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Thread: Zimbra responds slowly from time to time

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  1. #1
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    Default Zimbra responds slowly from time to time

    Hello,

    we have a problem with Zimbra network edition. From time to time, "java" process takes 90% of CPU time and 33% of memory.

    I did jps and it's this process:

    31825 com.zimbra.cs.launcher.TomcatLauncher -Xms709m -Xmx709m -XX:NewRatio=2 -Djava.awt.headless=true -Dcatalina.base=/opt/zimbra/apache-tomcat-5.5.15 -Dcatalina.home=/opt/zimbra/apache-tomcat-5.5.15 -Djava.io.tmpdir=/opt/zimbra/apache-tomcat-5.5.15/temp -Djava.library.path=/opt/zimbra/lib -Djava.endorsed.dirs=/opt/zimbra/apache-tomcat-5.5.15/common/endorsed

    Version is 4.5.6, running on Ubuntu.

    We have 2GB of memory, 15 users. This "downtime" and high load takes
    about five minutes and then continues.

    How can I debug this?


    Juraj.

  2. #2
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    Default Some more information

    Top:

    Code:
    top - 00:04:51 up 9 days, 18:01,  4 users,  load average: 3.47, 1.76, 0.91
    Tasks: 133 total,   6 running, 127 sleeping,   0 stopped,   0 zombie
    Cpu(s): 46.7% us, 51.5% sy,  0.0% ni,  0.2% id,  0.0% wa,  1.1% hi,  0.5% si
    Mem:   1815948k total,  1723604k used,    92344k free,    90164k buffers
    Swap:   939760k total,      108k used,   939652k free,   410928k cached
    
      PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND                                                                            
    31825 zimbra    16   0 1025m 585m  14m S   62 33.0  84:10.62 java
    20315 zimbra    25   0  251m 7920 5776 R   10  0.4   0:00.30 java
    20320 postfix   16   0  9104 3388 2676 S    7  0.2   0:00.21 smtpd
    17597 zimbra    25   0  9156 5384 2140 R    7  0.3   0:09.30 zmgengraphs
    20278 zimbra    22   0  5380 2708 1524 S    6  0.1   0:00.19 zmstatuslog
    Dstat output:

    Code:
    ----total-cpu-usage---- -disk/total -net/total- ---paging-- ---system--
    usr sys idl wai hiq siq|_read write|_recv _send|__in_ _out_|_int_ _csw_
      3   5  92   0   0   0|4980B   45k|   0     0 |   0   0.1 | 125   278 
     50  49   0   0   0   1|   0   268k|2700B 9430B|   0     0 | 157   243 
     51  44   0   0   3   1|   0     0 |7970B   20k|   0     0 | 243   343 
     48  50   0   0   1   1|   0  5120B|4922B   56k|   0     0 | 227   315 
     48  51   0   0   0   0|   0     0 |1046B 1126B|   0     0 | 118   244 
     35  62   0   0   2   0|   0   272k|3248B 2575B|   0     0 | 163   460 
     60  39   0   0   1   0|   0   236k|1748B 9128B|   0     0 | 140   295

    We have our /opt/zimbra/store, /opt/zimbra/index and /opt/zimbra/redolog
    on NFS server (actually running Solaris 10). I ran a zpool iostat 1 check and there was absolutely no traffic to the remote storage over NFS, so Zimbra
    did not touch any of these directories during that high load.

    What is pretty interesting is, that there's a lot of time spent in system
    (I saw 70% and also 100% few times in system cpu usage).

    Anything else I can have a look at?

    The Zimbra install is running under VMWare server.

  3. #3
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    Default

    Oh, NFS is bad.
    I'm actually surprised you got it working.

    Zimbra and NFS don't mix will (right now). My guess is that's where the problem is occurring.

  4. #4
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    Default Nfs?

    Really?

    Actually, when we switched to NFS, it was a lot better than before performance-wise.

    Anyways, it did the same thing without NFS, I just switched to NFS recently, because we brought 4.7TB NAS, so we wanted to put all mails there. Anyways, we had the same problem before we switched to NFS. Also as
    seen from the IOstat output, there was no NFS traffic in that particular time.

    Now I tried this KB article from vmware:

    VMware Knowledge Base - View Document

    I switched VMWare to use only one CPU for each guest (we run three guests on that machine). I added noapic nolapic nosmp options. I will let it run
    for a week and see if it helps.

  5. #5
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    Default

    Hi all,

    check this thread:
    http://www.zimbra.com/forums/adminis...s-zcs-oss.html
    I had the same issue (but local filesystems) and it was related to email stuck in the deferred queue.

    Kind Regards
    Andre

  6. #6
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    Default

    Quote Originally Posted by jholder View Post
    Oh, NFS is bad.
    I'm actually surprised you got it working.
    This is a fairly bold statement - do you have benchmarks and configuration info to back this up?

    I'm running a test implementation on NFS right now, primarily because it was an easy way to throw as much backed-up, snapshotted space into my environment as I needed. It's working fine.

    It would be nice to know what has and has not been tested on NFS, and what configurations were used. For example, the storage requirements of the MySQL store are very different from the message store. Putting them both on the same type of storage for an installation of any substantial size seems likely to be less than optimal.

  7. #7
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    I too am interested in utilizing an NFS resource to off load old email but using Zimbra's HSM function instead. Specifically adding a new volume declaring is a secondary volume and then mounting an nfs resource to that volume's path.

    My biggest concern is Zimbra's ability to recover if network issues arise between our zimbra server and the nfs server. Whether it is a "glitch" or an outage.

  8. #8
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    NFS has some known issues with IO performance with Zimbra. We do not recommend using it.

    If you can use something like netapp or symlinks, that's better.

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