Out Of MemoryError: Java heap space

[Zurab]

Good day,

I'm using datishnas for almost 2 months and using the system for our VM backup and saving more than 50% of disk sapce and currently for the first time I encountered IOException "Out Of MemoryError: Java heap space".

How can I resolved the error I encountered?

Details are the error and current configurations

Error log:

error,Garbage Collection,VM-image-backup,SDFS Volume Cleanup Failed because Java heap space,,Tue Jul 19 23:59:00 PHT 2016,Wed Jul 20 00:43:02 PHT 2016,4F381BE4-4D58-9FD8-5E30-E85F0C5D3842,,100,100
error,Garbage Collection,VM-image-backup,Garbage Collection failed Exception : java.io.IOException: java.lang.OutOfMemoryError: Java heap space,,Tue Jul 19 23:59:00 PHT 2016,Wed Jul 20 00:43:02 PHT 2016,BF6BB6A8-96EE-6DD9-BDED-92A1FC95A683,,1,1

mount.sdfs script:

# vi /sbin/mount.sdfs
#!/bin/bash
modprobe fuse > /dev/null
BASEMEMORY="1000"
CHUNKSZ="80"
CFG=""
MPTG=4
MU="M"
EXEC="/usr/share/sdfs/jsvc"
PF="sdfs-ncfg.pid"
if [[ ${1:0:1} == '-' ]]; then
while getopts ":v:" opt; do
  case $opt in
    v)
      CFG="/etc/sdfs/$OPTARG-volume-cfg.xml"
        PF="$OPTARG.pid"
        ;;
    z)
      MEM=$OPTARG
        ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done
else
        CFG="/etc/sdfs/$1-volume-cfg.xml"
        PF="$1.pid"
fi

if [ ! -n "$MEM" ]; then
if [ -n "$CFG" ] && [ -f "$CFG" ]; then
        ac=$(echo 'cat //subsystem-config/local-chunkstore/@allocation-size' | xmllint --shell "$CFG" | grep -v ">" | cut -f 2 -d "=" | tr -d - | tr -d \");
        bac=$(echo 'cat //subsystem-config/local-chunkstore/extended-config/@io-threads' | xmllint --shell "$CFG" | grep -v ">" | cut -f 2 -d "=" | tr -d - | tr -d \");
        MEMORY=$(((ac/10737418240*MPTG)+BASEMEMORY+(bac*CHUNKSZ)))
fi
else
        MEMORY=$MEM
fi

LD_PRELOAD="/usr/share/sdfs/bin/libfuse.so.2" $EXEC -server -outfile '&1' -errfile '&2' -Djava.library.path=/usr/share/sdfs/bin/ -home /usr/share/sdfs/bin/jre -Dorg.apache.commons.logging.Log=fuse.logging.FuseLog\
 -Dfuse.logging.level=INFO -Xmx$MEMORY$MU -Xms$MEMORY$MU \
-XX:+DisableExplicitGC -pidfile /var/run/$PF -XX:+UseG1GC -Djava.awt.headless=true \
"/sbin/mount.sdfs" 44 lines, 1463 characters

XML config:

# cat VM-image-backup-volume-cfg.xml
<?xml version="1.0" encoding="UTF-8" standalone="no"?><subsystem-config version="3.1.9">
<locations dedup-db-store="/opt/sdfs/metadata/VM-image-backup/ddb" io-log="/opt/sdfs/metadata/VM-image-backup/ioperf.log"/>
<io chunk-size="4" claim-hash-schedule="0 59 23 * * ?" dedup-files="true" hash-type="murmur3_128" log-level="1" max-file-inactive="900" max-file-write-buffers="1" max-open-files="1024" max-variable-segment-size="32" meta-file-cache="1024" read-ahead="false" safe-close="false" safe-sync="true" write-threads="8"/>
<permissions default-file="0644" default-folder="0755" default-group="0" default-owner="0"/>

<sdfscli enable="true" enable-auth="true" listen-address="0.0.0.0" password="5a24d6cf044a9dab25f2223041ba1356200002cf891fe723af9157d325f9dfd6" port="6442" salt="EqHAgv"/>
<local-chunkstore allocation-size="4398046511104" average-chunk-size="8192" chunk-store="/opt/sdfs/chunkdata/VM-image-backup" chunkstore-class="org.opendedup.sdfs.filestore.BatchFileChunkStore" cluster-config="/etc/sdfs/jgroups.cfg.xml" cluster-dse-password="admin" cluster-id="sdfs-cluster" compress="false" enabled="true" encrypt="false" encryption-iv="e729e9707a27862d19a20abd51e7d7a2" encryption-key="g27VHVaVi8QrC2G3QUfdUNvxLI+BJcNPFHVkNJ4NCjUen3e=2j7xDDd+HDu93+Mz" gc-class="org.opendedup.sdfs.filestore.gc.PFullGC" hash-db-store="/opt/sdfs/hashdb/VM-image-backup" hashdb-class="org.opendedup.collections.ProgressiveFileBasedCSMap" io-threads="8" max-repl-batch-sz="128">
<network enable="true" hostname="0.0.0.0" port="2222" use-ssl="false"/>
<extended-config allow-sync="false" block-size="60 MB" delete-unclaimed="true" io-threads="16" local-cache-size="10 GB" map-cache-size="100" read-speed="0" sync-files="false" upload-thread-sleep-time="150000" write-speed="0"/>
</local-chunkstore>
<volume allow-external-links="true" capacity="4 TB" closed-gracefully="false" cluster-block-copies="2" cluster-id="sdfs-cluster" cluster-rack-aware="false" cluster-response-timeout="4000" current-size="0" dse-comp-size="0" dse-size="0" duplicate-bytes="0" maximum-percentage-full="0.95" name="VM-image-backup" path="/opt/sdfs/metadata/VM-image-backup/files" perf-mon-file="/opt/sdfs//logs/volume-VM-image-backup-perf.json" read-bytes="0.0" read-timeout-seconds="-1" serial-number="1807226685" sync-files="false" use-dse-capacity="true" use-dse-size="true" use-perf-mon="false" volume-clustered="false" write-bytes="0" write-timeout-seconds="-1"/></


Thanks.

[Sam Silverberg]

Zubar,

Make sure that xmllint is on your system. If not, this is probably your issue. Otherwise, change the mount.sdfs script mptg from 4 to 5.

I'm guessing it's the xmllint.

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[Zurab]

Hi Sam

Good Day!

How can I check the xmllint if is working properly? As I checked xmllint  in on the system. I already increase the MPTG by 7 actually,  and restart the Datishnas appliance and after garbage collection run last night I still get the same error.


# which xmllint
/usr/bin/xmllint

# whereis xmllint
xmllint: /usr/bin/xmllint /usr/share/man/man1/xmllint.1.gz


Error log:

error,Garbage Collection,VM-image-backup,Garbage Collection failed Exception : java.io.IOException: java.lang.OutOfMemoryError: Java heap space,,Thu Jul 21 23:59:00 PHT 2016,Fri Jul 22 01:36:54 PHT 2016,4AF582F3-A4F2-49B6-DF1C-A2111E624CFD,,1,1


As I check the system also using high memory resources using more than 23 GB of memory out of 24 GB total RAM.

Memory status:

# free -m
             total       used       free     shared    buffers     cached
Mem:         24101      23888        212          0         38      18870
-/+ buffers/cache:       4978      19122
Swap:        47683          2      47681


 
Thanks.

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[Sam Silverberg]

Zurab,

I looks like xmllint is installed correctly. Can you run ps -ef while the volume is loaded? The shell script starts the sdfs volume with the correct amount of memory based on the maximum size of the volume. This can be hard coded in the script at 400MB per TB plus 1GB for overhead.

Change the variable $MEMORY$MU in the last line to 2600MB

 -Dfuse.logging.level=INFO -Xmx$MEMORY$MU -\

-XX:+DisableExplicitGC -pidfile /var/run/$PF -XX:+UseG1GC -Djava.awt.headless=true \
"/sbin/mount.sdfs" 44 lines, 1463 characters

XML config:

# cat VM-image-backup-volume-cfg.xml
<?xml version="1.0" encoding="UTF-8" standalone="no"?><subsystem-config version="3.1.9">
<locations dedup-db-store="/opt/sdfs/metadata/VM-image-backup/ddb" io-log="/opt/sdfs/metadata/VM-image-backup/ioperf.log"/>
<io chunk-size="4" claim-hash-schedule="0 59 23 * * ?" dedup-files="true" hash-type="murmur3_128" log-level="1" max-file-inactive="900" max-file-write-buffers="1" max-open-files="1024" max-variable-segment-size="32" meta-file-cache="1024" read-ahead="false" safe-close="false" safe-sync="true" write-threads="8"/>
<permissions default-file="0644" default-folder="0755" default-group="0" default-owner="0"/>

<sdfscli enable="true" enable-auth="true" listen-address="0.0.0.0" password="5a24d6cf044a9dab25f2223041ba1356200002cf891fe723af9157d325f9dfd6" port="6442" salt="EqHAgv"/>
<local-chunkstore allocation-size="4398046511104" average-chunk-size="8192" chunk-store="/opt/sdfs/chunkdata/VM-image-backup" chunkstore-class="org.opendedup.sdfs.filestore.BatchFileChunkStore" cluster-config="/etc/sdfs/jgroups.cfg.xml" cluster-dse-password="admin" cluster-id="sdfs-cluster" compress="false" enabled="true" encrypt="false" encryption-iv="e729e9707a27862d19a20abd51e7d7a2" encryption-key="g27VHVaVi8QrC2G3QUfdUNvxLI+BJcNPFHVkNJ4NCjUen3e=2j7xDDd+HDu93+Mz" gc-class="org.opendedup.sdfs.filestore.gc.PFullGC" hash-db-store="/opt/sdfs/hashdb/VM-image-backup" hashdb-class="org.opendedup.collections.ProgressiveFileBasedCSMap" io-threads="8" max-repl-batch-sz="128">
<network enable="true" hostname="0.0.0.0" port="2222" use-ssl="false"/>
<extended-config allow-sync="false" block-size="60 MB" delete-unclaimed="true" io-threads="16" local-cache-size="10 GB" map-cache-size="100" read-speed="0" sync-files="false" upload-thread-sleep-time="150000" write-speed="0"/>
</local-chunkstore>
<volume allow-external-links="true" capacity="4 TB" closed-gracefully="false" cluster-block-copies="2" cluster-id="sdfs-cluster" cluster-rack-aware="false" cluster-response-timeout="4000" current-size="0" dse-comp-size="0" dse-size="0" duplicate-bytes="0" maximum-percentage-full="0.95" name="VM-image-backup" path="/opt/sdfs/metadata/VM-image-backup/files" perf-mon-file="/opt/sdfs//logs/volume-VM-image-backup-perf.json" read-bytes="0.0" read-timeout-seconds="-1" serial-number="1807226685" sync-files="false" use-dse-capacity="true" use-dse-size="true" use-perf-mon="false" volume-clustered="false" write-bytes="0" write-timeout-seconds="-1"/></


Thanks.

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[zurab de vera]

Hi Sam,

Good day,

Thanks for the response.  Here is the result of my ps-ef. As I read the info on your website, yes I'm running out memory. Based on my volume setting with 4k block size and having a vitual size disk usage of more than 4TB.

I'll change the line variable $MEMORY$MU on the script to 2600MB after I finish my transfer of file. 

/# ps -ef

UID        PID  PPID  C STIME TTY          TIME CMD
root         1     0  0 Jul21 ?        00:00:01 /sbin/init
root         2     0  0 Jul21 ?        00:00:00 [kthreadd]
root         3     2  0 Jul21 ?        00:02:06 [ksoftirqd/0]
root         5     2  0 Jul21 ?        00:00:00 [kworker/0:0H]
root         7     2  0 Jul21 ?        00:05:29 [rcu_sched]
root         8     2  0 Jul21 ?        00:00:00 [rcu_bh]
root         9     2  0 Jul21 ?        00:02:03 [rcuos/0]
root        10     2  0 Jul21 ?        00:00:00 [rcuob/0]
root        11     2  0 Jul21 ?        00:00:00 [migration/0]
root        12     2  0 Jul21 ?        00:00:01 [watchdog/0]
root        13     2  0 Jul21 ?        00:00:01 [watchdog/1]
root        14     2  0 Jul21 ?        00:00:00 [migration/1]
root        15     2  0 Jul21 ?        00:00:01 [ksoftirqd/1]
root        17     2  0 Jul21 ?        00:00:00 [kworker/1:0H]
root        18     2  0 Jul21 ?        00:00:24 [rcuos/1]
root        19     2  0 Jul21 ?        00:00:00 [rcuob/1]
root        20     2  0 Jul21 ?        00:00:01 [watchdog/2]
root        21     2  0 Jul21 ?        00:00:00 [migration/2]
root        22     2  0 Jul21 ?        00:00:00 [ksoftirqd/2]
root        24     2  0 Jul21 ?        00:00:00 [kworker/2:0H]
root        25     2  0 Jul21 ?        00:00:24 [rcuos/2]
root        26     2  0 Jul21 ?        00:00:00 [rcuob/2]
root        27     2  0 Jul21 ?        00:00:01 [watchdog/3]
root        28     2  0 Jul21 ?        00:00:00 [migration/3]
root        29     2  0 Jul21 ?        00:00:01 [ksoftirqd/3]
root        31     2  0 Jul21 ?        00:00:00 [kworker/3:0H]
root        32     2  0 Jul21 ?        00:00:26 [rcuos/3]
root        33     2  0 Jul21 ?        00:00:00 [rcuob/3]
root        34     2  0 Jul21 ?        00:00:01 [watchdog/4]
root        35     2  0 Jul21 ?        00:00:00 [migration/4]
root        36     2  0 Jul21 ?        00:00:00 [ksoftirqd/4]
root        38     2  0 Jul21 ?        00:00:00 [kworker/4:0H]
root        39     2  0 Jul21 ?        00:01:25 [rcuos/4]
root        40     2  0 Jul21 ?        00:00:00 [rcuob/4]
root        41     2  0 Jul21 ?        00:00:01 [watchdog/5]
root        42     2  0 Jul21 ?        00:00:00 [migration/5]
root        43     2  0 Jul21 ?        00:00:00 [ksoftirqd/5]
root        44     2  0 Jul21 ?        00:00:00 [kworker/5:0]
root        45     2  0 Jul21 ?        00:00:00 [kworker/5:0H]
root        46     2  0 Jul21 ?        00:00:08 [rcuos/5]
root        47     2  0 Jul21 ?        00:00:00 [rcuob/5]
root        48     2  0 Jul21 ?        00:00:01 [watchdog/6]
root        49     2  0 Jul21 ?        00:00:00 [migration/6]
root        50     2  0 Jul21 ?        00:00:04 [ksoftirqd/6]
root        51     2  0 Jul21 ?        00:00:00 [kworker/6:0]
root        52     2  0 Jul21 ?        00:00:00 [kworker/6:0H]
root        53     2  0 Jul21 ?        00:00:36 [rcuos/6]
root        54     2  0 Jul21 ?        00:00:00 [rcuob/6]
root        55     2  0 Jul21 ?        00:00:01 [watchdog/7]
root        56     2  0 Jul21 ?        00:00:00 [migration/7]
root        57     2  0 Jul21 ?        00:00:02 [ksoftirqd/7]
root        58     2  0 Jul21 ?        00:00:00 [kworker/7:0]
root        59     2  0 Jul21 ?        00:00:00 [kworker/7:0H]
root        60     2  0 Jul21 ?        00:00:09 [rcuos/7]
root        61     2  0 Jul21 ?        00:00:00 [rcuob/7]
root        62     2  0 Jul21 ?        00:00:00 [khelper]
root        63     2  0 Jul21 ?        00:00:00 [kdevtmpfs]
root        64     2  0 Jul21 ?        00:00:00 [netns]
root        65     2  0 Jul21 ?        00:00:00 [perf]
root        66     2  0 Jul21 ?        00:00:00 [khungtaskd]
root        67     2  0 Jul21 ?        00:00:00 [writeback]
root        68     2  0 Jul21 ?        00:00:00 [ksmd]
root        69     2  0 Jul21 ?        00:00:07 [khugepaged]
root        70     2  0 Jul21 ?        00:00:00 [crypto]
root        71     2  0 Jul21 ?        00:00:00 [kintegrityd]
root        72     2  0 Jul21 ?        00:00:00 [bioset]
root        73     2  0 Jul21 ?        00:00:00 [kblockd]
root        74     2  0 Jul21 ?        00:00:00 [ata_sff]
root        75     2  0 Jul21 ?        00:00:00 [md]
root        76     2  0 Jul21 ?        00:00:00 [devfreq_wq]
root        80     2  0 Jul21 ?        00:07:02 [kswapd0]
root        81     2  0 Jul21 ?        00:00:00 [fsnotify_mark]
root        82     2  0 Jul21 ?        00:00:00 [ecryptfs-kthrea]
root        94     2  0 Jul21 ?        00:00:00 [kthrotld]
root        95     2  0 Jul21 ?        00:00:00 [acpi_thermal_pm]
root        96     2  0 Jul21 ?        00:00:00 [scsi_eh_0]
root        97     2  0 Jul21 ?        00:00:00 [scsi_tmf_0]
root        98     2  0 Jul21 ?        00:00:00 [scsi_eh_1]
root        99     2  0 Jul21 ?        00:00:00 [scsi_tmf_1]
root       101     2  0 Jul21 ?        00:00:00 [scsi_eh_2]
root       102     2  0 Jul21 ?        00:00:00 [scsi_tmf_2]
root       103     2  0 Jul21 ?        00:00:00 [scsi_eh_3]
root       104     2  0 Jul21 ?        00:00:00 [scsi_tmf_3]
root       110     2  0 Jul21 ?        00:00:00 [ipv6_addrconf]
root       131     2  0 Jul21 ?        00:00:00 [deferwq]
root       132     2  0 Jul21 ?        00:00:00 [charger_manager]
root       146     2  0 Jul21 ?        00:00:11 [kworker/4:1]
root       199     2  0 Jul21 ?        00:00:00 [scsi_eh_4]
root       200     2  0 Jul21 ?        00:00:00 [scsi_tmf_4]
root       201     2  0 Jul21 ?        00:00:00 [kpsmoused]
root       214     2  0 Jul21 ?        00:00:06 [jbd2/sda1-8]
root       215     2  0 Jul21 ?        00:00:00 [ext4-rsv-conver]
root       356     1  0 Jul21 ?        00:00:00 upstart-udev-bridge --daemon
root       365     1  0 Jul21 ?        00:00:00 /lib/systemd/systemd-udevd --daemon
root       416     2  0 Jul21 ?        00:00:08 [jbd2/sda4-8]
root       417     2  0 Jul21 ?        00:00:00 [ext4-rsv-conver]
root       440     2  0 Jul21 ?        00:00:00 [rpciod]
root       444     2  0 Jul21 ?        00:00:00 [nfsiod]
message+   457     1  0 Jul21 ?        00:00:00 dbus-daemon --system --fork
syslog     459     1  0 Jul21 ?        00:00:00 rsyslogd
root       467     1  0 Jul21 ?        00:00:00 upstart-file-bridge --daemon
root       493     1  0 Jul21 ?        00:00:00 /lib/systemd/systemd-logind
root       495     1  0 Jul21 ?        00:00:00 rpc.idmapd
root       508     2  0 Jul21 ?        00:00:00 [edac-poller]
root       542     2  0 Jul21 ?        00:00:00 [kvm-irqfd-clean]
root       792     1  0 Jul21 ?        00:00:00 upstart-socket-bridge --daemon
root       803     1  0 Jul21 ?        00:00:01 rpcbind
statd      840     1  0 Jul21 ?        00:00:00 rpc.statd -L
root       910     1  0 Jul21 tty4     00:00:00 /sbin/getty -8 38400 tty4
root       912     1  0 Jul21 tty5     00:00:00 /sbin/getty -8 38400 tty5
root       915     1  0 Jul21 tty2     00:00:00 /sbin/getty -8 38400 tty2
root       916     1  0 Jul21 tty3     00:00:00 /sbin/getty -8 38400 tty3
root       918     1  0 Jul21 tty6     00:00:00 /sbin/getty -8 38400 tty6
root       931     1  0 Jul21 ?        00:00:00 /usr/sbin/sshd -D
root       963     1  0 Jul21 ?        00:00:00 cron
root       987     2  0 Jul21 ?        00:00:00 [nfsd4]
root       988     2  0 Jul21 ?        00:00:00 [nfsd4_callbacks]
root       989     2  0 Jul21 ?        00:00:00 [lockd]
root       992     2  0 Jul21 ?        00:07:09 [nfsd]
root       993     2  0 Jul21 ?        00:07:26 [nfsd]
root       994     2  0 Jul21 ?        00:08:19 [nfsd]
root       995     2  0 Jul21 ?        00:09:07 [nfsd]
root       996     2  0 Jul21 ?        00:10:06 [nfsd]
root       997     2  0 Jul21 ?        00:19:07 [nfsd]
root       998     2  0 Jul21 ?        00:35:47 [nfsd]
root       999     2  0 Jul21 ?        00:54:28 [nfsd]
root      1002     1  0 Jul21 ?        00:00:00 /usr/sbin/rpc.mountd --manage-gids
root      1016     1  0 Jul21 ?        00:00:57 /usr/sbin/irqbalance
root      1025     2  0 Jul21 ?        00:00:01 [kworker/0:1H]
root      1030     2  0 Jul21 ?        00:00:00 [target_completi]
root      1031     2  0 Jul21 ?        00:00:00 [tmr-rd_mcp]
root      1032     2  0 Jul21 ?        00:00:00 [xcopy_wq]
root      1117     1  0 Jul21 ?        01:14:07 /usr/share/sdfs/bin/jre/bin/java -javaagent:/usr/share/datish_viewer/framework/play-1.4.2.jar -Dprecompiled=tr
root      1222  1117 18 Jul21 ?        1-10:13:13 /usr/share/sdfs/bin/jre/bin/java -Djava.library.path=/usr/share/sdfs/bin/ -Dorg.apache.commons.logging.Log=f
root      1293     2  0 Jul21 ?        00:00:00 [kworker/2:1H]
ntp       1337     1  0 Jul21 ?        00:00:18 /usr/sbin/ntpd -p /var/run/ntpd.pid -g -u 103:109
root      1345     2  0 Jul21 ?        00:00:00 [kauditd]
root      1384     2  0 Jul21 ?        00:00:00 [kworker/1:1H]
root      1386     2  0 Jul21 ?        00:00:00 [kworker/3:1H]
root      1461     2  0 Jul21 ?        00:00:00 [kworker/7:1H]
root      1466     2  0 Jul21 ?        00:00:00 [kworker/4:1H]
root      1471     2  0 Jul21 ?        00:00:00 [kworker/5:1H]
root      1475     2  0 Jul21 ?        00:00:00 [kworker/6:1H]
root      1646     2  0 Jul28 ?        00:00:03 [kworker/3:2]
root      1996     2  0 00:03 ?        00:00:03 [kworker/1:1]
root      2065     2  0 00:14 ?        00:00:01 [kworker/4:2]
root      2072     2  0 00:15 ?        00:00:02 [kworker/6:2]
root      2519     2  0 Jul21 ?        00:00:19 [kworker/3:0]
root      2883     2  0 Jul21 ?        00:00:05 [kworker/2:1]
root      3750     2  0 04:41 ?        00:00:04 [kworker/u48:1]
root      3890   931  0 Jul25 ?        00:00:00 sshd: root@pts/1
root      3921  3890  0 Jul25 pts/1    00:00:03 -bash
root      5958     2  0 10:33 ?        00:00:00 [kworker/u48:0]
root      6622  3921  0 12:21 pts/1    00:00:00 ps -ef
root      8047     2  0 Jul22 ?        00:00:01 [kworker/1:0]
root     10074     2  0 Jul22 ?        00:00:00 [nfsv4.0-svc]
root     21646     2  0 Jul27 ?        00:00:07 [kworker/5:2]
root     21739     2  0 Jul27 ?        00:00:10 [kworker/0:1]
root     22251     2  0 Jul27 ?        00:00:06 [kworker/7:1]
root     24374     2  0 Jul27 ?        00:00:11 [kworker/2:2]
root     24591     2  0 Jul27 ?        00:00:41 [kworker/0:0]
root     24679     1  0 Jul27 tty1     00:00:00 /sbin/getty -8 38400 tty1

Thanks..

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