mmap failure with address space quotas

[JonathanAnderson]

I'm having a problem where when I build from 3c7136e when I run julia, I get the error could not allocate pools If I run as a different user, Julia runs successfully.

I think there might be something specific to my user on this box, but I am happy to help identify what is happening here.

I think this is related to #8699

also, from the julia-users group: https://groups.google.com/forum/#!topic/julia-users/FSIC1E6aaXk

[JeffBezanson]

This error is from a failing mmap, where we try to allocate 8GB of virtual address space. There might be a quota on virtual memory for some users.

[pao]

Oops, misread the issue, sorry.

[ivarne]

-v: address space (kb) 8000000 (from the julia-users thread) seems to indicate that a 8GB allocation is guaranteed to cause trouble

[JeffBezanson]

@carnaval Could we decrease this to, say, 4GB, to make this issue less likely?

[tkelman]

an 8gb array is also too large for msvc to compile, fwiw

[tkelman]

Can you try reducing the number on

julia/src/gc.c

Line 88 in e1d6e56

#define REGION_PG_COUNT 16*8*4096 // 8G because virtual memory is cheap

by a factor of 2 or 4, see if it helps? I could also make a test branch with that change to have the buildbot make test binaries if that would be easier.

[carnaval]

We can certainly lower this. I set it that high under the reasoning that address space was essentially free on x64. As I understand it, operations are either O(f(number of memory mappings)) or O(f(size of resident portion)) so it should not hurt performance.
I didn't think of arbitrary quotas, but it's probably better to ask, does anyone know any other drawback in allocating "unreasonable" amounts of virtual memory on 64bit arch ?

[ScottPJones]

@carnaval Yes, indeed... lots of performance issues if you have very large amounts of memory mapped... which is why people use huge page support...

[carnaval]

Keep in mind I'm still talking about uncomitted memory. The advantage of huge pages is reducing TLB contention as far as I know, and uncomitted memory sure won't end up in the TLB.

Generally, as far as my understanding of the kernel VM system goes, "dense" data structures (such as the page table, for which the TLB acts as a cache) are only filled with committed memory. The mapping itself stays into a "sparse" structure (like a list of mappings), so you only pay costs relative to the number of mappings. I may be wrong though, so I'll be happy to be corrected.

[ScottPJones]

I'm talking about memory that has actually been touched, i.e. commited.
The issue is if you have an (opt-in at least) limit in the language, instead of just relying on things like ulimit, you can (at least in my experience) better control things, keep things from getting to the point where the OS goes bellyup. Say you have 60,000 processes running, which you know only need say 128M (unless they somehow get out of control, due to some bug)... having the limit protects you.
You may also have different classes of processes that need more memory (say, loading a huge XML document), it's important to be able to also be able to allow those to dynamically (based on user roles) have a higher limit).

[carnaval]

That's not what my question was about though. We are already careful to decommit useless pages.

The limit is another issue, to enforce it strictly would probably require parsing /proc/self/smaps from time to time anyway to be sure some C library is not sneaking around making mappings.

[ScottPJones]

Yes, but does the current system ever try to proactively cut down on caches, etc., so that it can free up some memory?

It doesn't really have to be done strictly, to be useful, without fancy approaches like parsing /proc/...
also, for people embedding julia, couldn't things be compiled so that at least malloc/calloc/realloc end up using a julia version, that does keep track?
Having some facility to try to increase stability is better than none, even if it can't handle external memory pressures.

[carnaval]

I'm not arguing that we should not do those things. But those are features. I was just trying to check if someone knew that some kernel would be slow with large mappings : it would be a regression, not a missing feature.

[mauro3]

I'm running into a could not allocate pools issue on a new build on a new machine (0.3 works fine).
(Not sure whether this warrants a new issue or not, let me know.)

It builds fine but it crashes on running the tests, the culprit is addprocs:

   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "help()" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.4.0-dev+6683 (2015-08-12 17:53 UTC)
 _/ |\__'_|_|_|\__'_|  |  Commit 103f7a3* (0 days old master)
|__/                   |  x86_64-linux-gnu

julia> addprocs(3; exeflags=`--check-bounds=yes --depwarn=error`)
could not allocate pools

However, addprocs(2; exeflags=``--check-bounds=yes --depwarn=error``) works. Also starting more than three REPLs at once produces the error.

As far as I can tell there are no relevant ulimits:

 $ ulimit -a
-t: cpu time (seconds)         unlimited
-f: file size (blocks)         unlimited
-d: data seg size (kbytes)     unlimited
-s: stack size (kbytes)        8192
-c: core file size (blocks)    0
-m: resident set size (kbytes) unlimited
-u: processes                  63889
-n: file descriptors           1024
-l: locked-in-memory size (kb) 64
-v: address space (kb)         unlimited
-x: file locks                 unlimited
-i: pending signals            63889
-q: bytes in POSIX msg queues  819200
-e: max nice                   0
-r: max rt priority            0
-N 15:                         unlimited

On my normal machine the -l option is unlimited, but limiting it there to 64 does not reproduce this behavior.

[mauro3]

The same problem arises using the Julia nightlies julia-0.4.0-24a92a9f5d-linux64.tar.gz.

Any ideas on how I could resolve this? Should I contact the admin of that machine to change some settings?

[carnaval]

yes, you can remove the 16* here

julia/src/gc.c

Line 164 in f40da0f

#define REGION_PG_COUNT 16*8*4096 // 8G because virtual memory is cheap

and recompile.

Maybe I should make that the default but it feels so silly to me for admins to restrict addr space, I don't get it really.

[mauro3]

Yes, that works, thanks! Just to clarify, my understanding from this thread is that it is limiting the -v: address space (kb) which causes this. However, this is unlimited on my machine. So which one is the culprit?

[waTeim]

As for me, this is happening on ARM for unclear reasons. The GC memory space is currently not expandable I take it. If it were, I think minimal low-end stuff could afford a heap size of at least 64M, without an issue while expecting size approaching 1G is ridiculous. Somewhere in between is the target.

Additionally, I request that this needs to be configurable via library jl_init or similar, and not expect to be controlled by running julia the executable.

[yuyichao]

The arm issue is completely different. This is only an issue for those who cannot control the virtual address limit. The amount of physical memory is irrelevant here.

[waTeim]

Well since the error message is the same it at least seems related. Are you saying this happens not because of the size of the allocation but the location? These aren't related? The previous discussion made it sound that people were having problems because the system prevented oversubscription which seems to indicate a problem with size. Well if that's the case, then that kind of makes sense too; it is true that there is a lack of OS support for 64-bit virtual addresses.

[r-barnes]

Attempting to compile on XSEDE's Comet raised this error. Removing 16* from gc.c allowed compilation to continue.

[eschnett]

Comet's front end has a severely restricted memory limit setting (ulimit). You can only allocate 2 GByte. The solution is to request a compute node interactively, and build there:

/share/apps/compute/interactive/qsubi.bash -p debug --nodes=1 --ntasks-per-node=24 -t 00:30:00 --export=ALL

[floswald]

Hi all,
is this going to be backported to 0.4.x at some point? I'm stuck with this problem on a cluster. thanks!

[tkelman]

#16385 was a pretty large change, I'm not sure whether it can be easily backported. Are you building from source or using binaries? If the former, just change the number in the code and recompile. If the latter, I guess we could trigger an unofficial build with a smaller value.

[floswald]

i was using binaries. building is a nightmare on that system as well, I run into diskspace quota exceeded on the login node all the time, and i can't get the build to work on a compute node either. If you can trigger an unofficial 0.4.5 build that would save my week. thanks.

[tkelman]

might take a while to build, but check back at https://build.julialang.org/builders/package_tarball64/builds/435 and when it's done it should be available at https://julianightlies.s3.amazonaws.com/bin/linux/x64/0.4/julia-0.4.6-c7cd8171df-linux64.tar.gz (assuming you want 64 bit linux, and dropping by a factor of 8 will get you below your ulimit)

[floswald]

Awesome! Thanks.

On Wednesday, 8 June 2016, Tony Kelman [email protected] wrote:

might take a while to build, but check back at
https://build.julialang.org/builders/package_tarball64/builds/435 and
when it's done it should be available at
julianightlies.s3.amazonaws.com/bin/linux/x64/0.4/julia-0.4.6-c7cd8171df-linux64.tar.gz
(assuming you want 64 bit linux)

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[floswald]

@tkelman thanks so much works out of the box like a charm! so much for "broken software". outstanding support as usual. 👍 👍 👍

[mauro3]

In case someone else stumbles over this: I was under the impression that this issue was resolve but it still surfaced for me with 0.5-rc4 binaries and source build for rc4, see #18477.

The error now looks a bit different for me with either just hanging at the tests when running make testall or when doing addprocs with a suitably high number I get Master process (id 1) could not connect within 60.0 seconds. The fix is as before but now in file src/gc-pages.c.

[StefanKarpinski]

Reopened to be fixed in 0.5.x.

[yuyichao]

As mentioned in the related issue, this is really #17987. It does not fail because we are asking for a huge fixed size anymore and the remaining is better handled by allowing users with special memory constraint to specify that directly.

[floswald]

Sorry to bother with this but I am still looking for a solution to this problem. I am working on a cluster where I have to request the max amount of virtual and physical memory that I will be using, and I have to request very large amounts in order for my job to run at all. This puts me on a significantly longer queue, because I basically need an entire compute node all for myself. julia v0.5-rc3.

my job has the following memory requirements when run on a single compute node on that same cluster.

• 2.5GB of RES, 7038MB VIRT: https://www.dropbox.com/s/jii21v56i5v86vr/Screenshot%202016-09-21%2010.43.14.png?dl=0
• when run on my office mac os: max RES is 2648MB, so same ballpark.
  https://www.dropbox.com/s/wkmawhxo0i78b95/Screenshot%202016-09-21%2010.40.00.png?dl=0

Any advice for how to deal with this greatly appreciated.