ 	</changelog>
+ 
+-	<package>amber-ROLLCOMPILER-ROLLNETWORK</package>
+-	<package>amber-module-ROLLCOMPILER-ROLLNETWORK</package>
+-	<package>amber-roll-test</package>
++	<package>amberGaMD-ROLLCOMPILER-ROLLNETWORK</package>
++	<package>amberGaMD-module-ROLLCOMPILER-ROLLNETWORK</package>
+ 
+ <post>
+ </post>
+
+--- amber.xml	2015-11-06 13:11:12.969386574 -0800
++++ amberGaMD.xml	2015-09-16 10:21:23.816037723 -0700
+@@ -15,9 +15,9 @@
+ 	<changelog>
+ 	</changelog>
+ 
+-	<edge from="base" to="amber-common"/>
++	<edge from="base" to="amberGaMD-common"/>
+ 	<order head="base">
+-		<tail>amber-common</tail>
++		<tail>amberGaMD-common</tail>
+ 	</order>
+ 
+ </graph>
diff --git a/README.rst b/README.rst
index e010513..fa8072b 100644
--- a/README.rst
+++ b/README.rst
@@ -70,6 +70,26 @@ Tthe roll installs amber and environment module files in: ::
     /opt/amber/benchmark/Amber14_Benchmark_Suite.tar.bz2 - benchmark suit distro
 
 
+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 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 patch to src/amber/ (patch received via email from author, source )
+
+See diffs for the above files in GaMD-diffs file at the top of the roll.
+After creating changes build `amberGaMD` roll
+
 **Testing**
 
 A test script ``amber.t`` can be run to verify proper