I'm working with someone who has some MATLAB code that they want to be sped up. They are currently trying to convert all of this code into CUDA to get it to run on a CPU. I think it would be faster to use MATLAB's parallel computing toolbox to speed this up, and run it on a cluster that has MATLAB's Distributed Computing Toolbox, allowing me to run this across several different worker nodes. Now, as part of the parallel computing toolbox, you can use things like GPUArray. However, I'm confused as to how this would work. Are using things like parfor (parallelization) and gpuarray (gpu programming) compatible with each other? Can I use both? Can something be split across different worker nodes (parallelization) while also making use of whatever GPUs are available on each worker?
They think its still worth exploring the time it takes to convert all of your matlab code to cuda code to run on a machine with multiple GPUs...but I think the right approach would be to use the features already built into MATLAB.
Any help, advice, direction would be really appreciated!
Thanks!
When you use parfor, you are effectively dividing your for loop into tasks, with one task per loop iteration, and splitting up those tasks to be computed in parallel by several workers where each worker can be thought of as a MATLAB session without an interactive GUI. You configure your cluster to run a specified number of workers on each node of the cluster (generally, you would choose to run a number of workers equal to the number of available processor cores on that node).
On the other hand, gpuarray indicates to MATLAB that you want to make a matrix available for processing by the GPU. Underneath the hood, MATLAB is marshalling the data from main memory to the graphics board's internal memory. Certain MATLAB functions (there's a list of them in the documentation) can operate on gpuarrays and the computation happens on the GPU.
The key differences between the two techniques are that parfor computations happen on the CPUs of nodes of the cluster with direct access to main memory. CPU cores typically have a high clock rate, but there are typically fewer of them in a CPU cluster than there are GPU cores. Individually, GPU cores are slower than a typical CPU core and their use requires that data be transferred from main memory to video memory and back again, but there are many more of them in a cluster. As far as I know, hybrid approaches are supposed to be possible, in which you have a cluster of PCs and each PC has one or more Nvidia Tesla boards and you use both parfor loops and gpuarrays. However, I haven't had occasion to try this yet.
If you are mainly interested in simulations, GPU processing is the perfect choice. However, if you want to analyse (big) data, go with Parallization. The reason for this is, that GPU processing is only faster than cpu processing if you don't have to copy data back and forth. In case of a simulation, you can generate most of the data on the GPU and only need to copy the result back. If you try to work with bigger data on the GPU you will very often run into out of memory problems.
Parallization is great if you have big data structures and more than 2 cores in your computer CPU.
If you write it in CUDA it is guaranteed to run in parallel at the chip-level versus going with MATLAB's best guess for a non-parallel architecture and your best effort to get it to run in parallel.
Kind of like drinking fresh mountain water run-off versus buying filtered water. Go with the purist solution.
Related
How can I get faster processing speeds for a single thread by combining multiple CPU cores, like training a custom neural network (not tensorflow) on a Google Compute Engine n1-highmem-64 machine type that has 64 CPU cores? Cluster computers or what? Not sure where to start... thanks!
Well you are asking for faster speeds on a single thread, but with multiple cores.
The only feasible way to get faster processing speeds off of a single thread, which is owned by a single core, is overclocking. You could also get a better chipset by getting newer cores.
It would be infeasible to accomplish this straightforward, you would likely have to patch the firmware to several of your components allowing them to communicate across cpus on a single thread utilizing an L3 cache or something.... very infeasible.
The opposite of that would be the way to go.
Multi-threading is used for processing different pieces of data concurrently on multiple cores.
General Purpose GPU use is for performing the same operation on a large set of data by farming the computation to the GPU. It has increased overhead time, but will give good results when the input is big enough.
It's funny that you mention not TensorFlow, because it actually implements both of these.
Even if you were able to implement something like this, it would probably just thrash over atomic locks unless you threaded it anyway.
Edit
If you are looking to use software as a service, Amazon (https://aws.amazon.com/tensorflow/ and other companies) have a range of services that are compatible with various deep-learning / machine-learning frameworks out of the box.
If I use the function:
net=feedfowardnet([60 60])
net2=train(net,x,t)
It takes about 20 minuets to train. (I have done this on multiple computers {with the same specs}, and the average time is always around 20 mins)
If I use the function:
parpool %//starts a local parallel pool connected to 2 workers
net2=train(net,x,t,'useParallel','yes')
It takes around 40 minuets to complete training. I have two cores, so this is counter intuitive, it should be twice as fast, not twice as slow. I am using the same starting network, and the same training inputs and targets.
Also, when I open the task manager during NN training, it shows that both CPUs are working at 100%, even when parpool and useParallel are turned off.
This page of the Mathworks website says that "Parallel Computing Toolbox™ allows Neural Network Toolbox™ to simulate and train networks faster and on larger datasets than can fit on one PC. Parallel training is currently supported for backpropagation training only, not for self-organizing maps."
I am using 2000 training examples in the data set. There are 32 inputs and 3 outputs so this is definitely a large data set. The parallel pool is also definitely turned off when I just use the net2=train(net,x,t) function.
I have tested the use of parpool with other functions, (ones containing parfor loops), and the calculation is usually twice as fast. It is just seems to be the neural network training that goes slower.
Is there any reason for this?
I am using an Intel Core 2 Duo E8400 Cpu #3GHz, and I am using MATLAB version R2013 b. I am also using a computer on a network (inside a university). I'm not sure if this makes a difference.
More info on the university computer network. I am using multiple computers on the network at the same time. I have not connected them together in a way to do distributed computing, each one is just doing its own thing using parallel computing on its own 2 processors. However I am not sure if the computers are still interfering with each other in some way because they are logged on with the same user. I load the training input and target data into the matlab workspace on each computer using:
load('H:\18-03-14\x.mat')
load('H:\18-03-14\net.mat')
load('H:\18-03-14\t.mat')
Where H: is the network drive. I am not sure if once these are in the matlab workspace, they are still somehow connected, and interfere with each other across different computers. Do they?
There are two types of parallelism going on: multicore and multithread. MATLAB implements basic matrix operations with multicore support, so even without the parallel computing toolbox, all your cores are being utilized.
The Parallel Computing Toolbox additionally allows for multiple threads. Multiple threads have two advantages. The first is that they allow calculations to be threaded across multiple PCs using MATLAB Distributed Computing Server for a reliable linear speed up. The second is less obvious, which is that multiple threads on a single PC can improve on already single-threaded multicore calculations, even though that might seem counter intuitive. However, there is extra overhead for using parallel threads so this is not always the case. More cores and large problems are more likely to see a speed up.
Your problem is not a large one. A large problem would be 10's of thousands of examples or more, whereas your problem only has 2000.
Also, two hidden layers with 60 neurons each is almost certainly a far larger network than you need. Your problem has 2000 samples * 3 outputs = 6000 constraints. Your network has 32*60+60*60+60*3 weights and 32+60+3 biases for a total of 5795 adjustable variables which is almost as many as the number of constraints. I would suggest far fewer weights and probably only a single hidden layer. This will train much faster, and is also likely to generalize better.
So maybe start with feedforwardnet(100) and then increase that if the desired accuracy is not found.
You can see the benefits of multiple threads on a larger problem using this Neural Network Toolbox example dataset with 68,308 examples:
[x,t] = vinyl_dataset;
net = feedforwardnet(140,'trainscg');
rng(0), tic, net2 = train(net,x,t); toc
parpool
rng(0), tic, net2 = train(net,x,t,'useParallel','yes'); toc
The 100% cpu load without use of the parallel computing toolbox shows, that the function train or the relevant called functions are implemented using multi threading. In these cases, the parallel computing toolbox only adds a useless overhead of inter process communication.
I'm asking on behalf of a friend working in numerical astrophysics.
Basically what he's doing is simulating a cloud of gas. There are a finite number of cells and the timestep is defined such that gas cannot cross more than one cell each step. Each cell has properties like density and temperature. Each timestep, these (and position) need to be calculated. It's mainly position that's the issue I believe as that is affected primarily by the interactions of gravity among the cells, all of which affect each other.
At the moment he's running this on a cluster of ~150 nodes but I wondered, if it's parallelizable like this, could it be run faster on a few GPUs with CUDA? At the moment it takes him a couple of days to finish a simulation. As GPUs generally have ~500 cores, it seemed like they could provide a boost.
Maybe I'm totally wrong.
Yes this sounds like a decent application for a GPU. GPU processing is most effective when it's running the same function on a large data set. If you've already got it running in parallel on a cluster computer, I'd say write it and test it on a single graphics card, and see if that's an improvement on a single cluster, then scale accordingly.
The task you describe is a good fit for the GPU. GPUs have successfully been used for dramatically improving the performance in areas such as particle, aerodynamics and fluid simulations.
Without knowing more details about the simulation it's impossible to say for sure whether it would gain a performance boost. Broadly speaking, algorithms that are memory bound ( that is, relatively few arithmetic operations per memory transaction ) tend to benefit most from offloading to the GPU.
For astrophysics simulations specifically, the following link may be of use : http://www.astrogpu.org/
I know for some machine learning algorithm like random forest, which are by nature should be implemented in parallel. I do a home work and find there are these three parallel programming framework, so I am interested in knowing what are the major difference between these three types of parallelism?
Especially, if some one can point me to some study compare the difference between them, that will be perfect!
Please list the pros and cons for each parallelism , thanks
MPI is a message passing paradigm of parallelism. Here, you have a root machine which spawns programs on all the machines in its MPI WORLD. All the threads in the system are independent and hence the only way of communication between them is through messages over network. The network bandwidth and throughput is one of the most crucial factor in MPI implementation's performance. Idea : If there is just one thread per machine and you have many cores on it, you can use OpenMP shared memory paradigm for solving subsets of your problem on one machine.
CUDA is a SMT paradigm of parallelism. It uses state of the art GPU architecture to provide parallelisim. A GPU contains (blocks of ( set of cores)) working on same instruction in a lock-step fashion (This is similar to SIMD model). Hence, if all the threads in your system do a lot of same work, you can use CUDA. But the amount of shared memory and global memory in a GPU are limited and hence you should not use just one GPU for solving a huge problem.
Hadoop is used for solving large problems on commodity hardware using Map Reduce paradigm. Hence, you do not have to worry about distributing data or managing corner cases. Hadoop also provides a file system HDFS for storing data on compute nodes.
Hadoop, MPI and CUDA are completely orthogonal to each other. Hence, it may not be fair to compare them.
Though, you can always use ( CUDA + MPI ) to solve a problem using a cluster of GPU's. You still need a simple core to perform the communication part of the problem.
With all the hype around parallel computing lately, I've been thinking a lot about parallelism, number crunching, clusters, etc...
I started reading Learn You Some Erlang. As more people are learning (myself included), Erlang handles concurrency in a very impressive, elegant way.
Then the author asserts that Erlang is not ideal for number crunching. I can understand that a language like Erlang would be slower than C, but the model for concurrency seems ideally suited to things like image handling or matrix multiplication, even though the author specifically says its not.
Is it really that bad? Is there a tipping point where Erlang's strength overcomes its local speed weakness? Are/what measures are being taken to deal with speed?
To be clear: I'm not trying to start a debate; I just want to know.
It's a mistake to think of parallelism as only about raw number crunching power. Erlang is closer to the way a cluster computer works than, say, a GPU or classic supercomputer.
In modern GPUs and old-style supercomputers, performance is all about vectorized arithmetic, special-purpose calculation hardware, and low-latency communication between processing units. Because communication latency is low and each individual computing unit is very fast, the ideal usage pattern is to load the machine's RAM up with data and have it crunch it all at once. This processing might involve lots of data passing among the nodes, as happens in image processing or 3D, where there are lots of CPU-bound tasks to do to transform the data from input form to output form. This type of machine is a poor choice when you frequently have to go to a disk, network, or some other slow I/O channel for data. This idles at least one expensive, specialized processor, and probably also chokes the data processing pipeline so nothing else gets done, either.
If your program requires heavy use of slow I/O channels, a better type of machine is one with many cheap independent processors, like a cluster. You can run Erlang on a single machine, in which case you get something like a cluster within that machine, or you can easily run it on an actual hardware cluster, in which case you have a cluster of clusters. Here, communication overhead still idles processing units, but because you have many processing units running on each bit of computing hardware, Erlang can switch to one of the other processes instantaneously. If it happens that an entire machine is sitting there waiting on I/O, you still have the other nodes in the hardware cluster that can operate independently. This model only breaks down when the communication overhead is so high that every node is waiting on some other node, or for general I/O, in which case you either need faster I/O or more nodes, both of which Erlang naturally takes advantage of.
Communication and control systems are ideal applications of Erlang because each individual processing task takes little CPU and only occasionally needs to communicate with other processing nodes. Most of the time, each process is operating independently, each taking a tiny fraction of the CPU power. The most important thing here is the ability to handle many thousands of these efficiently.
The classic case where you absolutely need a classic supercomputer is weather prediction. Here, you divide the atmosphere up into cubes and do physics simulations to find out what happens in each cube, but you can't use a cluster because air moves between each cube, so each cube is constantly communicating with its 6 adjacent neighbors. (Air doesn't go through the edges or corners of a cube, being infinitely fine, so it doesn't talk to the other 20 neighboring cubes.) Run this on a cluster, whether running Erlang on it or some other system, and it instantly becomes I/O bound.
Is there a tipping point where Erlang's strength overcomes its local speed weakness?
Well, of course there is. For example, when trying to find the median of a trillion numbers :) :
http://matpalm.com/median/question.html
Just before you posted, I happened to notice this was the number 1 post on erlang.reddit.com.
Almost any language can be parallelized. In some languages it's simple, in others it's a pain in the butt, but it can be done. If you want to run a C++ program across 8000 CPU's in a grid, go ahead! You can do that. It's been done before.
Erlang doesn't do anything that's impossible in other languages. If a single CPU running an Erlang program is less efficient than the same CPU running a C++ program, then two hundred CPU's running Erlang will also be slower than two hundred CPU's running C++.
What Erlang does do is making this kind of parallelism easy to work with. It saves developer time and reduces the chance of bugs.
So I'm going to say no, there is no tipping point at which Erlang's parallelism allows it to outperform another language's numerical number-crunching strength.
Where Erlang scores is in making it easier to scale out and do so correctly. But it can still be done in other languages which are better at number-crunching, if you're willing to spend the extra development time.
And of course, let's not forget the good old point that languages don't have a speed.
A sufficiently good Erlang compiler would yield perfectly optimal code. A sufficiently bad C compiler would yield code that runs slower than anything else.
There is pressure to make Erlang execute numeric code faster. The HiPe compiler compiles to native code instead of the BEAM bytecode for example, and it probably has its most effective optimization on code on floating points where it can avoid boxing. This is very beneficial for floating point code, since it can store values directly in FPU registers.
For the majority of Erlang usage, Erlang is plenty fast as it is. They use Erlang to write always-up control systems where the most important speed measurement that matters is low latency responses. Performance under load tends to be IO-bound. These users tend to stay away from HiPe since it is not as flexible/malleable in debugging live systems.
Now that servers with 128Gb of RAM are not that uncommon, and there's no reason they'll get even more memory, some IO-bound problems might shift over to be somewhat CPU bound. That could be a driver.
You should follow HiPe for the development.
Your examples of image manipulations and matrix multiplications seem to me as very bad matches for Erlang though. Those are examples that benefit from vector/SIMD operations. Erlang is not good at parallellism (where one does the same thing to multiple values at once).
Erlang processes are MIMD, multiple instructions multiple data. Erlang does lots of branching behind pattern matching and recursive loops. That kills CPU instruction pipelining.
The best architecture for heavily parallellised problems are the GPUs. For programming GPUs in a functional language I see the best potential in using Haskell for creating programs targeting them. A GPU is basically a pure function from input data to output data. See the Lava project in Haskell for creating FPGA circuits, if it is possible to create circuits so cleanly in Haskell, it can't be harder to create program data for GPUs.
The Cell architecture is very nice for vectorizable problems as well.
I think the broader need is to point out that parallelism is not necessarily or even typically about speed.
It is about how to express algorithms or programs in which the sequence of activities is partial-ordered.