diff --git a/doc/README.md b/doc/README.md
index 2e361bb2fabfa8c64fae504a69b59077a30fdb7f..024eedb51dc7a63bdd71f6ebaa7922a52f5b1b48 100644
--- a/doc/README.md
+++ b/doc/README.md
@@ -2,8 +2,8 @@ APARAPI Documentation
======================
-* [PrivateMemorySpace](privatememoryspace.md) Using __private memory space in Aparapi kernels.
-* [SettingUpLinuxHSAMachineForAparapi](settinguplinuxhsamachineforaparapi.md) How to setup a Linux HSA machine for testing HSA enabled Aparapi
+| [PrivateMemorySpace](privatememoryspace.md)| Using `__private` memory space in Aparapi kernels. |
+| [SettingUpLinuxHSAMachineForAparapi](settinguplinuxhsamachineforaparapi.md) | How to setup a Linux HSA machine for testing HSA enabled Aparapi |
* PossibleAparapiLambdaSyntaxOptions syntax suggestions for HSA enabled Aparapi Mar 2014 frost.g...@gmail.com
* HSAEnablementOfLambdaBranchSidebar Sidebar for HSAEnablementOfLambdaBranchAparapi Feb 2014 frost.g...@gmail.com
* HSAEnablementOfLambdaBranch Adding HSA Support to Aparapi lambda branch Feb 2014 frost.g...@gmail.com
diff --git a/doc/privatememoryspace.md b/doc/privatememoryspace.md
index 8c4d304255884134d918b38c296126a38dbc4744..1901c02094e9973feef0ec51ed4cb4fe5f0b9191 100644
--- a/doc/privatememoryspace.md
+++ b/doc/privatememoryspace.md
@@ -9,10 +9,10 @@ The private memory space is generally only suitable for smallish arrays, but is
##Details
In Aparapi there are two mechanisms available to mark a Kernel class member as belonging to the private memory space when mapped to OpenCL code (matching the equivalent functionality for marking items as belonging to the local memory space). Either the field can be named with a suffix plus buffer size, for example
-> protected short[] myBuffer_$private$32 = new short[32];
+ protected short[] myBuffer_$private$32 = new short[32];
or using the Annotation Kernel.PrivateMemorySpace, for example
-> protected @PrivateMemorySpace(32) short[] myBuffer = new short[32];
+ protected @PrivateMemorySpace(32) short[] myBuffer = new short[32];
The latter should be used in preference to the former.
Note that OpenCL requires that the size of a private array be fixed at compile time for any kernel. Thus it is not possible for a single Kernel subclass to support private buffers of varying size. Unfortunately this may entail creating multiple subclasses with varying buffer sizes in order to most efficiently support varying private buffer sizes.
diff --git a/doc/settinguplinuxhsamachineforaparapi.md b/doc/settinguplinuxhsamachineforaparapi.md
index cd6ccba95f565ecfbb817471df3dbbb54f9dc3e4..14353654a23402946b6a3956a20d34ed2b7a0da8 100644
--- a/doc/settinguplinuxhsamachineforaparapi.md
+++ b/doc/settinguplinuxhsamachineforaparapi.md
@@ -10,18 +10,22 @@ But for Aparapi users the main advantage is that we are no longer limited to the
##Hardware Required
These instructions were based on my experience setting up a platform using the following hardware.
-Component Suggested
-APU AMD A10-7850K APU http://www.amd.com/us/products/desktop/processors/a-series/Pages/a-series-apu.aspx
-Motherboard ASUS A88X-PRO or A88XM-A http://www.asus.com/Motherboards/A88XPRO http://www.asus.com/Motherboards/A88XMA
-Memory G.SKILL Ripjaws X Series 16GB (2 x 8GB) 240-Pin DDR3 SDRAM DDR3 2133
-Software Required
+|Component | Suggested |
+|-----------|-------------------------------------------------------------------------------------------------------------|
+|APU | AMD A10-7850K APU [http://www.amd.com/us/products/desktop/processors/a-series/Pages/a-series-apu.aspx](http://www.amd.com/us/products/desktop/processors/a-series/Pages/a-series-apu.aspx) |
+| Motherboard | ASUS A88X-PRO or A88XM-A [http://www.asus.com/Motherboards/A88XPRO http://www.asus.com/Motherboards/A88XMA](http://www.asus.com/Motherboards/A88XPRO http://www.asus.com/Motherboards/A88XMA) |
+|Memory | G.SKILL Ripjaws X Series 16GB (2 x 8GB) 240-Pin DDR3 SDRAM DDR3 2133 |
+
+##Software Required
We also have some software dependencies.
-Component Suggested
-Java 8 JDK http://www.oracle.com/technetwork/java/javase/downloads/ea-jsp-142245.html
-Ubuntu 13.10 64-bit edition http://www.ubuntu.com/download
-Ubuntu 13.10 64-bit edition HSA enabled kernel image https://github.com/HSAFoundation/Linux-HSA-Drivers-And-Images-AMD
-OKRA HSA enabled runtime https://github.com/HSAFoundation/Okra-Interface-to-HSA-Device
+|Component | Suggested |
+|-------------------------------------------------------|------------------------------------------------------------------------------|
+|Java 8 JDK | http://www.oracle.com/technetwork/java/javase/downloads/ea-jsp-142245.html |
+| Ubuntu 13.10 64-bit edition | http://www.ubuntu.com/download |
+| Ubuntu 13.10 64-bit edition HSA enabled kernel image | https://github.com/HSAFoundation/Linux-HSA-Drivers-And-Images-AMD |
+| OKRA HSA enabled runtime | https://github.com/HSAFoundation/Okra-Interface-to-HSA-Device |
+
The hope is that the list of HW/SW support widens, but for early adopters this is the set of HW/SW we have been testing with.
##Setting up your System
@@ -33,42 +37,38 @@ Remember HSA allows the GPU and CPU cores to share the same memory. IOMMU needs
##For the A88X-PRO board
For the recommended ASUS board above you will need to make sure that your BIOS is updated to version 0802. Here is a direct link to the 0802 version of the BIOS from ASUS's site as of 2/28/2014.
-http://dlcdnet.asus.com/pub/ASUS/mb/SocketFM2/A88X-PRO/A88X-PRO-ASUS-0802.zip
+[http://dlcdnet.asus.com/pub/ASUS/mb/SocketFM2/A88X-PRO/A88X-PRO-ASUS-0802.zip](http://dlcdnet.asus.com/pub/ASUS/mb/SocketFM2/A88X-PRO/A88X-PRO-ASUS-0802.zip)
Once you have the latest BIOS you will need to enable IOMMU in the system BIOS. This is done using the "CPU Configuration" screen under "Advanced Mode" and then enabling IOMMU.
##For the A88XM-A
You will need the 1102 (or later) version of the BIOS
-http://dlcdnet.asus.com/pub/ASUS/mb/SocketFM2/A88XM-A/A88XM-A-ASUS-1102.zip
+[http://dlcdnet.asus.com/pub/ASUS/mb/SocketFM2/A88XM-A/A88XM-A-ASUS-1102.zip](http://dlcdnet.asus.com/pub/ASUS/mb/SocketFM2/A88XM-A/A88XM-A-ASUS-1102.zip)
Once you have the latest BIOS you will need to enable IOMMU in the system BIOS. This is done using the "CPU Configuration" screen under "Advanced Mode" and then enabling IOMMU.
##Installing Ubuntu 13.10
-Once you have your BIOS setup you need to install Ubuntu http://www.ubuntu.com/download
+Once you have your BIOS setup you need to install Ubuntu [http://www.ubuntu.com/download](http://www.ubuntu.com/download)
Installing HSA enabled kernel + driver
Until all of the HSA drivers and features are available in stock linux and have been pulled down into Ubuntu distro we will need a special HSA enabled kernel image.
A Ubuntu compatible kernel can be pulled from github
->$ cd ~ # I put all of this in my home dir
-
->$ sudo apt-get install git
-
->$ git clone https://github.com/HSAFoundation/Linux-HSA-Drivers-And-Images-AMD.git
+ $ cd ~ # I put all of this in my home dir
+ $ sudo apt-get install git
+ $ git clone https://github.com/HSAFoundation/Linux-HSA-Drivers-And-Images-AMD.git
Or you can pull the zip and unzip using curl if you don't have git
->$ cd ~ # I put all of this in my home dir
-
->$ curl -L https://github.com/HSAFoundation/Linux-HSA-Drivers-And-Images-AMD/archive/master.zip > drivers.zip
-
->$ unzip drivers.zip
+ $ cd ~ # I put all of this in my home dir
+ $ curl -L https://github.com/HSAFoundation/Linux-HSA-Drivers-And-Images-AMD/archive/master.zip > drivers.zip
+ $ unzip drivers.zip
This will create the following subdir on your machine
-> Linux-HSA-Drivers-And-Images-AMD/
+ Linux-HSA-Drivers-And-Images-AMD/
LICENSE
README.md
ubuntu12.10-based-alpha1/
@@ -78,29 +78,29 @@ This will create the following subdir on your machine
From here we can install our new image and setup the HSA KFD (the driver for HSA)and reboot to the new kernel.
->$ cd ~/Linux-HSA-Drivers-And-Images-AMD
-$ echo "KERNEL==\"kfd\", MODE=\"0666\"" | sudo tee /etc/udev/rules.d/kfd.rules
-$ sudo dpkg -i ubuntu13.10-based-alpha1/linux-image-3.13.0-kfd+_3.13.0-kfd+-2_amd64.deb
-$ sudo cp ~/Linux-HSA-Drivers-And-Images-AMD/ubuntu13.10-based-alpha1/xorg.conf /etc/X11
-$ sudo reboot
+ $ cd ~/Linux-HSA-Drivers-And-Images-AMD
+ $ echo "KERNEL==\"kfd\", MODE=\"0666\"" | sudo tee /etc/udev/rules.d/kfd.rules
+ $ sudo dpkg -i ubuntu13.10-based-alpha1/linux-image-3.13.0-kfd+_3.13.0-kfd+-2_amd64.deb
+ $ sudo cp ~/Linux-HSA-Drivers-And-Images-AMD/ubuntu13.10-based-alpha1/xorg.conf /etc/X11
+ $ sudo reboot
##Installing OKRA RT
Now we need a runtime for executing HSAIL code. We share common infrastructure used by our sister OpenJDK project called Sumatra. Both Aparapi and Sumatra use OKRA to execute HSAIL code on a HSA enabled platform.
We can get the latest version using of OKRA (Offloadable Kernel Runtime API) from another HSA foundation repository.
->$ cd ~ # I put all of this in my home dir
-$ git clone https://github.com/HSAFoundation/Okra-Interface-to-HSA-Device.git
+ $ cd ~ # I put all of this in my home dir
+ $ git clone https://github.com/HSAFoundation/Okra-Interface-to-HSA-Device.git
or if you prefer curl/unzip
->$ cd ~ # I put all of this in my home dir
-$ curl -L https://github.com/HSAFoundation/Okra-Interface-to-HSA-Device/archive/master.zip > okra.zip
-$ unzip okra.zip
+ $ cd ~ # I put all of this in my home dir
+ $ curl -L https://github.com/HSAFoundation/Okra-Interface-to-HSA-Device/archive/master.zip > okra.zip
+ $ unzip okra.zip
This will create the following dir structure.
-> Okra-Interface-to-HSA-Device/
+ Okra-Interface-to-HSA-Device/
README.md
okra/
README
@@ -125,8 +125,8 @@ OKRA offers a C API (for those that are so inclined ;) ) as well as a java jar f
##Sanity check your HSA and OKRA install
So to sanity check your install you can run a small sample app (binary)
->$ cd ~/Okra-Interface-to-HSA-Device/okra/samples/
-$ sh runSquares.sh
+ $ cd ~/Okra-Interface-to-HSA-Device/okra/samples/
+ $ sh runSquares.sh
If everything is OK this should run the C Squares test app.
@@ -135,54 +135,54 @@ Congratulations, you have executed your first HSA enabled app.
##Getting OpenCL headers and libraries
We need OpenCL headers and libraries to build Aparapi (remember we still support OpenCL).
-My recommendation is to download AMD-APP-SDK-v2.9-lnx64.tgz from http://developer.amd.com/tools-and-sdks/heterogeneous-computing/amd-accelerated-parallel-processing-app-sdk/downloads and extract the libraries and headers.
+My recommendation is to download AMD-APP-SDK-v2.9-lnx64.tgz from [http://developer.amd.com/tools-and-sdks/heterogeneous-computing/amd-accelerated-parallel-processing-app-sdk/downloads](http://developer.amd.com/tools-and-sdks/heterogeneous-computing/amd-accelerated-parallel-processing-app-sdk/downloads) and extract the libraries and headers.
Note that we have nested zipped jars in this archive.
->$ cd ~
-$ gunzip ~/Downloads/AMD-APP-SDK-v2.9-lnx64.tgz
-$ tar xvf ~/Downloads/AMD-APP-SDK-v2.9-lnx64.tar
-$ rm ~/default-install_lnx_64.pl ~/icd-registration.tgz ~/Install-AMD-APP.sh ~/ReadMe.txt
-$ gunzip ~/AMD-APP-SDK-v2.9-RC-lnx64.tgz
-$ tar xvf ~/AMD-APP-SDK-v2.9-RC-lnx64.tar
-$ rm ~/AMD-APP-SDK-v2.9-RC-lnx64.tar
-$ rm -rf AMD-APP-SDK-v2.9-RC-lnx64/samples
+ $ cd ~
+ $ gunzip ~/Downloads/AMD-APP-SDK-v2.9-lnx64.tgz
+ $ tar xvf ~/Downloads/AMD-APP-SDK-v2.9-lnx64.tar
+ $ rm ~/default-install_lnx_64.pl ~/icd-registration.tgz ~/Install-AMD-APP.sh ~/ReadMe.txt
+ $ gunzip ~/AMD-APP-SDK-v2.9-RC-lnx64.tgz
+ $ tar xvf ~/AMD-APP-SDK-v2.9-RC-lnx64.tar
+ $ rm ~/AMD-APP-SDK-v2.9-RC-lnx64.tar
+ $ rm -rf AMD-APP-SDK-v2.9-RC-lnx64/samples
Note where AMD-APP-SDK-v2.9-RC-lnx64 is located, you need this in the following step.
##You will need Java 8
-Download Java 8 JDK from https://jdk8.java.net/download.html I chose to download the zipped tar and not install with RPM so I can control the location of the install.
+Download Java 8 JDK from [https://jdk8.java.net/download.html](https://jdk8.java.net/download.html) I chose to download the zipped tar and not install with RPM so I can control the location of the install.
->$ cd ~
-$ gunzip /home/gfrost/Downloads/jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz
-$ tar xvf ~/Downloads/jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar
+ >$ cd ~
+ $ gunzip /home/gfrost/Downloads/jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz
+ $ tar xvf ~/Downloads/jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar
I now have ~/jdk1.8.0 as my java 8 install dir.
Alternatively the following will pull from Oracles site using curl
->$ cd ~
-$ curl http://download.java.net/jdk8/archive/b132/binaries/jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz?q=download/jdk8/archive/b132/binaries/jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz > jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz
-$ gunzip jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz
-$ tar xvf jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar
+ $ cd ~
+ $ curl http://download.java.net/jdk8/archive/b132/binaries/jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz?q=download/jdk8/archive/b132/binaries/jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz > jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz
+ $ gunzip jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar.gz
+ $ tar xvf jdk-8-fcs-bin-b132-linux-x64-04_mar_2014.tar
I now have ~/jdk1.8.0 as my java 8 install dir.
You will need ant
->$ sudo apt-get install ant
+ $ sudo apt-get install ant
This takes a long time because in also installs a java7 jdk.
You will need g++
We use g++ to build the JNI side of Aparapi
->$ sudo apt-get install g++
+ $ sudo apt-get install g++
##Pulling the HSA enabled Aparapi branch and building
Now we can pull the Aparapi lambda/HSA branch from SVN
->$ sudo apt-get install subversion
-$ svn checkout https://aparapi.googlecode.com/svn/branches/lambda aparapi-lambda
+ $ sudo apt-get install subversion
+ $ svn checkout https://aparapi.googlecode.com/svn/branches/lambda aparapi-lambda
If you are familiar with Aparapi structure then this tree should not be that much of a surprise but there are a few subtle changes.
@@ -201,13 +201,13 @@ Here are how I set my vars.
It is recommended (thanks notzed ;) ) that you test your env.sh using sh env.sh until it stops reporting errors. Once you have finished I recommend sourcing it into your current shell before building with ant.
->$ cd ~aparapi-lambda
-$ . env.sh
-$ ant
+ $ cd ~aparapi-lambda
+ $ . env.sh
+ $ ant
If you get any problems check the env.sh vars first.
If all is well you should be able to run some samples.
->$ cd ~/aparapi-lambda/samples/mandel
-$ sh hsailmandel.sh
\ No newline at end of file
+ $ cd ~/aparapi-lambda/samples/mandel
+ $ sh hsailmandel.sh
\ No newline at end of file