I have something like this
outputs = Parallel(n_jobs=12, verbose=10)(delayed(_process_article)(article, config) for article in data)
Case 1: Run on ubuntu with 80 cores:
CPU(s): 80
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
There are a total of 90,000 tasks. At around 67k it fails and is terminated.
joblib.externals.loky.process_executor.BrokenProcessPool: A process in the executor was terminated abruptly, the pool is not usable anymore.
When I monitor the top at 67k I see a sharp fall in the memory
top - 11:40:25 up 2 days, 18:35, 4 users, load average: 7.09, 7.56, 7.13
Tasks: 32 total, 3 running, 29 sleeping, 0 stopped, 0 zombie
%Cpu(s): 7.6 us, 2.6 sy, 0.0 ni, 89.8 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 33554432 total, 40 free, 33520996 used, 33396 buff/cache
KiB Swap: 0 total, 0 free, 0 used. 40 avail Mem
Case 2: Mac with 8 cores
hw.physicalcpu: 4
hw.logicalcpu: 8
But on the mac it is much much slower .. And surprisingly it does not get killed at 67k..
Additionally, I reduced the parallelism (in case 1) to 2,4 and it still fails :(
Why is this happening? Has anyone faced this issue before and has a fix?
Note: when I run for 50,000 tasks it runs well and does not give any problems.
Thank you!
Got a machine with an increased memory of 128GB and that solved the problem!
Related
I just did a large import of renderd tiles for an osm server. I want to start my next process (running the import of nominatim) but it takes a lot of memory. The problem I have is that walwriter, background writer, checkpointer are consuming 131GB of memory. I checked pg_top and the processes are sleeping. Is there any way to clear these processes safely or just force postgres to complete the walwriter and background writer?
I am using Postgres v12, and shared_buffers is set to 128GB.
HTOP:
pg_top:
last pid: 628600; load avg 0.08, 0.03, 0.04; up 1+00:31:38 02:22:22
5 5 sleeping
CPU states: 0.0% user, 0.0% nice, 0.0% system, 100% idle, 0.0% iowait
Memory: 487G used, 16G free, 546M buffers, 253G cached
DB activity: 0 tps, 0 rollbs/s, 0 buffer r/s, 100 hit%, 43 row r/s, 0 row w/s -
DB I/O: 0 reads/s, 0 KB/s, 0 writes/s, 0 KB/s
DB disk: 3088.7 GB total, 2538.8 GB free (17% used)
Swap: 45M used, 8147M free, 588K cached
627692 postgres 20 0 131G 4368K sleep 0:00 0.00% 0.00% postgres: 12/main: background writer
627691 postgres 20 0 131G 6056K sleep 0:00 0.00% 0.00% postgres: 12/main: checkpointer
627693 postgres 20 0 131G 4368K sleep 0:00 0.00% 0.00% postgres: 12/main: walwriter
628601 postgres 20 0 131G 11M sleep 0:00 0.00% 0.00% postgres: 12/main: postgres postgres [local] idle
627695 postgres 20 0 131G 6924K sleep 0:00 0.00% 0.00% postgres: 12/main: logical replication launcher
pg_wal directory:
Everything is just fine, and htop is lying to you.
Of course the background processes that access shared buffers will use that memory, and since it is shared memory, it is reported for each of these processes. In reality, it is allocated only once.
The shared memory allocated by PostgreSQL is slightly bigger than shared_buffers, so if that parameter is set to 128GB, you reported data make sense and are perfectly normal.
If you set max_wal_size = 32GB, it is normal to have a lot of WAL segments.
My company is considering a self-hosted option for a combination of JIRA, Confluence and MySQL running behind an nginx proxy. We are a very small team of 5, and expect extremely mild usage for now. I hardly even expect any concurrent usage at this point.
I am a bit puzzled by the various guidelines posted by Atlassian:
https://confluence.atlassian.com/enterprise/jira-sizing-guide-461504623.html
https://confluence.atlassian.com/adminjiraserver075/jira-applications-installation-requirements-935390824.html
https://confluence.atlassian.com/doc/example-size-and-hardware-specifications-from-customer-survey-76840961.html
https://confluence.atlassian.com/doc/server-hardware-requirements-guide-30736403.html
It seems they don't want to bother providing actual minimum hardware requirements. For example, on the same page they could say "minimum heap size to allocate to Confluence is 1 GB and 1 GB for Synchrony (which is required for collaborative editing)" and also that " minimum hardware recommendation" is 6GB. The leap from 1 required plus 1 optional to 6 recommended minimum is bizarre, to say the least.
I think what I want to know is whether I will be able to fit this setup into a 2GB RAM machine or a 4GB RAM machine (both dual CPU).
OK, I have done a test with following configuration:
VM with 2 cores capped at ~2.2Ghz and 4GB RAM
Ubuntu 16.04 server
Docker and docker-compose
Containers:
nginx
jwilder/docker-gen
jrcs/letsencrypt-nginx-proxy-companion
cptactionhank/atlassian-jira-software
cptactionhank/atlassian-confluence
mysql
This 4GB RAM machine is barely capable of running this setup:
$ free -m
total used free shared buff/cache available
Mem: 3951 3553 107 0 291 157
Swap: 974 725 249
CPU usage was going up to 200% only during initialisation when JIRA and Confluence started with empty home dirs. The following top output is after:
creating a space and a page in Confluence
and a project with ~10 issues in JIRA
and linking JIRA and Confluence together
$ top -o %MEM | head -15
top - 16:14:33 up 6:12, 2 users, load average: 0.15, 0.04, 0.01
Tasks: 132 total, 1 running, 131 sleeping, 0 stopped, 0 zombie
%Cpu(s): 2.6 us, 0.5 sy, 0.0 ni, 95.8 id, 1.0 wa, 0.0 hi, 0.1 si, 0.0 st
KiB Mem : 4046364 total, 128808 free, 3638444 used, 279112 buff/cache
KiB Swap: 998396 total, 252956 free, 745440 used. 161144 avail Mem
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
6328 bin 20 0 3306232 1.468g 0 S 0.0 38.1 12:03.27 java
6418 bin 20 0 2860000 1.320g 0 S 0.0 34.2 10:56.24 java
7205 bin 20 0 2807088 476592 1724 S 0.0 11.8 1:58.37 java
5752 999 20 0 1815480 99804 4728 S 0.0 2.5 1:11.29 mysqld
1070 root 20 0 621908 28672 8904 S 0.0 0.7 0:30.74 dockerd
1179 root 20 0 623004 7536 2520 S 0.0 0.2 0:16.66 docker-containe
968 root 20 0 291352 6536 1912 S 0.0 0.2 0:00.77 snapd
8310 root 20 0 15388 5064 3056 S 0.0 0.1 0:21.39 docker-gen
Confluence also allocated ~500MB RAM to Synchrony:
$ ps aux --sort -rss | head -4
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
bin 6328 3.3 38.3 3306232 1551120 ? Ssl 10:14 12:12 /usr/lib/jvm/java-1.8-openjdk/bin/java -Djava.util.logging.config.file=/opt/atlassian/confluence...
bin 6418 2.9 34.1 2860000 1382868 ? Ssl 10:14 10:57 /usr/lib/jvm/java-1.8-openjdk/bin/java -Djava.util.logging.config.file=/opt/atlassian/jira/...
bin 7205 0.5 11.7 2807088 476588 ? Sl 10:44 1:59 /usr/lib/jvm/java-1.8-openjdk/jre/bin/java -classpath /opt/atlassian/confluence/temp/... synchrony.core sql
During JIRA and Confluence install stage, MySQL peaked at around 500MB RAM usage, and during normal operation it sits around 100MB.
In my attempts, a 2GB machine was only enough to run either JIRA or Confluence without MySQL.
Conclusion:
It looks like 4GB RAM Dual core machine is the absolute minimum required for JIRA+Confluence+MySQL. But keep in mind that such a machine is barely enough for a practically empty project.
I personally was not expecting these applications to be that RAM hungry being empty.
I recently started using a tool called pg_top that shows statistics for Postgres, however since I am not verify versed with the internals of Postgres I needed a bit of clarification on the output.
last pid: 6152; load avg: 19.1, 18.6, 20.4; up 119+20:31:38 13:09:41
41 processes: 5 running, 36 sleeping
CPU states: 52.1% user, 0.0% nice, 0.8% system, 47.1% idle, 0.0% iowait
Memory: 47G used, 16G free, 2524M buffers, 20G cached
DB activity: 151 tps, 0 rollbs/s, 253403 buffer r/s, 86 hit%, 1550639 row r/s,
21 row w/s
DB I/O: 0 reads/s, 0 KB/s, 35 writes/s, 2538 KB/s
DB disk: 233.6 GB total, 195.1 GB free (16% used)
Swap:
My question is under the DB Activity, the 1.5 million row r/s, is that a lot? If so what can be done to improve it? I am running puppetdb 2.3.8, with 6.8 million resources, 2500 nodes, and Postgres 9.1. All of this runs on a single 24 core box with 64GB of memory.
Customers are reporting problems almost every day on about the same hours. This app is running on 2 nodes. It is Metastorm BPM platform and it's calling our code.
In some dumps I noticed very long running threads (~50 minutes) but not in all of them. Administrators are also telling me that just before users report problems memory usage goes up. Then everything slows down to the point they can't work and admins have to restart platforms on both nodes. My first thought was deadlocks (long running threads) but didn't manage to confirm that. !syncblk isn't returning anything. Then I looked at memory usage. I noticed a lot of dynamic assemblies so thought maybe assemblies leak. But it looks it's not that. I have received dump from day where everything was working fine and number of dynamic assemblies is similar. So maybe memory leak I thought. But also cannot confirm that. !dumpheap -stat shows memory usage grows but I haven't found anything interesting with !gcroot. But there is one thing I don't know what it is. Threadpool Completion Port. There's a lot of them. So maybe sth is waiting on sth? Here is data I can give You so far that will fit in this post. Could You suggest anything that could help diagnose this situation?
Users not reporting problems:
Node1 Node2
Size of dump: 638MB 646MB
DynamicAssemblies 259 265
GC Heaps: 37MB 35MB
Loader Heaps: 11MB 11MB
Node1:
Number of Timers: 12
CPU utilization 2%
Worker Thread: Total: 5 Running: 0 Idle: 5 MaxLimit: 2000 MinLimit: 200
Completion Port Thread:Total: 2 Free: 2 MaxFree: 16 CurrentLimit: 4 MaxLimit: 1000 MinLimit: 8
!dumpheap -stat (biggest)
0x793041d0 32,664 2,563,292 System.Object[]
0x79332b9c 23,072 3,485,624 System.Int32[]
0x79330a00 46,823 3,530,664 System.String
0x79333470 22,549 4,049,536 System.Byte[]
Node2:
Number of Timers: 12
CPU utilization 0%
Worker Thread: Total: 7 Running: 0 Idle: 7 MaxLimit: 2000 MinLimit: 200
Completion Port Thread:Total: 3 Free: 1 MaxFree: 16 CurrentLimit: 5 MaxLimit: 1000 MinLimit: 8
!dumpheap -stat
0x793041d0 30,678 2,537,272 System.Object[]
0x79332b9c 21,589 3,298,488 System.Int32[]
0x79333470 21,825 3,680,000 System.Byte[]
0x79330a00 46,938 5,446,576 System.String
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Users start to report problems:
Node1 Node2
Size of dump: 662MB 655MB
DynamicAssemblies 236 235
GC Heaps: 159MB 113MB
Loader Heaps: 10MB 10MB
Node1:
Work Request in Queue: 0
Number of Timers: 14
CPU utilization 20%
Worker Thread: Total: 7 Running: 0 Idle: 7 MaxLimit: 2000 MinLimit: 200
Completion Port Thread:Total: 48 Free: 1 MaxFree: 16 CurrentLimit: 49 MaxLimit: 1000 MinLimit: 8
!dumpheap -stat
0x7932a208 88,974 3,914,856 System.Threading.ReaderWriterLock
0x79333054 71,397 3,998,232 System.Collections.Hashtable
0x24f70350 319,053 5,104,848 Our.Class
0x79332b9c 53,190 6,821,588 System.Int32[]
0x79333470 52,693 6,883,120 System.Byte[]
0x79333150 72,900 11,081,328 System.Collections.Hashtable+bucket[]
0x793041d0 247,011 26,229,980 System.Object[]
0x79330a00 644,807 34,144,396 System.String
Node2:
Work Request in Queue: 1
Number of Timers: 17
CPU utilization 17%
Worker Thread: Total: 6 Running: 0 Idle: 6 MaxLimit: 2000 MinLimit: 200
Completion Port Thread:Total: 48 Free: 2 MaxFree: 16 CurrentLimit: 49 MaxLimit: 1000 MinLimit: 8
!dumpheap -stat
0x7932a208 76,425 3,362,700 System.Threading.ReaderWriterLock
0x79332b9c 42,417 5,695,492 System.Int32[]
0x79333150 41,172 6,451,368 System.Collections.Hashtable+bucket[]
0x79333470 44,052 6,792,004 System.Byte[]
0x793041d0 175,973 18,573,780 System.Object[]
0x79330a00 397,361 21,489,204 System.String
Edit:
I downloaded debugdiag and let it analyze my dumps. Here is part of output:
The following threads in process_name name_of_dump.dmp are making a COM call to thread 193 within the same process which in turn is waiting on data to be returned from another server via WinSock.
The call to WinSock originated from 0x0107b03b and is destined for port xxxx at IP address xxx.xxx.xxx.xxx
( 18 76 172 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 210 211 212 213 214 215 216 217 218 224 225 226 227 228 229 231 232 233 236 239 )
14,79% of threads blocked
And the recommendation is:
Several threads making calls to the same STA thread can cause a performance bottleneck due to serialization. Server side COM servers are recommended to be thread aware and follow MTA guidelines when multiple threads are sharing the same object instance.
I checked using windbg what thread 193 does. It is calling our code. Our code is calling some Metastorm engine code and it hangs on some remoting call. But !runaway shows it is hanging for 8 seconds. So not that long. So I checked what are those waiting threads. All except thread 18 are:
System.Threading._IOCompletionCallback.PerformIOCompletionCallback(UInt32, UInt32, System.Threading.NativeOverlapped*) I could understand one, but why so many of them. Is it specific to business process modeling engine we're using or is it something typical? I guess it's taking threads that could be used by other clients and that's why the slowdown reported by users. Are those threads Completion Port Threads I asked about before? Can I do anything more to diagnose or did I found our code to be the cause?
From the looks of the output most of the memory is not on the .net heaps (only 35 MB out of ~650) so if you are looking at the .net heaps I think you are looking in the wrong place. The memory is probably either in assemblies or in native memory if you are using some native component for file transfers or similar. You would want to use Debug Diag to monitor that.
It is hard to say if you are leaking dynamic assemblies without looking at the pattern of growth so I would suggest for that that you look at perfmon and #current assemblies to see if it keeps growing over time, if it does then you would have to investigate that further by looking at what the dynamic assemblies are with !dda
I've been using prstat and prstat -m a lot to investigate performance issues lately, and I think I've basically understood the differences of sampling vs. microstate accounting in Solaris 10. So I don't expect both to always show the exactly same number.
Today I came across an occasion where the 2 showed so vastly different outputs, that I have problems interpreting them and making sense of the output. The machine is a heavily loaded 8-CPU Solaris 10, with several large WebSphere processes and an Oracle database. The system practically came to a halt today for about 15 minutes (load averages of >700). I had difficulties to get any prstat information, but was able to get some outputs from "prtstat 1 1" and "prtstat -m 1 1", issued shortly one after another.
The top lines of the outputs:
prstat 1 1:
PID USERNAME SIZE RSS STATE PRI NICE TIME CPU PROCESS/NLWP
8379 was 3208M 2773M cpu5 60 0 5:29:13 19% java/145
7123 was 3159M 2756M run 59 0 5:26:45 7.7% java/109
5855 app1 1132M 26M cpu2 60 0 0:01:01 7.7% java/18
16503 monitor 494M 286M run 59 19 1:01:08 7.1% java/106
7112 oracle 15G 15G run 59 0 0:00:10 4.5% oracle/1
7124 oracle 15G 15G cpu3 60 0 0:00:10 4.5% oracle/1
7087 app1 15G 15G run 58 0 0:00:09 4.0% oracle/1
7155 oracle 96M 6336K cpu1 60 0 0:00:07 3.6% oracle/1
...
Total: 495 processes, 4581 lwps, load averages: 74.79, 35.35, 23.8
prstat -m 1 1 (some seconds later)
PID USERNAME USR SYS TRP TFL DFL LCK SLP LAT VCX ICX SCL SIG PROCESS/NLWP
7087 app1 0.1 56 0.0 0.2 0.4 0.0 13 30 96 2 33 0 oracle/1
7153 oracle 0.1 53 0.0 3.2 1.1 0.0 1.0 42 82 0 14 0 oracle/1
7124 oracle 0.1 47 0.0 0.2 0.2 0.0 0.0 52 77 2 16 0 oracle/1
7112 oracle 0.1 47 0.0 0.4 0.1 0.0 0.0 52 79 1 16 0 oracle/1
7259 oracle 0.1 45 9.4 0.0 0.3 0.0 0.1 45 71 2 32 0 oracle/1
7155 oracle 0.0 42 11 0.0 0.5 0.0 0.1 46 90 1 9 0 oracle/1
7261 oracle 0.0 37 9.5 0.0 0.3 0.0 0.0 53 61 1 17 0 oracle/1
7284 oracle 0.0 32 5.9 0.0 0.2 0.0 0.1 62 53 1 21 0 oracle/1
...
Total: 497 processes, 4576 lwps, load averages: 88.86, 39.93, 25.51
I have a very hard time interpreting the output. prstat seems to tell me that a fair amount of Java processing is going on, together with some Oracle stuff, just as I would expect in normal situation. prtstat -m shows a machine totally dominated by Oracle, consuming huge amounts of system time, and the overall CPU being heavily overloaded (large numbers in LAT).
I'm inclined to believe the output of prstat -m, because that matches much mor closely to what the system felt like during this time. Totally sluggish, almost no more user request processing going on from WebSphere, etc. But why would prstat show so heavily differing numbers?
Any explanation of this would be welcome!
CU, Joe
There's a known problem with prstat -m on Solaris in the way cpu usage figures are calculated - the value you see has been averaged over all threads (LWPs) in a process, and hence is far far too low for heavily multithreaded processes - such as your Java app servers, which can have hundreds of threads each (see your NLWP). Less than a dozen of them are probably CPU hogs hence the CPU usage by java looks "low". You'd need to call it with prstat -Lm to get the per-LWP (thread) breakdown to see that effect. Reference:
http://bugs.opensolaris.org/bugdatabase/view_bug.do?bug_id=6780169
Without further performance monitoring data it's hard to give non-speculative explanations of what you've seen there. I assume lock contention within java. One particular workload that can cause this is heavily multithreaded memory mapped I/O, they'll all pile up on the process address space lock. But it could be a purely java userside lock of course. A plockstat on one of the java processes, and/or simple dtrace profiling would be helpful.