EJB thread pausing for 28 seconds

We have a weblogic application running with a JDMK package to receive and process SNMP packets. This processor is running on a separate thread off a EJB. We just recently encountered an issue where after processing several packets the thread pauses in the middle of processing for about 28 seconds, then continues processing again for a second and pauses again. This keeps occurring. Note the times vary and the pause spot in the processing can also vary.
Moreover, depending on what Linux system weblogic is running on, the problem may go away. In all cases the Linux systems never get more than 20% busy by CPU time.
Any thoughts?

Turns out the issue was related to OS level SNMP port IO timeout. There were routing issues causing DNS lookups a long time to resolve. This in-turn caused delays up to 28+ seconds in the JDMK SNMP manager during some snmpGet of OIDs and MIB tables. Since the same JDMK SNMP manager is used from trap recipient and listener it also caused delays in processing traps. We solved the issue by updating the resolv.conf to something that worked. This was verified using nslookup and traceroute commands on Linux.

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width: 64 bits
clock: 100MHz
capabilities: x86-64 fpu fpu_exception wp vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms cpufreq
configuration: cores=4 enabledcores=4 threads=8
*-pci
description: Host bridge
product: 3rd Gen Core processor DRAM Controller
vendor: Intel Corporation
physical id: 100
bus info: pci@0000:00:00.0
version: 09
width: 32 bits
clock: 33MHz
configuration: driver=agpgart-intel
resources: irq:0
*-pci:0
description: PCI bridge
product: Xeon E3-1200 v2/3rd Gen Core processor PCI Express Root Port
vendor: Intel Corporation
physical id: 1
bus info: pci@0000:00:01.0
version: 09
width: 32 bits
clock: 33MHz
capabilities: pci pm msi pciexpress normal_decode bus_master cap_list
configuration: driver=pcieport
resources: irq:40 ioport:e000(size=4096) memory:f6000000-f70fffff ioport:e0000000(size=301989888)
*-display UNCLAIMED
description: VGA compatible controller
product: NVIDIA Corporation
vendor: NVIDIA Corporation
physical id: 0
bus info: pci@0000:01:00.0
version: a1
width: 64 bits
clock: 33MHz
capabilities: pm msi pciexpress vga_controller cap_list
configuration: latency=0
resources: memory:f6000000-f6ffffff memory:e0000000-efffffff memory:f0000000-f1ffffff ioport:e000(size=128) memory:f7000000-f707ffff
*-display
description: VGA compatible controller
product: 3rd Gen Core processor Graphics Controller
vendor: Intel Corporation
physical id: 2
bus info: pci@0000:00:02.0
version: 09
width: 64 bits
clock: 33MHz
capabilities: msi pm vga_controller bus_master cap_list rom
configuration: driver=i915 latency=0
resources: irq:45 memory:f7400000-f77fffff memory:d0000000-dfffffff ioport:f000(size=64)
*-usb:0
description: USB controller
product: 7 Series/C210 Series Chipset Family USB xHCI Host Controller
vendor: Intel Corporation
physical id: 14
bus info: pci@0000:00:14.0
version: 04
width: 64 bits
clock: 33MHz
capabilities: pm msi xhci bus_master cap_list
configuration: driver=xhci_hcd latency=0
resources: irq:46 memory:f7900000-f790ffff
*-communication
description: Communication controller
product: 7 Series/C210 Series Chipset Family MEI Controller #1
vendor: Intel Corporation
physical id: 16
bus info: pci@0000:00:16.0
version: 04
width: 64 bits
clock: 33MHz
capabilities: pm msi bus_master cap_list
configuration: driver=mei latency=0
resources: irq:43 memory:f791b000-f791b00f
*-usb:1
description: USB controller
product: 7 Series/C210 Series Chipset Family USB Enhanced Host Controller #2
vendor: Intel Corporation
physical id: 1a
bus info: pci@0000:00:1a.0
version: 04
width: 32 bits
clock: 33MHz
capabilities: pm debug ehci bus_master cap_list
configuration: driver=ehci_hcd latency=0
resources: irq:16 memory:f7918000-f79183ff
*-multimedia
description: Audio device
product: 7 Series/C210 Series Chipset Family High Definition Audio Controller
vendor: Intel Corporation
physical id: 1b
bus info: pci@0000:00:1b.0
version: 04
width: 64 bits
clock: 33MHz
capabilities: pm msi pciexpress bus_master cap_list
configuration: driver=snd_hda_intel latency=0
resources: irq:41 memory:f7910000-f7913fff
*-pci:1
description: PCI bridge
product: 7 Series/C210 Series Chipset Family PCI Express Root Port 1
vendor: Intel Corporation
physical id: 1c
bus info: pci@0000:00:1c.0
version: c4
width: 32 bits
clock: 33MHz
capabilities: pci pciexpress msi pm normal_decode bus_master cap_list
configuration: driver=pcieport
resources: irq:16
*-pci:2
description: PCI bridge
product: 7 Series/C210 Series Chipset Family PCI Express Root Port 3
vendor: Intel Corporation
physical id: 1c.2
bus info: pci@0000:00:1c.2
version: c4
width: 32 bits
clock: 33MHz
capabilities: pci pciexpress msi pm normal_decode bus_master cap_list
configuration: driver=pcieport
resources: irq:18 ioport:d000(size=4096) ioport:f2100000(size=1048576)
*-network
description: Ethernet interface
product: RTL8111/8168B PCI Express Gigabit Ethernet controller
vendor: Realtek Semiconductor Co., Ltd.
physical id: 0
bus info: pci@0000:03:00.0
logical name: eth0
version: 07
serial: 00:6b:9e:03:62:f4
size: 10Mbit/s
capacity: 1Gbit/s
width: 64 bits
clock: 33MHz
capabilities: pm msi pciexpress msix vpd bus_master cap_list ethernet physical tp mii 10bt 10bt-fd 100bt 100bt-fd 1000bt 1000bt-fd autonegotiation
configuration: autonegotiation=on broadcast=yes driver=r8169 driverversion=2.3LK-NAPI duplex=half firmware=rtl8168e-3_0.0.4 03/27/12 latency=0 link=no multicast=yes port=MII speed=10Mbit/s
resources: irq:44 ioport:d000(size=256) memory:f2104000-f2104fff memory:f2100000-f2103fff
*-pci:3
description: PCI bridge
product: 7 Series/C210 Series Chipset Family PCI Express Root Port 6
vendor: Intel Corporation
physical id: 1c.5
bus info: pci@0000:00:1c.5
version: c4
width: 32 bits
clock: 33MHz
capabilities: pci pciexpress msi pm normal_decode bus_master cap_list
configuration: driver=pcieport
resources: irq:17 memory:f7800000-f78fffff
*-network
description: Wireless interface
product: AR9462 Wireless Network Adapter
vendor: Atheros Communications Inc.
physical id: 0
bus info: pci@0000:04:00.0
logical name: wlan0
version: 01
serial: 00:6b:9e:00:ab:6f
width: 64 bits
clock: 33MHz
capabilities: pm msi pciexpress bus_master cap_list rom ethernet physical wireless
configuration: broadcast=yes driver=ath9k driverversion=3.5.4-1-ARCH firmware=N/A ip=192.168.1.139 latency=0 link=yes multicast=yes wireless=IEEE 802.11abgn
resources: irq:17 memory:f7800000-f787ffff memory:f7880000-f788ffff
*-usb:2
description: USB controller
product: 7 Series/C210 Series Chipset Family USB Enhanced Host Controller #1
vendor: Intel Corporation
physical id: 1d
bus info: pci@0000:00:1d.0
version: 04
width: 32 bits
clock: 33MHz
capabilities: pm debug ehci bus_master cap_list
configuration: driver=ehci_hcd latency=0
resources: irq:23 memory:f7917000-f79173ff
*-isa
description: ISA bridge
product: HM77 Express Chipset LPC Controller
vendor: Intel Corporation
physical id: 1f
bus info: pci@0000:00:1f.0
version: 04
width: 32 bits
clock: 33MHz
capabilities: isa bus_master cap_list
configuration: driver=lpc_ich latency=0
resources: irq:0
*-storage
description: RAID bus controller
product: 82801 Mobile SATA Controller [RAID mode]
vendor: Intel Corporation
physical id: 1f.2
bus info: pci@0000:00:1f.2
version: 04
width: 32 bits
clock: 66MHz
capabilities: storage msi pm bus_master cap_list
configuration: driver=ahci latency=0
resources: irq:42 ioport:f0b0(size=8) ioport:f0a0(size=4) ioport:f090(size=8) ioport:f080(size=4) ioport:f060(size=32) memory:f7916000-f79167ff
*-serial UNCLAIMED
description: SMBus
product: 7 Series/C210 Series Chipset Family SMBus Controller
vendor: Intel Corporation
physical id: 1f.3
bus info: pci@0000:00:1f.3
version: 04
width: 64 bits
clock: 33MHz
configuration: latency=0
resources: memory:f7915000-f79150ff ioport:f040(size=32)
*-scsi:0
physical id: 1
logical name: scsi0
capabilities: emulated
*-disk
description: ATA Disk
product: ST1000LM024 HN-M
vendor: Seagate
physical id: 0.0.0
bus info: scsi@0:0.0.0
logical name: /dev/sda
version: 2AR1
serial: S2R8J9CC612158
size: 931GiB (1TB)
capabilities: partitioned partitioned:dos
configuration: ansiversion=5 sectorsize=4096 signature=0002dcaf
*-volume:0
description: EXT4 volume
vendor: Linux
physical id: 1
bus info: scsi@0:0.0.0,1
logical name: /dev/sda1
logical name: /home
version: 1.0
serial: 86f08c55-b73d-4c19-a427-04c076aa2956
size: 928GiB
capacity: 928GiB
capabilities: primary journaled extended_attributes large_files huge_files dir_nlink recover extents ext4 ext2 initialized
configuration: created=2012-09-29 11:54:11 filesystem=ext4 lastmountpoint=/home modified=2012-10-04 09:08:33 mount.fstype=ext4 mount.options=rw,relatime,data=ordered mounted=2012-10-04 09:08:33 state=mounted
*-volume:1
description: Linux swap volume
physical id: 2
bus info: scsi@0:0.0.0,2
logical name: /dev/sda2
version: 1
serial: 839f0cea-c59f-4e7b-90e5-c28d3e2fcca4
size: 3053MiB
capacity: 3053MiB
capabilities: primary nofs swap initialized
configuration: filesystem=swap pagesize=4096
*-scsi:1
physical id: 2
logical name: scsi1
capabilities: emulated
*-disk
description: ATA Disk
product: Toshiba THNSNW03
vendor: Toshiba
physical id: 0.0.0
bus info: scsi@1:0.0.0
logical name: /dev/sdb
version: L041
serial: 23RJ613KAFSK
size: 29GiB (32GB)
capabilities: partitioned partitioned:dos
configuration: ansiversion=5 sectorsize=512 signature=00051de3
*-volume
description: Linux filesystem partition
vendor: Linux
physical id: 1
bus info: scsi@1:0.0.0,1
logical name: /dev/sdb1
logical name: /
version: 1.0
serial: a9ba0f2f-aba4-47ae-b3bc-78ced3fb41d5
size: 29GiB
capacity: 29GiB
capabilities: primary bootable extended_attributes large_files ext2 initialized
configuration: filesystem=ext2 lastmountpoint=/ modified=2012-10-05 11:51:10 mount.fstype=ext2 mount.options=rw,relatime mounted=2012-10-04 09:08:33 state=mounted
*-scsi:2
physical id: 3
bus info: usb@1:3
logical name: scsi6
capabilities: emulated scsi-host
configuration: driver=usb-storage
*-disk
description: SCSI Disk
physical id: 0.0.0
bus info: scsi@6:0.0.0
logical name: /dev/sdc
size: 465GiB (500GB)
capabilities: partitioned partitioned:dos
configuration: sectorsize=512 signature=9c3c778f
*-volume
description: EXT3 volume
vendor: Linux
physical id: 1
bus info: scsi@6:0.0.0,1
logical name: /dev/sdc1
logical name: /data
version: 1.0
serial: 334c8b3e-ab70-4702-81f1-0bd0ce6af1e9
size: 465GiB
capacity: 465GiB
capabilities: primary bootable journaled extended_attributes large_files recover ext3 ext2 initialized
configuration: created=2012-01-26 18:25:12 filesystem=ext3 lastmountpoint=/data modified=2012-10-04 10:24:08 mount.fstype=ext3 mount.options=rw,relatime,data=ordered mounted=2012-10-04 10:24:08 state=mounted
lsmod
Module Size Used by
sg 25423 0
udf 79515 1
crc_itu_t 1363 1 udf
loop 18160 2
bbswitch 5042 0
joydev 9991 0
btusb 11892 0
bluetooth 193532 2 btusb
ums_realtek 7391 0
snd_hda_codec_cirrus 17229 1
uvcvideo 72339 0
videobuf2_vmalloc 2468 1 uvcvideo
videobuf2_memops 2246 1 videobuf2_vmalloc
videobuf2_core 20575 1 uvcvideo
videodev 100564 2 uvcvideo,videobuf2_core
media 10405 2 uvcvideo,videodev
microcode 12377 0
aesni_intel 42907 2
iTCO_wdt 5989 0
aes_x86_64 7508 1 aesni_intel
aes_generic 26138 2 aesni_intel,aes_x86_64
ghash_clmulni_intel 4237 0
iTCO_vendor_support 1929 1 iTCO_wdt
cryptd 8741 2 ghash_clmulni_intel,aesni_intel
arc4 1410 2
usb_storage 44760 2 ums_realtek
mxm_wmi 1425 0
uas 8823 0
ath9k 93564 0
ath9k_common 2096 1 ath9k
snd_hda_intel 25700 4
ath9k_hw 341950 2 ath9k_common,ath9k
snd_hda_codec 97432 2 snd_hda_intel,snd_hda_codec_cirrus
i915 473038 2
snd_hwdep 6300 1 snd_hda_codec
ath 15393 3 ath9k_common,ath9k,ath9k_hw
kvm 363714 0
mac80211 416391 1 ath9k
i2c_algo_bit 5391 1 i915
snd_pcm 74926 3 snd_hda_codec,snd_hda_intel
coretemp 6006 0
snd_page_alloc 7217 2 snd_pcm,snd_hda_intel
drm_kms_helper 32749 1 i915
snd_timer 18966 2 snd_pcm
crc32c_intel 1987 0
evdev 10266 12
cfg80211 173210 3 ath,ath9k,mac80211
snd 60021 12 snd_hwdep,snd_timer,snd_pcm,snd_hda_codec,snd_hda_intel,snd_hda_codec_cirrus
drm 220804 3 i915,drm_kms_helper
r8169 51909 0
rfkill 15604 3 cfg80211,bluetooth
soundcore 5442 1 snd
pcspkr 1899 0
mei 32583 0
intel_agp 11096 1 i915
i2c_i801 8212 0
lpc_ich 10545 0
intel_gtt 14478 3 i915,intel_agp
mfd_core 2833 1 lpc_ich
i2c_core 20508 6 drm,i915,i2c_i801,drm_kms_helper,i2c_algo_bit,videodev
mii 4123 1 r8169
acpi_cpufreq 5933 0
thermal 7959 0
mperf 1267 1 acpi_cpufreq
processor 27015 9 acpi_cpufreq
wmi 8475 1 mxm_wmi
video 11308 1 i915
button 4502 1 i915
vboxdrv 1823501 0
ext4 438999 3
crc16 1359 2 ext4,bluetooth
jbd2 78720 1 ext4
mbcache 5977 1 ext4
sd_mod 29271 7
hid_generic 1113 0
usbhid 36812 0
hid 85608 2 hid_generic,usbhid
ehci_hcd 41058 0
ahci 20549 3
libahci 20023 1 ahci
libata 167675 2 ahci,libahci
scsi_mod 133152 5 sg,uas,usb_storage,libata,sd_mod
xhci_hcd 84338 0
usbcore 147434 8 uas,btusb,uvcvideo,ums_realtek,usb_storage,ehci_hcd,usbhid,xhci_hcd
usb_common 954 1 usbcore

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