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add info about GaMD patch build
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nadyawilliams committed Nov 6, 2015
1 parent d7dd94e commit 6342930
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117 changes: 117 additions & 0 deletions GaMD-diffs
Original file line number Diff line number Diff line change
@@ -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>
20 changes: 20 additions & 0 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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
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