Server with multi-processor, how to launch code - parallel-processing

I don't have a big knowledge in hardware, GPU and CPU so I'm trying to create it. I have a server with N processor, the description for each of them is more or less the following one:
processor : 63
vendor_id : AuthenticAMD
cpu family : 25
model : 1
model name : AMD EPYC 7313 16-Core Processor
stepping : 1
microcode : 0xa001119
cpu MHz : 3724.322
cache size : 512 KB
physical id : 1
siblings : 32
core id : 15
cpu cores : 16
apicid : 63
initial apicid : 63
fpu : yes
fpu_exception : yes
cpuid level : 16
wp : yes
I don't have a job scheduler, so I'm using tmux or screen to deal with my code.
My question is, how can I deal with the processor and use like 3 of them, or less or more, and run my python code? I'm very confused about that.
Thank you

You probably want to divide your work into tasks that can run independently from each other and then have them in their own processes via forking (if they don't need to communicate with each other and e.g. just store their results somewhere on disk) or create threads to run them.
A single thread will always only use a single CPU, you need multiple threads to use more CPUs. Each process has at least one thread, that's why creating multiple processes would work, too.
Since you mention tmux, maybe bash's job control can help you - short example would be my_script.py input_file & my_script.py another_input_file, starting two instances of my_script.py to run at the same time.

Related

Different profiling modes for different cores using perf

I have the following questions regarding perf.
a) Is it possible that I run different profiling modes on different cores simultaneously. e.g. Core 0 with event based sampling (sampling every N events) and Core 1 with free running counter based sampling?
b) In case a) is not possible. Then is it possible to get a snapshot of the PMU counters on the other cores (Core 1) for every sample (overflow at N events) on Core 0?
P.S: The platform is a RPi 3b+ based on the Arm Cortex A53
It is possible to operate different profiling modes on different cores of the CPU simultaneously.
perf also has a processor-wide mode wherein all threads running on the designated processors are monitored. Counts and samples are thus aggregated per CPU/core.
-C, --cpu=
Count only on the list of CPUs provided. Multiple CPUs can be
provided as a comma-separated list with no space: 0,1. Ranges of
CPUs are specified with -: 0-2. In per-thread mode, this option
is ignored. The -a option is still necessary to activate
system-wide monitoring. Default is to count on all CPUs.
Running both the free-running counter as well as the sampling mechanism of perf simultaneously, is possible on different cores of the CPU like below -
eg. for cpu 0:
perf stat --cpu 0 -B dd if=/dev/zero of=/dev/null count=1000000
and for cpu 1:
perf record --cpu 1 sleep 20

How force 32 processes to run on 32 different cores?

I am running a simulation of a many-core system. I have a benchmark which has an option of selecting the number of processes as an option. This is set to 32.
Now when I run this bench mark, it correctly produces 32 processes.
Sample :
Now I want to force it to run on 32 cores. For this I have tried :
NOTE : I am running my application through busybox.
./busybox taskset 0xFFFFFFFF ./fmm <input
Here fmm is the benchmark I am running.
This whole system is being run in a simulator called qsim and when I run this, the processes get attached to only one or two cores (18th and 19th).
I understand that the mask is only an indicator to the OS that it can run on the given cores, but is there any way to force the OS to run the 32 processes on 32 cores ?
I guess you could try to set CPU affinity och each thread.

How to enlarge the memory in Microblaze for software applications?

I wrote a C program, which has a big size . However, it is known that the Microblaze by default uses only 64KB. So I change the amount of BRAM in the EDK to 512K but when I generate the bitsream I got this errors:
- C:\Users\slim\Desktop\hs\system.mhs line 74
IPNAME: plb_v46, INSTANCE: mb_plb - 2 master(s) : 1 slave(s)
IPNAME: lmb_v10, INSTANCE: ilmb - 1 master(s) : 1 slave(s)
IPNAME: lmb_v10, INSTANCE: dlmb - 1 master(s) : 1 slave(s)
ERROR:EDK:440 - platgen failed with errors!
Done!
On a Spartan-6, EDK's blockRAM memory block are limited to 64kB if they are 32 bits large, 128kB if they are 64 bits large and 256kB if they are 128 bits large. Besides, the spartan-6 LX45 has only 238kB of BlockRAM memory available, so this is impossible altogether on your platform.
The memory the microblaze use to store it's program is limited to 32 bits, as far as I know. To use the larger memories you would need to connect it to an AXI port. Otherwise, Xilinx has an answer record on how to use 2 differents 64kB memory to present 128kB to the microblaze.
Do you really need that much memory? If the answer is "yes", you should use a microblaze with external memory instead. You will have much more memory available (your board has 128MB DDR ready to use) with minimal performance impact if you have sufficient caches.

Linux Multi-Threaded Performance Enhancements for File open()

I’m working on tuning performance on a high-performance, high-capacity data engine which ultimately services an end-user web experience. Specifically, the piece delegated to me revolves around characterizing multi-threaded file IO and memory mapping of the data to local cache. In writing test applications to isolate the timing tall-poles, several questions have been exposed. The code has been minimized to perform only a system file open (open(O_RDONLY)) call. I’m hoping that the result of this query helps us understand the fundamental low-level system processes so that a complete predictive (or at least relational) timing model can be understood. Suggestions are always welcome. We’ve seemed to hit a timing barrier, and would like to understand the behavior and determine whether that barrier can be broken.
The test program:
Is written in C, compiled using the gnu C compiler as noted below;
Is minimally written to isolate the discovered issues to a single system file “open()”;
Is configurable to simultaneously launch a requested number of pthreads;
loads a list of 1000 text files of ~8K size;
creates the threads (simply) with no attribute modifications;
each thread performs multiple, sequential file open() calls on the next available file from the pre-determined list of files until the file list is exhausted in such a way that a single thread should open all 1000 files, 2 threads should theoretically open 500 files (not proven as of yet), etc.);
We’ve run tests multiple times, parametrically varying the thread count, file sizes, and whether the files are located on a local or remote server. Several questions have come up.
Observed results (opening remote files):
File open times are higher the first time through (as expected, due to file caching);
Running the test app with one thread to load all the remote files takes X seconds;
It appears that running the app with a thread count between 1 and # of available CPUs on the machine results in times that are proportional to the number of CPUs (nX seconds).
Running the app using a thread count > #CPUs results in run times that seem to level out at the approx same value as the time is takes to run with #CPUs threads (is this coincidental, or a systematic limit, or what?).
Running multiple, concurrent processes (for example, 25 concurrent instances of the same test app) results in the times being approximately linear with number of processes for a selected thread count.
Running app on different servers shows similar results
Observed results (opening files residing locally):
Orders of magnitude faster times (as to be expected);
With increasing the thread count, a LOW timing inflection point occurs at around 4-5 active threads, then increases again until the number of threads equals the CPU count, then levels off again;
Running multiple, concurrent processes (same test) results in the times being approximately linear with number of processes for a constant thread count (same result as #5 above).
Also, we noticed that Local opens take about .01 ms and sequential network opens are 100x slower at 1ms. Opening network files, we get a linear throughput increase up to 8x with 8 threads, but 9+ threads do nothing. The network open calls seem to block after more than 8 simultaneous requests. What we expected was an initial delay equal to the network roundtrip, and then approximately the same throughput as local. Perhaps there is extra mutex locking done on the local and remote systems that takes 100x longer. Perhaps there is some internal queue of remote calls that only holds 8.
Expected results and questions to be answered either by test or by answers from forums like this one:
Running multiple threads would result in the same work done in shorter time;
Is there an optimal number of threads;
Is there a relationship between the number of threads and CPUs available?
Is there some other systematic reason that an 8-10 file limit is observed?
How does the system call to “open()” work in a multi-threading process?
Each thread gets its context-switched time-slice;
Does the open() call block and wait until the file is open/loaded into file cache? Or does the call allow context switching to occur while the operation is in progress?
When the open() completes, does the scheduler reprioritize that thread to execute sooner, or does the thread have to wait until its turn in round-robin way;
Would having the mounted volume on which the 1000 files reside set as read-only or read/write make a difference?
When open() is called with a full path, is each element in the path stat()ed? Would it make more sense to open() a common directory in the list of files tree, and then open() the files under that common directory by relative path?
Development test setup:
Red Hat Enterprise Linux Server release 5.4 (Tikanga)
8-CPUS, each with characteristics as shown below:
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 23
model name : Intel(R) Xeon(R) CPU X5460 # 3.16GHz
stepping : 6
cpu MHz : 1992.000
cache size : 6144 KB
physical id : 0
siblings : 4
core id : 1
cpu cores : 4
apicid : 1
fpu : yes
fpu_exception : yes
cpuid level : 10
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall lm constant_tsc pni monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr sse4_1 lahf_lm
bogomips : 6317.47
clflush size : 64
cache_alignment : 64
address sizes : 38 bits physical, 48 bits virtual
power management:
GNU C compiler, version:
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)
Not sure if this is one of your issues, but it may be of use.
The one thing that struck me, while optimizing thousands of random reads on a single SATA disk, was that performing non-blocking I/O isn't so easy to do in linux in a clean way, without extra threads.
It is (currently) impossible to issue a non-blocking read() on a block device; i.e. it will block for the 5 ms seek time the disk needs (and 5 ms is an eternity, at 3 GHz). Specifying O_NONBLOCK to open() only served some purpose for backward compatibility, with CD burners or something (this was a rather vague issue). Normally, open() doesn't block or cache anything, it's mostly just to get a handle on a file to do some data I/O later.
For my purposes, mmap() seemed to get me as close to the kernel handling of the disk as possible. Using madvise() and mincore() I was able to fully exploit the NCQ capabilities of the disk, which was simply proved by varying the queue depth of outstanding requests, which turned out to be inversely proportional to the total time taken to issue 10k reads.
Thanks to 64 bit memory addressing, using mmap() to map an entire disk to memory is no problem at all. (on 32 bit platforms, you would need to map the parts of the disk you need using mmap64())

GNU make: should the number of jobs equal the number of CPU cores in a system?

There seems to be some controversy on whether the number of jobs in GNU make is supposed to be equal to the number of cores, or if you can optimize the build time by adding one extra job that can be queued up while the others "work".
Is it better to use -j4 or -j5 on a quad core system?
Have you seen (or done) any benchmarking that supports one or the other?
I've run my home project on my 4-core with hyperthreading laptop and recorded the results. This is a fairly compiler-heavy project but it includes a unit test of 17.7 seconds at the end. The compiles are not very IO intensive; there is very much memory available and if not the rest is on a fast SSD.
1 job real 2m27.929s user 2m11.352s sys 0m11.964s
2 jobs real 1m22.901s user 2m13.800s sys 0m9.532s
3 jobs real 1m6.434s user 2m29.024s sys 0m10.532s
4 jobs real 0m59.847s user 2m50.336s sys 0m12.656s
5 jobs real 0m58.657s user 3m24.384s sys 0m14.112s
6 jobs real 0m57.100s user 3m51.776s sys 0m16.128s
7 jobs real 0m56.304s user 4m15.500s sys 0m16.992s
8 jobs real 0m53.513s user 4m38.456s sys 0m17.724s
9 jobs real 0m53.371s user 4m37.344s sys 0m17.676s
10 jobs real 0m53.350s user 4m37.384s sys 0m17.752s
11 jobs real 0m53.834s user 4m43.644s sys 0m18.568s
12 jobs real 0m52.187s user 4m32.400s sys 0m17.476s
13 jobs real 0m53.834s user 4m40.900s sys 0m17.660s
14 jobs real 0m53.901s user 4m37.076s sys 0m17.408s
15 jobs real 0m55.975s user 4m43.588s sys 0m18.504s
16 jobs real 0m53.764s user 4m40.856s sys 0m18.244s
inf jobs real 0m51.812s user 4m21.200s sys 0m16.812s
Basic results:
Scaling to the core count increases the performance nearly linearly. The real time went down from 2.5 minutes to 1.0 minute (2.5x as fast), but the time taken during compile went up from 2.11 to 2.50 minutes. The system noticed barely any additional load in this bit.
Scaling from the core count to the thread count increased the user load immensely, from 2.50 minutes to 4.38 minutes. This near doubling is most likely because the other compiler instances wanted to use the same CPU resources at the same time. The system is getting a bit more loaded with requests and task switching, causing it to go to 17.7 seconds of time used. The advantage is about 6.5 seconds on a compile time of 53.5 seconds, making for a 12% speedup.
Scaling from thread count to double thread count gave no significant speedup. The times at 12 and 15 are most likely statistical anomalies that you can disregard. The total time taken increases ever so slightly, as does the system time. Both are most likely due to increased task switching. There is no benefit to this.
My guess right now: If you do something else on your computer, use the core count. If you do not, use the thread count. Exceeding it shows no benefit. At some point they will become memory limited and collapse due to that, making the compiling much slower. The "inf" line was added at a much later date, giving me the suspicion that there was some thermal throttling for the 8+ jobs. This does show that for this project size there's no memory or throughput limit in effect. It's a small project though, given 8GB of memory to compile in.
I would say the best thing to do is benchmark it yourself on your particular environment and workload. Seems like there are too many variables (size/number of source files, available memory, disk caching, whether your source directory & system headers are located on different disks, etc.) for a one-size-fits-all answer.
My personal experience (on a 2-core MacBook Pro) is that -j2 is significantly faster than -j1, but beyond that (-j3, -j4 etc.) there's no measurable speedup. So for my environment "jobs == number of cores" seems to be a good answer. (YMMV)
I, personally, use make -j n where n is "number of cores" + 1.
I can't, however, give a scientific explanation: I've seen a lot of people using the same settings and they gave me pretty good results so far.
Anyway, you have to be careful because some make-chains simply aren't compatible with the --jobs option, and can lead to unexpected results. If you're experiencing strange dependency errors, just try to make without --jobs.
Both are not wrong. To be at peace with yourself and with author of software you're compiling (different multi-thread/single-thread restrictions apply at software level itself), I suggest you use:
make -j`nproc`
Notes: nproc is linux command that will return number of cores/threads(modern CPU) available on system. Placing it under ticks ` like above will pass the number to the make command.
Additional info: As someone mentioned, using all cores/threads to compile software can literally choke your box to near death (being unresponsive) and might even take longer than using less cores. As I seen one Slackware user here posted he had dual core CPU but still provided testing up to j 8, which stopped being different at j 2 (only 2 hardware cores that CPU can utilize). So, to avoid unresponsive box i suggest you run it like this:
make -j`nproc --ignore=2`
This will pass the output of nproc to make and subtract 2 cores from its result.
Ultimately, you'll have to do some benchmarks to determine the best number to use for your build, but remember that the CPU isn't the only resource that matters!
If you've got a build that relies heavily on the disk, for example, then spawning lots of jobs on a multicore system might actually be slower, as the disk will have to do extra work moving the disk head back and forth to serve all the different jobs (depending on lots of factors, like how well the OS handles the disk-cache, native command queuing support by the disk, etc.).
And then you've got "real" cores versus hyper-threading. You may or may not benefit from spawning jobs for each hyper-thread. Again, you'll have to benchmark to find out.
I can't say I've specifically tried #cores + 1, but on our systems (Intel i7 940, 4 hyperthreaded cores, lots of RAM, and VelociRaptor drives) and our build (large-scale C++ build that's alternately CPU and I/O bound) there is very little difference between -j4 and -j8. (It's maybe 15% better... but nowhere near twice as good.)
If I'm going away for lunch, I'll use -j8, but if I want to use my system for anything else while it's building, I'll use a lower number. :)
I just got an Athlon II X2 Regor proc with a Foxconn M/B and 4GB of G-Skill memory.
I put my 'cat /proc/cpuinfo' and 'free' at the end of this so others can see my specs. It's a dual core Athlon II x2 with 4GB of RAM.
uname -a on default slackware 14.0 kernel is 3.2.45.
I downloaded the next step kernel source (linux-3.2.46) to /archive4;
extracted it (tar -xjvf linux-3.2.46.tar.bz2);
cd'd into the directory (cd linux-3.2.46);
and copied the default kernel's config over (cp /usr/src/linux/.config .);
used make oldconfig to prepare the 3.2.46 kernel config;
then ran make with various incantations of -jX.
I tested the timings of each run by issuing make after the time command, e.g.,
'time make -j2'. Between each run I 'rm -rf' the linux-3.2.46 tree and reextracted it, copied the default /usr/src/linux/.config into the directory, ran make oldconfig and then did my 'make -jX' test again.
plain "make":
real 51m47.510s
user 47m52.228s
sys 3m44.985s
bob#Moses:/archive4/linux-3.2.46$
as above but with make -j2
real 27m3.194s
user 48m5.135s
sys 3m39.431s
bob#Moses:/archive4/linux-3.2.46$
as above but with make -j3
real 27m30.203s
user 48m43.821s
sys 3m42.309s
bob#Moses:/archive4/linux-3.2.46$
as above but with make -j4
real 27m32.023s
user 49m18.328s
sys 3m43.765s
bob#Moses:/archive4/linux-3.2.46$
as above but with make -j8
real 28m28.112s
user 50m34.445s
sys 3m49.877s
bob#Moses:/archive4/linux-3.2.46$
'cat /proc/cpuinfo' yields:
bob#Moses:/archive4$ cat /proc/cpuinfo
processor : 0
vendor_id : AuthenticAMD
cpu family : 16
model : 6
model name : AMD Athlon(tm) II X2 270 Processor
stepping : 3
microcode : 0x10000c8
cpu MHz : 3399.957
cache size : 1024 KB
physical id : 0
siblings : 2
core id : 0
cpu cores : 2
apicid : 0
initial apicid : 0
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmo
v pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rd
tscp lm 3dnowext 3dnow constant_tsc nonstop_tsc extd_apicid pni monitor cx16 p
opcnt lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowpre
fetch osvw ibs skinit wdt npt lbrv svm_lock nrip_save
bogomips : 6799.91
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate
processor : 1
vendor_id : AuthenticAMD
cpu family : 16
model : 6
model name : AMD Athlon(tm) II X2 270 Processor
stepping : 3
microcode : 0x10000c8
cpu MHz : 3399.957
cache size : 1024 KB
physical id : 0
siblings : 2
core id : 1
cpu cores : 2
apicid : 1
initial apicid : 1
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmo
v pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rd
tscp lm 3dnowext 3dnow constant_tsc nonstop_tsc extd_apicid pni monitor cx16 p
opcnt lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowpre
fetch osvw ibs skinit wdt npt lbrv svm_lock nrip_save
bogomips : 6799.94
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate
'free' yields:
bob#Moses:/archive4$ free
total used free shared buffers cached
Mem: 3991304 3834564 156740 0 519220 2515308
Just as a ref:
From Spawning Multiple Build Jobs section in LKD:
where n is the number of jobs to spawn. Usual practice is to spawn one or two jobs per processor. For example, on a dual processor machine, one might do
$ make j4
From my experience, there must be some performance benefits when adding extra jobs.
It is simply because disk I/O is one of the bottle necks besides CPU. However it is not easy to decide on the number of extra jobs as it is highly inter-connected with the number of cores and types of the disk being used.
Many years later, the majority of these answers are still correct. However, there has been a bit of a change: Using more jobs than you have physical cores now gives a genuinely significant speedup. As an addendum to Dascandy's table, here's my times for compiling a project on a AMD Ryzen 5 3600X on linux. (The Powder Toy, commit c6f653ac3cef03acfbc44e8f29f11e1b301f1ca2)
I recommend checking yourself, but I've found with input from others that using your logical core count for job count works well on Zen. Alongside that, the system does not seem to lose responsiveness. I imagine this applies to recent Intel CPUs as well. Do note I have an SSD, as well, so it may be worth it to test your CPU yourself.
scons -j1 --release --native 120.68s user 9.78s system 99% cpu 2:10.60 total
scons -j2 --release --native 122.96s user 9.59s system 197% cpu 1:07.15 total
scons -j3 --release --native 125.62s user 9.75s system 292% cpu 46.291 total
scons -j4 --release --native 128.26s user 10.41s system 385% cpu 35.971 total
scons -j5 --release --native 133.73s user 10.33s system 476% cpu 30.241 total
scons -j6 --release --native 144.10s user 11.24s system 564% cpu 27.510 total
scons -j7 --release --native 153.64s user 11.61s system 653% cpu 25.297 total
scons -j8 --release --native 161.91s user 12.04s system 742% cpu 23.440 total
scons -j9 --release --native 169.09s user 12.38s system 827% cpu 21.923 total
scons -j10 --release --native 176.63s user 12.70s system 910% cpu 20.788 total
scons -j11 --release --native 184.57s user 13.18s system 989% cpu 19.976 total
scons -j12 --release --native 192.13s user 14.33s system 1055% cpu 19.553 total
scons -j13 --release --native 193.27s user 14.01s system 1052% cpu 19.698 total
scons -j14 --release --native 193.62s user 13.85s system 1076% cpu 19.270 total
scons -j15 --release --native 195.20s user 13.53s system 1056% cpu 19.755 total
scons -j16 --release --native 195.11s user 13.81s system 1060% cpu 19.692 total
( -jinf test not included, as it is not supported by scons.)
Tests done on Ubuntu 19.10 w/ a Ryzen 5 3600X, Samsung 860 Evo SSD (SATA), and 32GB RAM
Final note: Other people with a 3600X may get better times than me. When doing this test, I had Eco mode enabled, reducing the CPU's speed a little.
YES! On my 3950x, I run -j32 and it saves hours of compile time! I can still watch youtube, browse the web, etc. during compile without any difference. The processor isn't always pegged even with a 1TB 970 PRO nvme or 1TB Auros Gen4 nvme and 64GB of 3200C14. Even when it is, I don't notice UI wise. I plan on testing with -j48 in the near future on some big upcoming projects. I expect, as you probably do, to see some impressive improvement. Those still with a quad-core might not get the same gains....
Linus himself just upgraded to a 3970x and you can bet your bottom dollar, he is at least running -j64.

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