[Mochi-devel] RPC latency question

Tue Nov 2 13:37:44 CDT 2021

I’m glad you were able to reproduce it on a different system, thanks for letting me know. I’m not sure what the overlaps between Frontera and Cooley are (that aren’t shared by Summit); a quick look shows they are both Intel, and both FDR, but there’s probably more salient details.

On Nov 2, 2021, at 2:24 PM, Phil Carns <carns at mcs.anl.gov<mailto:carns at mcs.anl.gov>> wrote:

Ok.  Interesting.  I didn't see anything unusual in the timing on my laptop with sm (other than it being a bit slow, but I wasn't tuning or worrying about core affinity or anything).  On Cooley, a somewhat older Linux cluster with InfiniBand, I see the 4th and 8th RPC delay you were talking about:

{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047385464.750000,"dur":33077.620054,"args":{"GUID":3,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047418850.000000,"dur":458.322054,"args":{"GUID":5,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047419519.250000,"dur":205.328054,"args":{"GUID":7,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047419939.500000,"dur":2916.470054,"args":{"GUID":9,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047423046.750000,"dur":235.460054,"args":{"GUID":11,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047423426.000000,"dur":208.722054,"args":{"GUID":13,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047423809.000000,"dur":155.962054,"args":{"GUID":15,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047424096.250000,"dur":3573.288054,"args":{"GUID":17,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047427857.000000,"dur":243.386054,"args":{"GUID":19,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635877047428328.000000,"dur":154.338054,"args":{"GUID":21,"Parent GUID":0}},

(assuming the first is high due to connection establishment)

I'll check some other systems/transports, but I wanted to go ahead and share that I've been able to reproduce what you were seeing.

thanks,

-Phil

On 11/2/21 1:49 PM, Philip Davis wrote:
Glad that’s working now.

It is the put_wait events, and “dur” is the right field. Those units are microseconds.

On Nov 2, 2021, at 1:12 PM, Phil Carns <carns at mcs.anl.gov<mailto:carns at mcs.anl.gov>> wrote:

Thanks Philip, the "= {0};" initialization of that struct got me going.

I can run the test case now and it is producing output in the client and server perf dirs.  Just to sanity check what to look for, I think the problem should be exhibited in the "put_wait" or maybe "do_put" trace events on the client?  For example on my laptop I see this:

carns-x1-7g ~/w/d/d/m/client.perf [SIGINT]> grep do_put trace_events.0.json
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352591977.250000,"dur":350.464053,"args":{"GUID":2,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352593065.000000,"dur":36.858053,"args":{"GUID":4,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352593617.000000,"dur":32.954053,"args":{"GUID":6,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352594193.000000,"dur":36.026053,"args":{"GUID":8,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352594850.750000,"dur":34.404053,"args":{"GUID":10,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352595400.750000,"dur":33.524053,"args":{"GUID":12,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352595927.500000,"dur":34.390053,"args":{"GUID":14,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352596416.000000,"dur":37.922053,"args":{"GUID":16,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352596870.000000,"dur":35.506053,"args":{"GUID":18,"Parent GUID":0}},
{"name":"do_put","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352597287.500000,"dur":34.774053,"args":{"GUID":20,"Parent GUID":0}},
carns-x1-7g ~/w/d/d/m/client.perf> grep put_wait trace_events.0.json
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352592427.750000,"dur":570.428053,"args":{"GUID":3,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352593122.750000,"dur":429.156053,"args":{"GUID":5,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352593671.250000,"dur":465.616053,"args":{"GUID":7,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352594248.500000,"dur":547.054053,"args":{"GUID":9,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352594906.750000,"dur":428.964053,"args":{"GUID":11,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352595455.750000,"dur":416.796053,"args":{"GUID":13,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352595981.250000,"dur":371.040053,"args":{"GUID":15,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352596485.500000,"dur":334.758053,"args":{"GUID":17,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352596934.250000,"dur":298.168053,"args":{"GUID":19,"Parent GUID":0}},
{"name":"put_wait","cat":"CPU","ph":"X","pid":0,"tid":0,"ts":1635872352597342.250000,"dur":389.624053,"args":{"GUID":21,"Parent GUID":0}},

I should look at the "dur" field right?  What are the units on that?

I'll see if I can run this on a "real" system shortly.

thanks!

-Phil

On 11/2/21 12:11 PM, Philip Davis wrote:
Hi Phil,

Sorry the data structures are like that; I wanted to preserve as much of the RPC size and ordering in case it ended up being important.

I’m surprised in.odsc.size is troublesome, as I set in.odsc.size with the line `in.odsc.size = sizeof(odsc);`. I’m not sure what could be corrupting that value in the meantime.

I don’t set in.odsc.gdim_size (which was an oversight, since that’s non-zero normally), so I’m less surprised that’s an issue. I thought I initialized `in` to zero, but I see I didn’t do that after all.

Maybe change the line `bulk_gdim_t in;` to `bulk_gdim_t in = {0};`

On Nov 2, 2021, at 11:48 AM, Phil Carns <carns at mcs.anl.gov<mailto:carns at mcs.anl.gov>> wrote:

Awesome, thanks Philip.  It came through fine.

I started by modifying the job script slightly to just run it on my laptop with sm (I wanted to make sure I understood the test case, and how to use apex, before trying elsewhere).  Does in.size needs to be set in client.c?  For me there is a random value in that field and it is causing the encoder on the forward to attempt a very large allocation.  The same might be true of gdim_size if it got past that step.  I started to alter them but then I wasn't sure what the implications were.

(fwiw I needed to include stdlib.h in common.h, but I've hit that a couple of times recently on codes that didn't previously generate warnings; I think something in Ubuntu has gotten strict about that recently).

thanks,

-Phil

On 11/1/21 4:51 PM, Philip Davis wrote:
Hi Phil,

I’ve attached the reproducer. I see the 4th and 8th issue on Frontera, but not Summit. Hopefully it will build and run without too much modification. Let me know if there are any issues with running it (or if the anl listserv eats the tarball, which I kind of expect).

Thanks,
Philip

On Nov 1, 2021, at 11:14 AM, Phil Carns <carns at mcs.anl.gov<mailto:carns at mcs.anl.gov>> wrote:

Hi Philip,

(FYI I think the first image didn't come through in your email, but I think the others are sufficient to get across what you are seeing)

I don't have any idea what would cause that.  The recently released libfabric 1.13.2 (available in spack from the mochi-spack-packages repo) includes some fixes to the rxm provider that could be relevant to Frontera and Summit, but nothing that aligns with what you are observing.

If it were later in the sequence (much later) I would speculate that memory allocation/deallocation cycles were eventually causing a hiccup.  We've seen something like that in the past, and it's a theory that we could then test with alternative allocators like jemalloc.  That's not memory allocation jitter that early in the run though.

Please do share your reproducer if you don't mind!  We can try a few systems here to at least isolate if it is something peculiar to the InfiniBand path or if there is a more general problem in Margo.

thanks,

-Phil

On 10/29/21 3:20 PM, Philip Davis wrote:
Hello,

I apologize in advance for the winding nature of this email. I’m not sure how to ask my question without explaining the story of my results some.

I’m doing some characterization of our server performance under load, and I have a quirk of performance that I wanted to run by people to see if they make sense. My testing so far has been to iteratively send batches of RPCs using margo_iforward, and then measure the wait time until they are all complete. On the server side, handling the RPC includes a margo_bulk_transfer as a pull initiated on the server to pull (for now) 8 bytes. The payload of the RPC request is about 500 bytes, and the response payload is 4 bytes.

I’ve isolated my results down to one server rank and one client rank, because it’s an easier starting point to reason from. Below is a graph of some of my initial results. These results are from Frontera. The median times are good (a single RPC takes on the order of 10s of microseconds, which seems fantastic). However, the outliers are fairly high (note the log scale of the y-axis). With only one RPC per timestep, for example, there is a 30x spread between the median and the max.

[cid:5EB5DF63-97AA-48FC-8BBE-E666E933D79F]

I was hoping (expecting) the first timestep would be where the long replies resided, but that turned out not to be the case. Below are traces from the 1 RPC (blue) and 2 RPC  (orange) per timestep cases, 5 trials of 10 timesteps for each case (normalized to fix the same x-axis):

<PastedGraphic-6.png>

What strikes me is how consistent these results are across trials. For the 1 RPC per timestep case, the 3rd and 7th timestep are consistently slow (and the rest are fast). For the 2 RPC per timestep case, the 2nd and 4th timestep are always slow and sometimes the 10th is. These results are repeatable with very rare variation.

For the single RPC case, I recorded some timers on the server side, and attempted to overlay them with the client side (there is some unknown offset, but probably on the order of 10s of microseconds at worst, given the pattern):

<PastedGraphic-7.png>

I blew up the first few timesteps of one of the trials:
<PastedGraphic-8.png>

The different colors are different segments of the handler, but there doesn’t seem to be anything too interesting going on inside the handler. So it looks like the time is being introduced before the 3rd RPC handler starts, based on the where the gap appears on the server side.

To try and isolate any dataspaces-specific behavior, I created a pure Margo test case that just sends a single rpc of the same size as dataspaces iteratively, whre the server side does an 8-byte bulk transfer initiated by the server, and sends a response. The results are similar, except that it is now the 4th and 8th timestep that are slow (and the first timestep is VERY long, presumably because rxm communication state is being established. DataSpaces has an earlier RPC in its init that was absorbing this latency).

I got margo profiling results for this test case:

```
3
18446744025556676964,ofi+verbs;ofi_rxm://192.168.72.245:39573
0xa2a1,term_rpc
0x27b5,put_rpc
0xd320,__shutdown__
0x27b5 ,0.000206208,10165,18446744027256353016,0,0.041241646,0.000045538,0.025733232,200,18446744073709551615,286331153,0,18446744073709551615,286331153,0
0x27b5 ,0;0.041241646,200.000000000, 0;
0xa2a1 ,0.000009298,41633,18446744027256353016,0,0.000009298,0.000009298,0.000009298,1,18446744073709551615,286331153,0,18446744073709551615,286331153,0
0xa2a1 ,0;0.000009298,1.000000000, 0;
```

So I guess my question at this point is, is there any sensible reason why the 4th and 8th RPC sent would have a long response time? I think I’ve cleared my code on the client side and server side, so it appears to be latency being introduced by Margo, LibFabric, Argobots, or the underlying OS. I do see long timesteps occasionally after this (perhaps every 20-30 timesteps) but these are not consistent.

One last detail: this does not happen on Summit. On summit, I see about 5-7x worse single-RPC performance (250-350 microseconds per RPC), but without the intermittent long timesteps.

I can provide the minimal test case if it would be helpful. I am using APEX for timing results, and the following dependencies with Spack:

argobots at 1.1<mailto:argobots at 1.1>  json-c at 0.15<mailto:json-c at 0.15>  libfabric at 1.13.1<mailto:libfabric at 1.13.1>  mercury at 2.0.1<mailto:mercury at 2.0.1>  mochi-margo at 0.9.5<mailto:mochi-margo at 0.9.5>  rdma-core at 20

Thanks,
Philip

_______________________________________________
mochi-devel mailing list
mochi-devel at lists.mcs.anl.gov<mailto:mochi-devel at lists.mcs.anl.gov>
https://lists.mcs.anl.gov/mailman/listinfo/mochi-devel<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.mcs.anl.gov%2Fmailman%2Flistinfo%2Fmochi-devel&data=04%7C01%7Cphilip.e.davis%40rutgers.edu%7Ca14ae84bf41946615a7708d99e2e081a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637714743421137006%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=FsRuBITz1gZaU6RMPLdSfa3TKPCqopMc1VoOZhA1NS8%3D&reserved=0>
https://www.mcs.anl.gov/research/projects/mochi<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mcs.anl.gov%2Fresearch%2Fprojects%2Fmochi&data=04%7C01%7Cphilip.e.davis%40rutgers.edu%7Ca14ae84bf41946615a7708d99e2e081a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637714743421147002%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Gb4zp0QRN5yfdkjt%2FpTcM1mrFRK3odkl5O5gmJ1xRuo%3D&reserved=0>

_______________________________________________
mochi-devel mailing list
mochi-devel at lists.mcs.anl.gov<mailto:mochi-devel at lists.mcs.anl.gov>
https://lists.mcs.anl.gov/mailman/listinfo/mochi-devel<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.mcs.anl.gov%2Fmailman%2Flistinfo%2Fmochi-devel&data=04%7C01%7Cphilip.e.davis%40rutgers.edu%7Ca14ae84bf41946615a7708d99e2e081a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637714743421147002%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=fwq0wjfEcW1t1StE5IKFrNy1krIP7jTsGXp7qeWM72s%3D&reserved=0>
https://www.mcs.anl.gov/research/projects/mochi<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mcs.anl.gov%2Fresearch%2Fprojects%2Fmochi&data=04%7C01%7Cphilip.e.davis%40rutgers.edu%7Ca14ae84bf41946615a7708d99e2e081a%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637714743421157001%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=zl1uuK5Hz%2BPXjbvlF0fNkBDOF1lYsaPXI5fF2gtZ7Zw%3D&reserved=0>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/mochi-devel/attachments/20211102/93ab5e91/attachment-0001.html>