@everywhere is slow on HPC with multi-node environment #39291
Comments
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related issue #28966 |
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Hey @algorithmx I'm facing exactly the same issue you describe, have you found any workaround yet? Could it be realted to this? JuliaLang/Pkg.jl#1219 |
not yet :-( |
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So I have been able to reduce the delay quite significantly by using the latest Julia 1.6 release (seems that the faster compilation speed helps), and also changing the using Distributed, ClusterManagers
pids = addprocs_slurm(...)
@everywhere pushfirst!(Base.DEPOT_PATH, "/tmp/julia.cache") |
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I've also run into this problem (posted on discourse here), and traced it back to just using @everywhere 1+2It so happens that most of us run This is a real killer for my use case, which involves scaling up to thousands of processors, which will waste (and has wasted for me) thousands of cpu-hours just running that first |
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If possible, it would be good to run a bisect between julia 1.0 and 1.3 to find out if there was a specific commit that caused the regression. |
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Yes |
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I've also noticed this on Julia 1.6.2 and it's not just multi-node environments. When I am on a 128 core AMD machine and perform I have a video of what this looks like on a single node here: |
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Workaround described here. Basically, you have to precompile the code that lets processes talk to each other. |
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thanks @moble! I guess what I wonder is why is seems like precompilation problem is worse with many more processors? In other words, why aren't they all just precompiling simultaneously (the video makes it look like they're doing it one by one almost)? |
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I don't actually know how things work under the hood, but I have tested it and found that the timing increases linearly with the number of processes. So my mental model is that But the primary must do this in serial to some extent, meaning it doesn't start sending the instruction to the next worker until it has whatever confirmation it needs. Normally this wouldn't be a problem, because confirmation is presumably almost instantaneous the great majority of the time. But compiling the code required to confirm takes ~1 second. And that's the part that has to happen on each worker in serial. That 1 second is not used in compiling the statement itself (which I know because I've tried statements that take much longer to compile); it must be just some piece of code required to let the primary know it got the message. By precompiling something as simple as |
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maybe the precompilation in #42156 didn't fix this issue? maybe there is some other code that's needs to be precompiled on the worker end that isn't precompiled by just calling |
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Maybe. I don't know how julia's own build process works; maybe the image you used isn't being built with multiple processes. Also, I'll point out that in the workaround I linked above, I actually used the |
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Is it possible that his bug also affects
# all precompile(...) calls
function main()
MPI.Initialized()
MPI.Init(threadlevel=:multiple)
base_comm = MPI.COMM_WORLD
print(" comm size: $(MPI.Comm_size(base_comm)) ---")
base_grp = MPI.Comm_group(base_comm)
id_group = MPI.Group_incl(base_grp, Int32[0])
comm = MPI.Comm_create_group(base_comm, id_group, 42)
MPI.Barrier(base_comm)
fh = MPI.File.open(comm, "path/to/file/foo.bar"; append=true, write=true, create=true)
MPI.File.seek_shared(fh, 0)
MPI.File.write_ordered(fh, Int32[42,420])
MPI.File.write_at_all(fh, 1, Int32[69])
MPI.File.write_at(fh, 0, Int32[1])
close(fh)
end
main()And I then just execute |
Unlikely, since |
Sure, thank you. I'm now trying investigating on it so that i have more informations about it |
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com>
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com> (cherry picked from commit 62e0729)
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com> (cherry picked from commit 62e0729)
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com> (cherry picked from commit 62e0729)
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com> (cherry picked from commit 62e0729)
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com> (cherry picked from commit 62e0729)
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com> (cherry picked from commit 62e0729)
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com> (cherry picked from commit 62e0729)
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes JuliaLang/julia#44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see JuliaLang/julia#44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes JuliaLang/julia#39291. - JuliaLang/julia#42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with JuliaLang/julia#38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com> (cherry picked from commit 3b57a49)
* avoid using `@sync_add` on remotecalls It seems like @sync_add adds the Futures to a queue (Channel) for @sync, which in turn calls wait() for all the futures synchronously. Not only that is slightly detrimental for network operations (latencies add up), but in case of Distributed the call to wait() may actually cause some compilation on remote processes, which is also wait()ed for. In result, some operations took a great amount of "serial" processing time if executed on many workers at once. For me, this closes #44645. The major change can be illustrated as follows: First add some workers: ``` using Distributed addprocs(10) ``` and then trigger something that, for example, causes package imports on the workers: ``` using SomeTinyPackage ``` In my case (importing UnicodePlots on 10 workers), this improves the loading time over 10 workers from ~11s to ~5.5s. This is a far bigger issue when worker count gets high. The time of the processing on each worker is usually around 0.3s, so triggering this problem even on a relatively small cluster (64 workers) causes a really annoying delay, and running `@everywhere` for the first time on reasonable clusters (I tested with 1024 workers, see #44645) usually takes more than 5 minutes. Which sucks. Anyway, on 64 workers this reduces the "first import" time from ~30s to ~6s, and on 1024 workers this seems to reduce the time from over 5 minutes (I didn't bother to measure that precisely now, sorry) to ~11s. Related issues: - Probably fixes #39291. - #42156 is a kinda complementary -- it removes the most painful source of slowness (the 0.3s precompilation on the workers), but the fact that the wait()ing is serial remains a problem if the network latencies are high. May help with #38931 Co-authored-by: Valentin Churavy <vchuravy@users.noreply.github.com>
julia/stdlib/Distributed/src/macros.jl
Line 207 in 7647ab5
Please check here for descriptions of the problem by three Julia users:
https://discourse.julialang.org/t/everywhere-takes-a-very-long-time-when-using-a-cluster/35724
I have tested
@everywhereandpmap()on an HPC. Test code and result available herehttps://github.com/algorithmx/nodeba
Basically I just put timestamps between the lines. You can see in t*.log files that the largest gap is the one between timestamp 3 and 4. More interestingly, I found that increasing nworkers() causes the gap to increase linearly. I believe that this gap represents the execution time of the macro
@everywhere, seen from master.The vesion info is :
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