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<p>I am seeing something similar here on Tom's Novelty Search |
Distance: hamming | Super Anagrams - run 0 job (maybe would happen
on any job):</p>
<p>-The node is not running out of RAM and there are no errors</p>
<p>-However, before the job actually starts doing anything, there is
a long (5-10 minute or longer) delay after initial memory
allocation:</p>
<p><br>
</p>
<p>top - 12:04:09 up 2 days, 19:38, 1 user, load average: 0.00,
0.11, 0.09<br>
Tasks: 714 total, 1 running, 713 sleeping, 0 stopped, 0
zombie<br>
Cpu(s): 0.1%us, 0.1%sy, 0.0%ni, 99.9%id, 0.0%wa, 0.0%hi,
0.0%si, 0.0%st<br>
Mem: 66012900k total, 3158436k used, 62854464k free, 157252k
buffers<br>
Swap: 2047996k total, 0k used, 2047996k free, 609584k
cached<br>
<br>
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+
COMMAND <br>
63928 thelmuth 20 0 18.7g 330m 11m S 0.0 0.5 0:09.82
java <br>
63986 thelmuth 20 0 18.7g 327m 11m S 0.0 0.5 0:10.52
java <br>
64232 thelmuth 20 0 18.7g 252m 11m S 0.0 0.4 0:06.68
java <br>
64053 thelmuth 20 0 18.7g 185m 11m S 0.0 0.3 0:05.85
java <br>
64112 thelmuth 20 0 18.7g 182m 11m S 0.0 0.3 0:05.47
java <br>
63838 thelmuth 20 0 18.7g 177m 11m S 0.0 0.3 0:05.90
java <br>
64172 thelmuth 20 0 18.7g 173m 11m S 0.0 0.3 0:04.80
java <br>
63780 thelmuth 20 0 18.7g 169m 11m S 0.0 0.3 0:05.52
java <br>
</p>
<p>Very little CPU is being used - the network isn't sluggish - it's
not out of RAM (though that's a LOT of VIRT RAM for each job to
claim... but Java just kinda seems to do that)... occasionally
you'll see one of the processes use some CPU for a second... and
in a few minutes they will all start chugging away. Weird and I'm
not sure what's up at the moment, but it doesn't seem to exactly
harm anything - just weird.<br>
</p>
<p> -Josiah</p>
<p> <br>
</p>
<p><br>
</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 7/19/17 10:55 AM, Wm. Josiah Erikson
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:8410f858-dc8b-a67a-9055-81dae081bebf@hampshire.edu">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<p>I just saw one of Tom's jobs do the same thing (run rack0 nodes
out of RAM - not sure if any of the jobs actually crashed yet,
but still...), so I did two things:</p>
<p>1. Set the per-blade "sh" limit to 8 (previously unlimited)<br>
</p>
<p>2. Set the number of slots on Rack 0 nodes to 8 (previously 16)<br>
</p>
<p> -Josiah</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 7/19/17 9:40 AM, Wm. Josiah
Erikson wrote:<br>
</div>
<blockquote type="cite"
cite="mid:c5cc0cfa-7e80-81c6-b1c9-0efc88e76b43@hampshire.edu">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8">
<p>Also, some additional notes:</p>
<p>1. I've set the "bash" limit tag to 8 per node. Tom seems to
use sh instead of bash, so this won't affect him, I think.<br>
</p>
<p>2. If you want to do 4 per node instead, just add the limit
tag "4pernode" to a RemoteCmd in the .alf file, like this:</p>
<p> RemoteCmd "bash -c "env blah blah" -tags "4pernode"
-service "tom"</p>
<p>3. There's also a 2pernode tag</p>
<p> -Josiah</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 7/19/17 9:30 AM, Wm. Josiah
Erikson wrote:<br>
</div>
<blockquote type="cite"
cite="mid:53149407-f293-d666-8194-a9cdb4f44b52@hampshire.edu">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8">
<p>Yeah, it ran out of RAM - probably tried to take 16 jobs
simultaneously. It's got 64GB of RAM, so should be able to
do quite a few. It's currently running at under 1/3 RAM
usage with 3 jobs, so 8 jobs should be safe. I'll limit
"bash" limit tag jobs (what yours default to since you
didn't set one explicitly and that's the command you're
running) to 8 per node. I could lower it to 4 if you prefer.
Let me know.<br>
</p>
<p> -Josiah</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 7/19/17 8:38 AM, Thomas
Helmuth wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CABgVVjfn0FW28918bU4GDky0NCX-4kyv4+uApHwUcBzhWWd8NA@mail.gmail.com">
<div dir="auto">Moving today, so I'll be brief.
<div dir="auto"><br>
</div>
<div dir="auto">This sounds like the memory problems we've
had on rack 4. There, there are just too many cures for
the amount of memory, so if too many runs start, none
get enough memory. That's why rack 4 isn't on the Tom or
big go service tags. Probably means we should remove
rack 0 from those tags for now until we figure it out.</div>
<div dir="auto"><br>
</div>
<div dir="auto">I've done runs on rack 4 by limiting each
run to 1GB of memory.</div>
<div dir="auto"><br>
</div>
<div dir="auto">Tom</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Jul 19, 2017 7:46 AM, "Lee
Spector" <<a href="mailto:lspector@hampshire.edu"
moz-do-not-send="true">lspector@hampshire.edu</a>>
wrote:<br type="attribution">
<blockquote class="quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
I launched some runs this morning (a couple of hours
ago -- I'm in Europe) that behaved oddly. I don't know
if this is related to recent upgrades/reconfiguration,
or what, but I thought I'd share them here.<br>
<br>
First, there were weird delays between launches and
the generation of the initial output. I'm accustomed
to delays of a couple of minutes at this point, which
I think we've determined (or just guessed) are due to
the necessity of re-downloading dependencies on fly
nodes, which doesn't occur when running on other
machines. But these took much longer, maybe 30-45
minutes or longer (not sure of the exact times, but
they were on that order). And weirder still, there
were long times during which many had launched but
only one was producing output and proceeding for a
long time, with others really kicking in only after
the early one(s) finished. I'd understand this if the
non-producing ones weren't launched at all, because
they were waiting for free slots.... but that's not
what was happening.<br>
<br>
And then one crashed, on compute-0-1 (this was
launched with the "tom" service tag, using the run-fly
script in Clojush), with nothing in the .err file
(from standard error) but the following in the .out
file (from standard output):<br>
<br>
Producing offspring...<br>
Java HotSpot(TM) 64-Bit Server VM warning: INFO:
os::commit_memory(<wbr>0x00000006f0e00000, 1059061760,
0) failed; error='Cannot allocate memory' (errno=12)<br>
#<br>
# There is insufficient memory for the Java Runtime
Environment to continue.<br>
# Native memory allocation (malloc) failed to allocate
1059061760 bytes for committing reserved memory.<br>
# An error report file with more information is saved
as:<br>
# /home/lspector/runs/july19a-<wbr>9235/Clojush/hs_err_pid57996.<wbr>log<br>
<br>
-Lee<br>
<br>
--<br>
Lee Spector, Professor of Computer Science<br>
Director, Institute for Computational Intelligence<br>
Hampshire College, Amherst, Massachusetts, 01002, USA<br>
<a href="mailto:lspector@hampshire.edu"
moz-do-not-send="true">lspector@hampshire.edu</a>, <a
href="http://hampshire.edu/lspector/"
rel="noreferrer" target="_blank"
moz-do-not-send="true">http://hampshire.edu/lspector/</a><wbr>,
<a href="tel:413-559-5352" value="+14135595352"
moz-do-not-send="true">413-559-5352</a><br>
<br>
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</blockquote>
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<br>
<pre class="moz-signature" cols="72">--
Wm. Josiah Erikson
Assistant Director of IT, Infrastructure Group
System Administrator, School of CS
Hampshire College
Amherst, MA 01002
(413) 559-6091
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Wm. Josiah Erikson
Assistant Director of IT, Infrastructure Group
System Administrator, School of CS
Hampshire College
Amherst, MA 01002
(413) 559-6091
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Wm. Josiah Erikson
Assistant Director of IT, Infrastructure Group
System Administrator, School of CS
Hampshire College
Amherst, MA 01002
(413) 559-6091
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Wm. Josiah Erikson
Assistant Director of IT, Infrastructure Group
System Administrator, School of CS
Hampshire College
Amherst, MA 01002
(413) 559-6091
</pre>
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