I am running the termstrc yield curve analysis package in R across 10 years of daily bond price data for 5 different countries. This is highly compute intensive, it takes 3200 seconds per country on a standard lapply, and if I use foreach and %dopar% (with doSNOW) on my 2009 i7 mac, using all 4 cores (8 with hyperthreading) I get this down to 850 seconds. I need to re-run this analysis every time I add a country (to compute inter-country spreads), and I have 19 countries to go, with many more credit yield curves to come in the future. The time taken is starting to look like a major issue. By the way, the termstrc analysis function in question is accessed in R but is written in C.
Now, we're a small company of 12 people (read limited budget), all equipped with 8GB ram, i7 PCs, of which at least half are used for mundane word processing / email / browsing style tasks, that is, using 5% maximum of their performance. They are all networked using gigabit (but not 10-gigabit) ethernet.
Could I cluster some of these underused PCs using MPI and run my R analysis across them? Would the network be affected? Each iteration of the yield curve analysis function takes about 1.2 seconds so I'm assuming that if the granularity of parallel processing is to pass a whole function iteration to each cluster node, 1.2 seconds should be quite large compared with the gigabit ethernet lag?
Can this be done? How? And what would the impact be on my co-workers. Can they continue to read their emails while I'm taxing their machines?
I note that Open MPI seems not to support Windows anymore, while MPICH seems to. Which would you use, if any?
Perhaps run an Ubuntu virtual machine on each PC?
Yes you can. There are a number of ways. One of the easiest is to use redis as a backend (as easy as calling sudo apt-get install redis-server on an Ubuntu machine; rumor has that you could have a redis backend on a windows machine too).
By using the doRedis package, you can very easily en-queue jobs on a task queue in redis, and then use one, two, ... idle workers to query the queue. Best of all, you can easily mix operating systems so yes, your co-workers' windows machines qualify. Moreover, you can use one, two, three, ... clients as you see fit and need and scale up or down. The queue does not know or care, it simply supplies jobs.
Bost of all, the vignette in the doRedis has working examples of a mix of Linux and Windows clients to make a bootstrapping example go faster.
Perhaps not the answer you were looking for, but - this is one of those situations where an alternative is sooo much better that it's hard to ignore.
The cost of AWS clusters is ridiculously low (my emphasis) for exactly these types of computing problems. You pay only for what you use. I can guarantee you that you will save money (at the very least in opportunity costs) by not spending the time trying to convert 12 windows machines into a cluster. For your purposes, you could probably even do this for free. (IIRC, they still offer free computing time on clusters)
References:
Using AWS for parallel processing with R
http://blog.revolutionanalytics.com/2011/01/run-r-in-parallel-on-a-hadoop-cluster-with-aws-in-15-minutes.html
http://code.google.com/p/segue/
http://www.vcasmo.com/video/drewconway/8468
http://aws.amazon.com/ec2/instance-types/
http://aws.amazon.com/ec2/pricing/
Some of these instances are so powerful you probably wouldn't even need to figure out how to setup your work on a cluster (given your current description). As you can see from the references costs are ridiculously low, ranging from 1-4$ per hour of compute time.
What about OpenCL?
This would require rewriting the C code, but would allow potentially large speedups. The GPU has immense computing power.
Related
I'm running models in the r package 'secr'. The simplest models take days to complete on a 4G macbook and I've already done everything possible within the model's setup to decrease run time. Parallel (multicore) processing is possible and straightforward in secr, but benefits are minimal and run time may actually increase. Am I likely to see improvement in run time if I switch to a high-powered virtual machine in the cloud (e.g. AWS's EC2 with 16 RAM and 4 vCPUs), or do the EC2's four vCPUs function like a multicore system (in which case I would only benefit from one vCPU despite having 4)?
I've asked this question in a couple of different forums and received conflicting answers.
You can think of the vCPUs just like a multicore system. They would appear as multiple cores to any software running on the system.
Good question. It depends. You may see a improvement in runtime if you switch to a EC2 instance type with better virtual hardware specifications. AWS runs a custom version of the Xen hypervisor, and your getting vCPUs as you pointed out. Performance will depend on the variability of the other guests's workloads. If the vCPUs are all assigned to instances, and each instance is running CPU heavy workloads, your going to see a downward trend in performance. It depends on the pattern of usage of all the instances running on the hypervisor. This article from Citrix explains some of the nuances of balancing vCPU time between instances on Xen and why performance will vary:
Citrix on Xen vCPU Performance
The instance type matters, not only the vCPUs and RAM. Avoid the T2 instances because they are 'burstable' and CPU performance will certainly vary. This article from AWS recommends to try M4 instance types for parallelization with R:
Running R on AWS
For specific types of EC2 instances you can control the C-state (sleep levels a core can enter when it is idle) and P-State (desired performance in frequency from a core). This would allow you to tune your instance performance for your workload. The following link explains in detail what instance types allow for C-State and P-State control and shows you how to use the utility "stress" to benchmark and tune different configurations.
EC2: Processor State Control
It would be best to design a test when you first provision the instance to see if it the type meets your performance requirements and then run the test again later to see if the performance benchmark holds.
I'm running an MCMC algorithm and Microsoft R open on Windows 7 has improved my speed a lot. But right now I need to run tons of simulations using my algorithm, so I used the R snow package to parallel my code. However, it doesn't work.
To be specific, the Microsfot R open on my PC is using 4 cores for calculation, while there are 8 cores in total. So I'm thinking I will parallel 2 process on my PC since each will need 4 cores for MKL library. But the parallel isn't real at all. I set up all my 8 cores when paralleling. My test program will need 5 minutes to run. But if I'm paralleling my program with a copy of that, I hope the 2 process will take 5 minutes as well. But actually it took 10 minutes, just like running the 2 process sequentially.
The same thing happened if I tried to open two R sessions and run the programs in the two R sessions. Usually it will only need 5 mins, but now each of them will take 10 mins.
So where am I messing up? Is that the problems about two layers of parallel? One is at my level, the other one is at the intel MKL level?
There are way too many factors at play here to figure it out without knowing certain details about your code. For example, what is the affinity mask in effect for each process? What is the Tread Ideal Processor for threads in concurrent processes? It is possible, that your processes are trying to compete for the same cores. You can find more details by looking at the SetThreadIdealProcessor and SetProcessAffinityMask APIs. It is also possible that your code is using a shared resource protected by a critical section or other synchronization object. I would start by downloading Process Explorer from Sysinternals and looking at the thread list for each process. This would tell you how many physical threads are running and how many context switches are there for each thread. This will give you something to start with.
I'm running a foreach loop with the snow back-end on a windows machine. I have 8 cores to work with. The rscript is exectuted via a system call embedded in a python script, so there would be an active python instance too.
Is there any benefit to not have #workers=#cores and instead #workers<#cores so there is always an opening for system processes or the python instance?
It successfully runs having #workers=#cores but do I take a performance hit by saturating the cores (max possible threads) with the r worker instances?
It will depend on
Your processor (specifically hyperthreading)
How much info has to be copied to/from the different images
If you're implementing this over multiple boxes (LAN)
For 1) hyperthreading helps. I know my machine does it so I typically have twice as many workers are cores and my code completes in about 85% of the time compared to if I matched the number of workers with cores. It won't improve more than that.
2) If you're not forking, using sockets for instance, you're working as if you're in a distributed memory paradigm, which means creating one copy in memory for every worker. This can be a non-trivial amount of time. Also, multiple images in the same machine may take up a lot of space, depending on what you're working on. I often match the number of workers with number because doubling workers will make me run out of memory.
This is compounded by 3) network speeds over multiple workstations. Locally between machines our switch will transfer things at about 20 mbytes/second which is 10x faster than my internet download speeds at home, but is a snail's pace compared to making copies in the same box.
You might consider increasing R's nice value so that the python has priority when it needs to do something.
I'm a researcher in statistical pattern recognition, and I often run simulations that run for many days. I'm running Ubuntu 12.04 with Linux 3.2.0-24-generic, which, as I understand, supports multicore and hyper-threading. With my Intel Core i7 Sandy Bridge Quadcore with HTT, I often run 4 simulations (programs that take a long time) at the same time. Before I ask my question, here are the things that I already (think I) know.
My OS (Ubuntu 12.04) detects 8 CPUs due to hyper-threading.
The scheduler in my OS is clever enough never to schedule two programs to run on two logical (virtual) cores belonging to the same physical core, because the OS supports SMP (Simultaneous Multi-Threading).
I have read the Wikipedia page on Hyper-Threading.
I have read the HowStuffWorks page on Sandy Bridge.
OK, my question is as follows. When I run 4 simulations (programs) on my computer at the same time, they each run on a separate physical core. However, due to hyper-threading, each physical core is split into two logical cores. Therefore, is it true that each of the physical cores is only using half of its full capacity to run each of my simulations?
Thank you very much in advance. If any part of my question is not clear, please let me know.
This answer is probably late, but I see that nobody offered an accurate description of what's going on under the hood.
To answer your question, no, one thread will not use half a core.
One thread can work inside the core at a time, but that one thread can saturate the whole core processing power.
Assume thread 1 and thread 2 belong to core #0. Thread 1 can saturate the whole core's processing power, while thread 2 waits for the other thread to end its execution. It's a serialized execution, not parallel.
At a glance, it looks like that extra thread is useless. I mean the core can process 1 thread at once right?
Correct, but there are situations in which the cores are actually idling because of 2 important factors:
cache miss
branch misprediction
Cache miss
When it receives a task, the CPU searches inside its own cache for the memory addresses it needs to work with. In many scenarios the memory data is so scattered that it is physically impossible to keep all the required address ranges inside the cache (since the cache does have a limited capacity).
When the CPU doesn't find what it needs inside the cache, it has to access the RAM. The RAM itself is fast, but it pales compared to the CPU's on-die cache. The RAM's latency is the main issue here.
While the RAM is being accessed, the core is stalled. It's not doing anything. This is not noticeable because all these components work at a ridiculous speed anyway and you wouldn't notice it through some CPU load software, but it stacks additively. One cache miss after another and another hampers the overall performance quite noticeably.
This is where the second thread comes into play. While the core is stalled waiting for data, the second thread moves in to keep the core busy. Thus, you mostly negate the performance impact of core stalls.
I say mostly because the second thread can also stall the core if another cache miss happens, but the likelihood of 2 threads missing the cache in a row instead of 1 thread is much lower.
Branch misprediction
Branch prediction is when you have a code path with more than one possible result. The most basic branching code would be an if statement.
Modern CPUs have branch prediction algorithms embedded into their microcode which try to predict the execution path of a piece of code. These predictors are actually quite sophisticated and although I don't have solid data on prediction rate, I do recall reading some articles a while back stating that Intel's Sandy Bridge architecture has an average successful branch prediction rate of over 90%.
When the CPU hits a piece of branching code, it practically chooses one path (path which the predictor thinks is the right one) and executes it. Meanwhile, another part of the core evaluates the branching expression to see if the branch predictor was indeed right or not. This is called speculative execution.
This works similarly to 2 different threads: one evaluates the expression, and the other executes one of the possible paths in advance.
From here we have 2 possible scenarios:
The predictor was correct. Execution continues normally from the speculative branch which was already being executed while the code path was being decided upon.
The predictor was wrong. The entire pipeline which was processing the wrong branch has to be flushed and start over from the correct branch.
OR, the readily available thread can come in and simply execute while the mess caused by the misprediction is resolved. This is the second use of hyperthreading.
Branch prediction on average speeds up execution considerably since it has a very high rate of success. But performance does incur quite a penalty when the prediction is wrong.
Branch prediction is not a major factor of performance degradation since, like I said, the correct prediction rate is quite high.
But cache misses are a problem and will continue to be a problem in certain scenarios.
From my experience hyperthreading does help out quite a bit with 3D rendering (which I do as a hobby). I've noticed improvements of 20-30% depending on the size of the scenes and materials/textures required. Huge scenes use huge amounts of RAM making cache misses far more likely. Hyperthreading helps a lot in overcoming these misses.
Since you are running on a Linux kernel you are in luck because the scheduler is smart enough to make sure your tasks is divided on between your physical cores.
Linux became hyperthredding aware in kernel 2.4.17 ( ref: http://kerneltrap.org/node/391 )
Note that the reference is from the old O(1) scheduler. Linux now uses the CFS scheduling algorithm which was introduced in kernel 2.6.23 and should be even better.
But as already suggested you can experiment by disabling hyper threading in bios and see if your particular workload runs faster or slower with or without hyperthreading enabled. If you start 8 tasks instead of 4 you will probably find that the total executing time for 8 tasks on hyperthreading is faster than two separate runs with 4 tasks but again the best thing to do is to experiment. Good luck!
If you are really want just 4 dedicated cores, you should be able to disable hyperthreading in your BIOS page. Also, and this part I'm less clear on, I believe that the processor is smart enough to do more work on a single thread if its second logical core is idle.
No, it's not exactly true. A hyperthreaded core is not two cores. Some things can run in parallel, but not as much as on two separate cores.
I want to use the highest possible number of threads (to use less computers) but without making the bottleneck to be in the client.
JMeter can simulate a very High Load provided you use it right.
Don't listen to Urban Legends that say JMeter cannot handle high load.
Now as for answer, it depends on:
your machine power
your jvm 32 bits or 64 bits
your jvm allocated memory -Xmx
your test plan ( lot of beanshell, post processor, xpath ... Means lots of cpu)
your os configuration (tunable)
Gui / non gui mode
So there is no theorical answer but following Best Practices will ensure JMeter performs well.
Note that with jmeter you can distribute load through remote testing, read:
Remote Testing > 15.4 Using a different sample sender
And finally use cloud based testing if it's not enough.
Read this for tuning tips:
http://www.ubik-ingenierie.com/blog/jmeter_performance_tuning_tips/
Read this book for doing load testing and using JMeter correctly.
I have used JMeter a fair bit and found it is not great at generating really high load. On a 2Ghz Core2 Duo with 2Gb memory you can reasonably expect about 100 threads.
That being said, it is best to run it on your hardware so that the CPU of the PC does not peak at 100% - a stable 80%-90% is best otherwise the results are affected.
I have also tried WAPT 5 - it successfully ran 1000+ threads from the same PC. It is not free but it is more useable than JMeter but doesn't have all of the features.
Outdated answer since at least version 2.6 see https://stackoverflow.com/a/11922239/460802 for a more up to date one.
The JMeter Wiki reports cases where JMeter was used with as much as 1000 threads. I have used it with at most 100 threads, but the Links in the Wiki suggest resource reductions I never tried.
One of the issues we had with running JMeter on Windows XP was the Windows XP TCP Connection Limit. Limit should be removed in order to run use the JMeter to workstation’s full potential
More info here. AFAIK, does not apply to other OS.
I used JMeter since 2004 and i launched lot of load tests.
With PC Windows 7 64 bits 4Go RAM iCore5.
I think JMeter can support 300 to 400 concurrent threads for Http (Sampler) protocol with only one "Aggregate Report Listener" who writes in the log file results and timers between call pages.
For a big load test you could configure JMeter with slaves (load generators) like this
http://jmeter-plugins.org/wiki/HttpSimpleTableServer/
I have already done tests with 11 PC slaves to simulate 5000 threads.
I have not used JMeter, but the answer probably depends on your hardware. Best bet might be to establish metrics of performance, guess at the number of threads and then run a binary search as follows.
Source was Wikipedia.
Number guessing game...
This rather simple game begins something like "I'm thinking of an integer between forty and sixty inclusive, and to your guesses I'll respond 'High', 'Low', or 'Yes!' as might be the case." Supposing that N is the number of possible values (here, twenty-one as "inclusive" was stated), then at most questions are required to determine the number, since each question halves the search space. Note that one less question (iteration) is required than for the general algorithm, since the number is already constrained to be within a particular range.
Even if the number we're guessing can be arbitrarily large, in which case there is no upper bound N, we can still find the number in at most steps (where k is the (unknown) selected number) by first finding an upper bound by repeated doubling. For example, if the number were 11, we could use the following sequence of guesses to find it: 1, 2, 4, 8, 16, 12, 10, 11
One could also extend the technique to include negative numbers; for example the following guesses could be used to find −13: 0, −1, −2, −4, −8, −16, −12, −14, −13
It is more dependent on the kind of performance testing you do(load, spike, endurance etc) on a specific server (a little on hardware dependency)
Keep in mind around these parameters
- the client machine on which you are targeting the run of jmeter, there will be a certain amount of heap memory allocated, ensure to have a healthy allocation so that the script does not error out. The highest i had run on jmeter was 1500 on a local environment ( client - server arch), On a Web arch, the highest i had a run was based upon Non- functional requirement were limited to 250 threads,
so it ideally depends on the kinds of performance testing and deployment style and so on..
There is not standard number for this. The maximum number of threads that you can generate from one computer depends completely on the computer's hardware and the OS. The OS by default occupies certain amount of CPU and the RAM.
To find out the maximum threads your computer can handle you can prepare a sample test and run it with only a few threads. Then with each cycle of test run increase the number of threads gradually. During this you also need to monitor the CPU, RAM, Disk I/O and Network I/O of your computer. The moment any of these reach near or beyond 80% (Again for you to decide if near is okay for you or beyond), that is the maximum number of threads your computer can handle. To be on the safer side I would stop at the number when the resource utilization reaches 70%.
It'll depend on the hardware you run on as well as the underlying script. I've always felt that this fuzziness is the biggest problem with traditional load testing tools. If you've got a small budget ($200 or so gets you a LOT of testing), check out my company's load testing service, BrowserMob.
Besides our Real Browser Users (RBUs) which control thousands on actual browsers for the purpose of performance and load testing, we also have traditional virtual users (VUs). Scripts are written in JavaScript and can make various HTTP calls.
The reason I bring it up is that I always felt that the game of trying to figure out how many VUs you can fit on your load gen hardware is dangerous. It's so easy to get bad results without realizing it.
To solve that for BrowserMob, we took an extremely conservative approach on the number of VUs and RBUs per CPU core: no more than 1 browser or 50 threads per CPU core, and sometimes much less. In the world of cloud computing, CPU cycles are so cheap that it just doesn't make sense to try to overload machines.