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Accelerating HPC: Installing and Running nVidia CUDA
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Accelerating HPC: Installing and Running nVidia CUDA

by deadline
Published on February 26th, 2010 02:43 AM 0 Comments
A low cost tutorial on how to install and evaluate the CUDA environment

Experimenting with a new technology always takes time. If the technology is plug-and-play (like an Ethernet switch) it is often easy to install and test it. If, however, the technology is more hands-on (like a new programming language), then a more detailed analysis is warranted. Indeed, a new programming paradigm often means that there are two tasks involved in the evaluation. The first is finding the right hardware/software platform and installing the software. The second task is actually sitting down and trying out some new things. Obviously the second task requires the first task to be complete before you can "play with the software."

In some cases downloading a new software tool is as simple as installing an RPM or similar package on your Linux box. In other cases, if the software is designed for multi-core or GP-GPU processing then it is important to make sure you have the right hardware. In still other cases, specific versions of Linux or libraries may be required in order for the software to work. In this article, we will be discussing how to install the nVidia CUDA software suite on standard desktop hardware. For some this step can be challenging because it requires assembling and installing both hardware and software, so this article will help with your first steps. In terms of cost, the nVidia software is freely available as are some of the supported versions of Linux. You may have to scrounge a bit to find some hardware, but the CUDA toolkit works on many existing nVidia graphics cards.

Once you get everything working, you will be able to run programs like the mandelbrot example. Using this program allows you to compare the difference between the GPU and the CPU. Plus you get to look at pretty pictures like those in Figure One below. While this level of experimentation does not utilize a cluster, it is a great (and inexpensive) way to learn about GP-GPU computing, which is becoming popular in many HPC circles.



Hardware Setup

One of the advantages with the nVidia CUDA software is that it will work on many older video cards. For testing purposes this is a big advantage as there is no need to buy a new $250+ video card to try CUDA programming. The nVidia website states that CUDA will work with GeForce 8, 9, 100, 200-series GPUs with a minimum of 256MB of local graphics memory. To check that your video card will work, go to the CUDA GPUs web page and check for you model. For this article, I am using a rather old GeForce 8500 GT. The specifications are given in Table One below.

CUDA Cores 16
Core Clock (MHz) 450
Shader Clock (MHz) 900
Memory Clock (MHz) 400
Memory Amount 512MB DDR2
Memory Interface 128-bit
Memory Bandwidth (GB/sec) 12.8
Texture Fill Rate (billion/sec) 3.6


Table One: GeForce 8500 GT specification

As you can see the specifications are a bit lacking by todays standards. In particular, the 8500 GT only has 16 CUDA cores. While this is certainly not enough for production work, it is enough to test and play with the CUDA toolkit. Indeed, the scalable nature of CUDA applications means that I can develop on my existing hardware and then move to a much large number of CUDA cores with no re-programming

My host processor is an Intel Core2 Duo Model 6400 (2.1 GHz) with 2 GB or memory and a GigByte GA 945GM motherboard. Again, nothing spectacular by todays hardware standards, but that is the point. There is no need to buy new hardware to test CUDA software.

Software Setup

I had previously installed Fedora 8 on the test hardware and the new version of CUDA (Version 2.3) requires Fedora 10. Not being one to make extra work for myself, I decided to upgrade my Fedora version and keep everything within the nVidia recommend environment. CUDA 2.3 also supports Red Hat Enterprise Linux 4.3-4.7, or 5.0-5.3, and SUSE Enterprise Desktop 10-SP2 or 11, or Open SUSE 11, or Ubuntu 8.10 or 9.04

A note about upgrading Fedora. In the past, I have had little success upgrading Fedora versions. I usually end up reinstalling everything. I am pleased to say that my upgrade of Fedora 8 to Fedora 10 occurred without issue (of course upgrading/installing 1600+ packages over the web took a little time). Nice job, Fedora team

Before we get to the installation, I want to provide a little background on CUDA. First, CUDA stands for "Compute Unified Device Architecture." The CUDA designers quite wisely did not invent a completely new language and based CUDA on ANSI C. They intentionally designed a minimal set of extensions to standard C so that users could experiment in a familiar environment. There is support for Fortran which I'll mention at the end of this article.

Another advantage of CUDA is that it allows the user to take small increasing more advanced steps. Users can take an existing C program and add CUDA code incrementally. Progressing in this fashion users can usually see some benefit for a small amount of work so that the user does not have to rip their program apart and rebuild it in order to see if CUDA will provide some increased speed. This feature coupled with a low cost development environment that can be easily scaled to better hardware has made CUDA very popular.

Downloads and System Preparation

The first step is to download the CUDA software. The CUDA Toolkit is available from the nVidia download page. For the purposes of this article you will need to download the Linux packages listed below. (Note if not using Fedora, select the one for your supported OS environment). You will also need to select a 32 or 64-bit version depending on your host system.
CUDA Toolkit - cudatoolkit_2.3_linux_64_fedora10.run
CUDA Getting Started Guide - CUDA_Getting_Started_2.3_Linux.pdf
Current Video Driver - NVIDIA-Linux-x86_64-190.53-pkg2.run
CUDA SDK - cudasdk_2.3_linux.run
The "CUDA Getting Started Guide" will provide additional background and help if you get stuck following this article. We will trace some of the basic steps outlined in the Guide here, and add some Fedora specific hints as well.
The first step recommend by nVidia is to verify your installation is one of the supported versions. They recommend running:

Code:
uname -i && cat /etc/*release
to get the architecture and Linux distribution version. Keep in mind that you may be able to use other versions of Linux, but you will be responsible for adding and updating libraries, kernels etc. CUDA also needs gcc. To verify that this is installed, run "gcc --version." If gcc is not installed, you can easily install it using "yum install gcc" if you are connected to the Internet.
The next step is installing the most recent nVidia driver. If you have already done this you can skip this step. If you do not have the nVidia driver installed or if you have an old version, then you should install/upgrade the latest driver as it is required for newer versions of CUDA. To install the driver, simply enter:

Code:
# chmod u+x NVIDIA-Linux-x86_64-190.53-pkg2.run
# ./NVIDIA-Linux-x86_64-190.53-pkg2.run
The driver installation if self explanatory and should proceed without any problems if you have a valid hardware environment. Make sure you reboot your system after the driver is installed. To make sure the new driver was installed properly, execute the following command:

Code:
# dmesg|grep nvidia
nvidia: module license 'NVIDIA' taints kernel.
nvidia 0000:01:00.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16
nvidia 0000:01:00.0: setting latency timer to 64
If nothing is returned or an error is indicated, then the driver has not installed properly. At that point you may want to check the nVidia support forums for more information. There should also be an NVIDIA X Server Settings under the Systems/Preferences menu in the top menu bar. You can check driver version and change settings if needed from this applications.

Installing CUDA Toolkit and SDK

If everything has worked thus far, it is time to install the CUDA software. The installation is very simple. Enter the following commands, and when asked for the installation location, use the default (/usr/local/cuda).
Code:
# chmod u+x cudatoolkit_2.3_linux_64_fedora10.run
#./cudatoolkit_2.3_linux_64_fedora10.run
The next steps involve setting the correct paths. First, you will need to set the path for the CUDA binaries. For now you can enter (enter appropriate command for csh):

Code:
export PATH=$PATH:/usr/local/cuda/bin
Add this to your .bashrc file as well (use appropriate command for .cshrc if using csh). The location of CUDA libraries also needs to be configured. I recommend using /etc/ld.so.conf instead of setting a LD_LIBRARY_PATH in your environment. To register the libraries, simply add

Code:
/usr/local/cuda/lib64
to the end of /etc/ld.so.conf and run ldconfig. If you are using a 32 bit environment, add /usr/local/cuda/lib instead of the lib64 path. At this point the CUDA toolkit kit should be installed.

Install the SDK

In order to test our installation, we need to install the CUDA SDK. As with the other packages, simply enter:
Code:
# chmod u+x cudasdk_2.3_linux.run
# ./cudasdk_2.3_linux.run
For my system, I used /usr/local/NVIDIA_GPU_Computing_SDK as the installation path. In order to test CUDA, it is best to compile and run code as a user. Therefore, open another window and log in under a user account. The SDK installs example codes under /usr/local/NVIDIA_GPU_Computing_SDK. A preferred strategy is to leave these files in their pristine form and make a copy for your own use so that if you accidentally delete or change smomething the originals will still be available. Also, don't forget to set your PATH variable using export PATH=$PATH:/usr/local/cuda/bin . The following steps will install the SDK into your home directory:

Code:
$ mkdir CUDA
$ cd CUDA
$ cp -rp /usr/local/NVIDIA_GPU_Computing_SDK .
Next we need to compile the CUDA programs. $ cd NVIDIA_GPU_Computing_SDK/C $ make
On my installation, I got the error /usr/bin/ld: cannot find -lglut, which is odd because the freeglut RPM was installed. On further inspection I found that the following fixed the problem (do this as root):

Code:
# ln -s /usr/lib64/libglut.so.3.8.0 /usr/lib64/libglut.so
The packages take a while to build, but when done, change to the executable files by entering:

Code:
$cd /bin/linux/release
The first program to run is called deviceQuery. This program will return important information about your video card and ensure that CUDA is working. Your output should look something like the following.

Code:
$ ./deviceQuery
CUDA Device Query (Runtime API) version (CUDART static linking)
There is 1 device supporting CUDA

Device 0: "GeForce 8500 GT"
CUDA Driver Version: 2.30
CUDA Runtime Version: 2.30
CUDA Capability Major revision number: 1
CUDA Capability Minor revision number: 1
Total amount of global memory: 536150016 bytes
Number of multiprocessors: 2
Number of cores: 16
Total amount of constant memory: 65536 bytes
Total amount of shared memory per block: 16384 bytes
Total number of registers available per block: 8192
Warp size: 32
Maximum number of threads per block: 512
Maximum sizes of each dimension of a block: 512 x 512 x 64
Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
Maximum memory pitch: 262144 bytes
Texture alignment: 256 bytes
Clock rate: 0.92 GHz
Concurrent copy and execution: Yes
Run time limit on kernels: Yes
Integrated: No
Support host page-locked memory mapping: No
Compute mode: Default (multiple host
threads can use this device simultaneously)

Test PASSED

Press ENTER to exit...
Now The Fun Begins

If everything has worked thus far, you can run the CUDA example programs to further your confidence in the installation. An example of the nbody code is shown in Figure Two below. The examples provide many types of applications and source code from which you can learn more about CUDA. Your next step is to download the CUDA Programming Guide and work on your own killer application. You can also find more examples (some freely available) at the CUDA Zone.



Figure Two: Example nbody program in action

CUDA and Clusters

At this point you should be able to explore CUDA for your own applications. If you use Fortran, you will be pleased to know that The Portland Group (PGI) and nVidia have teamed up to offer PGI CUDA Fortran. PGI has a 15-day trial offer that will let you play a bit with the tools

One final question you may ask is, "How do I use CUDA on my HPC cluster?" At this point, if your cluster nodes do not have access to nVidia hardware, then you obviously cannot use CUDA programs. Many installations are considering adding "CUDA nodes" equipped with nVidia Tesla cards, which can be used to run CUDA applications. In one sense, the use of GP-GPUs is like adding a low cost array processor to your nodes. You can also consider a stand-alone CUDA workstation that includes multiple Tesla GPU boards. The important question however, has been answered. By using a low cost hardware and freely available software you will know for sure if CUDA and nVidia GP-GPUs will work for your applications. If the answer is "yes," you now have a new world of hardware acceleration available.
Attached Images
mandelbrot-475..jpg (14.1 KB, 18187 views)
nbody-475..jpg (16.4 KB, 2600 views)
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