I have a laptop running Ubuntu on Intel(R) Core(TM) i5-2410M CPU # 2.30GHz. According to Intel website for the above processor (located here), this processor has two cores and can run 4 threads at a time in parallel (because although it has 2 physical cores it has 4 logical cores).
When I start matlabpool it starts with local configuration and says it has connected to 2 labs. I suppose this means that it can run 2 threads in parallel. Does it not know that the CPU can actually run 4 threads in parallel?
In my experience, the local configuration of matlabpool uses, by default, the number of physical cores a machine possesses, rather than the number of logical cores. Hence on your machine, matlabpool only connects to two labs.
However, this is just a setting and can be overwritten with the following command:
matlabpool poolsize n
where n is an integer between 1 and 12 denoting the number of labs you want Matlab to use.
Now we get to the interesting bit that I'm a bit better equipped to answer thanks to a quick lesson from #RodyOldenhuis in the comments.
Hyper-threading implies a given physical core can have two threads run through it at the same time. Of course, they can't literally be processed simultaneously. The idea goes more like this: If one of the threads is inefficient in allocating tasks to the core, then the core may exhibit some "down-time". A second thread can take advantage of this "down-time" to get some work done.
In my experience, Matlab is often efficient in its allocation of threads to cores, therefore with one Matlab thread (ie one lab) running through it, a core may have very little "down-time" and hence there will be very little advantage to hyper-threading. My desktop is a core-i7 with 4 physical cores but 8 logical cores. However, I notice very little difference between running a parfor loop with 4 labs versus 8 labs. In fact, 8 labs is often slower due to the start-up costs associated with initializing the extra labs.
Of course, this is probably all complicated by other external factors such as what other programs you might be running simultaneously to Matlab too.
In summary, my suspicion is that even though you could force Matlab to initialize 4 labs (or even 12 labs), you won't see much of a speed-up over 2 labs, since Matlab is generally fairly efficient at allocating tasks to the processor.
Related
I have 16000 jobs to perform.
Each job is independent. There is no shared memory, no interprocess communication, no lock or mutex.
I am on ubuntu 16.06. c++11. Intel® Core™ i7-8550U CPU # 1.80GHz × 8
I use std::async to split jobs between cores.
If I split the jobs into 8 (2000 per core), computation time is 145.
If I split the jobs into 4 (4000 per core), computation time is 60.
Output after reduce is the same in both case.
If I monitor the CPU during computation (just using htop), things happen as expected (8 cores are used at 100% in first case, only 4 cores are used 100% in second case).
I am very confused why 4 cores would process much faster than 8.
The i7-8550U has 4 cores and 8 threads.
What is the difference? Quoting How-To Geek:
Hyper-threading was Intel’s first attempt to bring parallel
computation to consumer PCs. It debuted on desktop CPUs with the
Pentium 4 HT back in 2002. The Pentium 4’s of the day featured just a
single CPU core, so it could really only perform one task at a
time—even if it was able to switch between tasks quickly enough that
it seemed like multitasking. Hyper-threading attempted to make up for
that.
A single physical CPU core with hyper-threading appears as two logical
CPUs to an operating system. The CPU is still a single CPU, so it’s a
little bit of a cheat. While the operating system sees two CPUs for
each core, the actual CPU hardware only has a single set of execution
resources for each core. The CPU pretends it has more cores than it
does, and it uses its own logic to speed up program execution. In
other words, the operating system is tricked into seeing two CPUs for
each actual CPU core.
Hyper-threading allows the two logical CPU cores to share physical
execution resources. This can speed things up somewhat—if one virtual
CPU is stalled and waiting, the other virtual CPU can borrow its
execution resources. Hyper-threading can help speed your system up,
but it’s nowhere near as good as having actual additional cores.
By splitting the jobs to more cores than available - you are paying a big penalty.
I have been running several scientific program package in conjunction with MPI by using the following command
nohup mpirun -np N -x OMP_NUM_THREADS=M program.exe < input > output &
where the value of N and M depend on the physical CPU cores of my machine. For example, my machine has the specification like this
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 24
On-line CPU(s) list: 0-23
Thread(s) per core: 2
Core(s) per socket: 6
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 45
Model name: Intel(R) Xeon(R) CPU E5-2440 0 # 2.40GHz
Stepping: 7
In this case, I first tried setting with N = 24 and M = 1, so the calculation ran very slowly. Then I changed N and M to 12 and 2 respectively. So I found that the latter had obviously provided me the fastest computation.
I was wondering that why did I set N & M are 12 and 2 provide more performance higher than the first case ?
there is no absolute rule on how to run MPI+OpenMP application.
the only advice is not to run an OpenMP process on more than one socket
(OpenMP was designed for SMP machines with flat memory access, but today, most systems are NUMA)
then just experiment.
some apps run best in flat MPI (e.g. one thread per task), while some other work best with one MPI task per socket, and all available cores for OpenMP.
last but not least, if you run more than one OpenMP thread per MPI task, make sure your MPI library bound the MPI tasks as expected.
for example, if you run with 12 OpenMP threads but MPI bind tasks to one core, you will end up doing time sharing and performance will be horrible.
or if you run with 12 OpenMP threads, and MPI task was bound to 12 cores, make sure the 12 cores are on the same socket (and not 6 on each socket)
There is no general rule about this because, most of the time, this performance is dependent on the computation properties of the application itself.
Applications with coarse synchronization granularity may scale well using plain MPI code (no multithreading).
If the synchronization granularity is fine, then using shared memory multithreading (such as OpenMP) and placing all the threads in a process close to each other (in the same socket) becomes more important: synchronization is cheaper and memory access latency is critical.
Finally, compute-bound applications (performance is limited by the processor) are likely not to benefit from hyper-threading at all, since two threads sharing a core contend for the functional units it contains. In this case, you may find applications that perform better using N=2 and M=6 than using N=2 and M=12.
indeeed there is no absolute rule on how to run MPI+OpenMP application.
I agree with all Gilles said.
so I want to talk about the CPU in your case.
in the specification you give, it shows the system enables hyper-thread.
but this not always helps. your computer has 12 physical cores in fact.
so I advice you try some combinations that make M * N = 12 to 24,
like 12*1, 6*2, 6*3
which one is best, depends on how well your application.
Here is my situation:
my company need to run tests on tons of test samples. But if we start a single process on a windows PC machine, this test could last for hours, even days. so we try to split the test set and start a process to test each one of the slices on a multi-core linux server.
we expect a linear performance improvement for the server solution, but the truth is we could only observe a 2~3 times improvement when the test task finished by 10~20 processes.
I tried several means to locate the problem:
disable hyper-threading;
use max-performance power policy
use taskset to pin each process on different core
but no luck, the problem remains.
Why does this happen? which is the root cause, our code, OS or hardware?
here is the info of my pc and server:
PC: os: win10; cpu: i5-4570, 2 physical core; mem : 16gb
server: os: redhat 6.5 cpu: E5-2630 v3, 2 physical core; mem : 32gb
Edit:
About CPU: the server has 2 processors, and each of them has 8 physical cores. check this link for more information.
About My Test: it's handwriting recognition related(that's why it's a cpu-sensitive task).
About IO: the performance check points do not involve much IO if logging doesn't count.
we expect a linear performance improvement for the server solution,
but the truth is we could only observe a 2~3 times improvement when
the test task finished by 10~20 processes.
This seems very logical considering there are only 2 cores on the system. Starting 10-20 processes will only add some overhead due to task switching.
Also, I/O could be a bottleneck here too, if multiple processes are reading from disk at the same time.
Ideally, the number of running threads should not exceed 2 x the number of cores.
I'm a bit confused here about cores and threads on CPUs
Often in configuration files eg. nginx, golang you have to define the number of cores to get the best performance
If you look at this CPU
http://ark.intel.com/products/52213/Intel-Core-i7-2600-Processor-8M-Cache-up-to-3_80-GHz
How many "cores" does it have?
In the specs it has 4 cores and 8 threads.. Does that mean 4*8 = 32 "cores" ??
No, the CPU you linked to has four cores. It can, however, run two threads at the same time per core with a technology called Hyper-Threading (HT), thus has 8 "threads". The OS will be presented with 8 processors, unless you disable HT in the BIOS or elsewhere.
Note that hyper threading works in a special way: It uses unused execution units (in the sense of a superscalar processor) of a core for the second thread. AFAIK there are really good algorithms that re-order instructions for this to be most effective, but bear in mind that the hyper threads may not bring the best performance for all applications. For example: if you already use all floating point execution units in the four "real" threads all the time, the hyper threads will not be able to use them most of the time.
I have my own multithreaded C program which scales in speed smoothly with the number of CPU cores.. I can run it with 1, 2, 3, etc threads and get linear speedup.. up to about 5.5x speed on a 6-core CPU on a Ubuntu Linux box.
I had an opportunity to run the program on a very high end Sunfire x4450 with 4 quad-core Xeon processors, running Red Hat Enterprise Linux. I was eagerly anticipating seeing how fast the 16 cores could run my program with 16 threads..
But it runs at the same speed as just TWO threads!
Much hair-pulling and debugging later, I see that my program really is creating all the threads, they really are running simultaneously, but the threads themselves are slower than they should be. 2 threads runs about 1.7x faster than 1, but 3, 4, 8, 10, 16 threads all run at just net 1.9x! I can see all the threads are running (not stalled or sleeping), they're just slow.
To check that the HARDWARE wasn't at fault, I ran SIXTEEN copies of my program independently, simultaneously. They all ran at full speed. There really are 16 cores and they really do run at full speed and there really is enough RAM (in fact this machine has 64GB, and I only use 1GB per process).
So, my question is if there's some OPERATING SYSTEM explanation, perhaps some per-process resource limit which automatically scales back thread scheduling to keep one process from hogging the machine.
Clues are:
My program does not access the disk or network. It's CPU limited. Its speed scales linearly on a
single CPU box in Ubuntu Linux with
a hexacore i7 for 1-6 threads. 6
threads is effectively 6x speedup.
My program never runs faster than
2x speedup on this 16 core Sunfire
Xeon box, for any number of threads
from 2-16.
Running 16 copies of
my program single threaded runs
perfectly, all 16 running at once at
full speed.
top shows 1600% of
CPUs allocated. /proc/cpuinfo shows
all 16 cores running at full 2.9GHz
speed (not low frequency idle speed
of 1.6GHz)
There's 48GB of RAM free, it is not swapping.
What's happening? Is there some process CPU limit policy? How could I measure it if so?
What else could explain this behavior?
Thanks for your ideas to solve this, the Great Xeon Slowdown Mystery of 2010!
My initial guess would be shared memory bottlenecks. From what you say, your performance pretty much flatlines after 2 CPUs. You initially blame Redhat, but I'd be curious to see what happens if you install Ubuntu on the same hardware. I assume, of course, that you're running 64 bit SMP kernels across both tests.
It's probably not possible that the motherboard would peak at utilizing 2 CPUs. You have another machine with multiple cores that has provided better performance. Do you have hyperthreading turned on with the new machine? (and how does that answer compare to the old machine?). You're not, by chance, running in a virtualized environment?
Overall, your evidence is pointing to a ludicrously slow bottleneck somewhere. As you said, you're not I/O bound, so that leaves the CPU and memory. Either something is wrong with the hardware, or something is wrong with the hardware. Test one by changing the other, and you'll narrow down your possibilities quickly.
Do some research on rlimit - it's quite possible the shell/user acct you're running in has some RH-default or admin-set resource limits in place.
When you see this kind of odd scaling behaviour, especially if problems are seen with multiple threads, but not multiple processes, one thing to start looking at is the impacts of lock contention and other synchronisation primitives, which can cause threads running on different processors to have to wait for each other, potentially forcing multiple cores to flush their cache to main memory.
This means memory architecture starts to come into play, and that's going to be substantially faster when you have 6 cores on a single piece of silicon than when you're coordinating across 4 separate processors. Specifically, the single CPU case likely isn't needing to hit main memory for locking operations at all - everything is likely being handled at the L3 cache level, allowing the CPU to get on with things while data is flushed to main memory in the background.
While I expect the OP has lost interest in the question after all this time (or may not even have access to the hardware any more), one way to check this would be to see if the scaling up to 4 threads improves if the process affinity is set to lock it to a single physical CPU. Even better though would be to profile the application itself to see where it is spending it's time.As you change architectures and increase the number of cores, it gets harder and harder to guess where the bottlenecks are, so you really need to start measuring things directly, as in this example: http://postgresql.1045698.n5.nabble.com/Sun-Donated-a-Sun-Fire-T2000-to-the-PostgreSQL-community-td2057445.html