Print file information:
RUN_IN_PLACE=no
LINUXCNC_DIR=
LINUXCNC_BIN_DIR=/usr/bin
LINUXCNC_TCL_DIR=/usr/lib/tcltk/linuxcnc
LINUXCNC_SCRIPT_DIR=
LINUXCNC_RTLIB_DIR=/usr/realtime-2.6.32-122-rtai/modules/linuxcnc
LINUXCNC_CONFIG_DIR=
LINUXCNC_LANG_DIR=/usr/share/linuxcnc/tcl/msgs
INIVAR=inivar
HALCMD=halcmd
LINUXCNC_EMCSH=/usr/bin/wish8.5
LINUXCNC - 2.5.1
Machine configuration directory is '/home/shay/linuxcnc/configs/my_LinuxCNC_machine'
Machine configuration file is 'my_LinuxCNC_machine.ini'
INIFILE=/home/shay/linuxcnc/configs/my_LinuxCNC_machine/my_LinuxCNC_machine.ini
PARAMETER_FILE=linuxcnc.var
TASK=milltask
HALUI=halui
DISPLAY=axis
Starting LinuxCNC...
Starting LinuxCNC server program: linuxcncsvr
Loading Real Time OS, RTAPI, and HAL_LIB modules
Starting LinuxCNC IO program: io
Starting HAL User Interface program: halui
Shutting down and cleaning up LinuxCNC...
Running HAL shutdown script
Killing task linuxcncsvr, PID=2307
Removing HAL_LIB, RTAPI, and Real Time OS modules
Removing NML shared memory segments
Cleanup done

Debug file information:
Can not find -sec MOT -var MOT -num 1 
Can not find -sec IO -var IO -num 1 
Can not find -sec LINUXCNC -var NML_FILE -num 1 
Can not find -sec EMC -var NML_FILE -num 1 
my_LinuxCNC_machine.hal:198: Pin 'hm2_5i25.0.encoder.00.position' was already linked to signal 'x-pos-fb'
2307
  PID TTY      STAT   TIME COMMAND
Stopping realtime threads
Unloading hal components

Kernel message information:
[  856.648658] I-pipe: Domain RTAI registered.
[  856.648676] RTAI[hal]: <3.8.1> mounted over IPIPE-NOTHREADS 2.6-03.
[  856.648683] RTAI[hal]: compiled with gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5) .
[  856.648804] RTAI[hal]: mounted (IPIPE-NOTHREADS, IMMEDIATE (INTERNAL IRQs DISPATCHED), ISOL_CPUS_MASK: 0).
[  856.648811] PIPELINE layers:
[  856.648818] fa75de20 9ac15d93 RTAI 200
[  856.648825] c085cb20 0 Linux 100
[  856.694261] RTAI[malloc]: global heap size = 2097152 bytes, <BSD>.
[  856.695278] RTAI[sched]: IMMEDIATE, MP, USER/KERNEL SPACE: <with RTAI OWN KTASKs>, kstacks pool size = 524288 bytes.
[  856.695290] RTAI[sched]: hard timer type/freq = APIC/12500328(Hz); default timing: periodic; linear timed lists.
[  856.695298] RTAI[sched]: Linux timer freq = 250 (Hz), TimeBase freq = 1799708000 hz.
[  856.695303] RTAI[sched]: timer setup = 999 ns, resched latency = 2944 ns.
[  856.695429] RTAI[usi]: enabled.
[  856.760416] RTAI[math]: loaded.
[  856.886427] hm2: loading Mesa HostMot2 driver version 0.15
[  856.891936] hm2_pci: loading Mesa AnyIO HostMot2 driver version 0.7
[  856.892008] hm2_pci 0000:05:00.0: PCI INT A -> GSI 20 (level, low) -> IRQ 20
[  856.892019] hm2_pci: discovered 5i25 at 0000:05:00.0
[  856.893506] hm2/hm2_5i25.0: Smart Serial Firmware Version 38
[  856.954281] hm2/hm2_5i25.0: 34 I/O Pins used:
[  856.954290] hm2/hm2_5i25.0:     IO Pin 000 (P3-01): IOPort
[  856.954296] hm2/hm2_5i25.0:     IO Pin 001 (P3-14): IOPort
[  856.954303] hm2/hm2_5i25.0:     IO Pin 002 (P3-02): StepGen #3, pin Step (Output)
[  856.954310] hm2/hm2_5i25.0:     IO Pin 003 (P3-15): StepGen #3, pin Direction (Output)
[  856.954317] hm2/hm2_5i25.0:     IO Pin 004 (P3-03): StepGen #2, pin Step (Output)
[  856.954325] hm2/hm2_5i25.0:     IO Pin 005 (P3-16): StepGen #2, pin Direction (Output)
[  856.954332] hm2/hm2_5i25.0:     IO Pin 006 (P3-04): StepGen #1, pin Step (Output)
[  856.954339] hm2/hm2_5i25.0:     IO Pin 007 (P3-17): StepGen #1, pin Direction (Output)
[  856.954346] hm2/hm2_5i25.0:     IO Pin 008 (P3-05): StepGen #0, pin Step (Output)
[  856.954353] hm2/hm2_5i25.0:     IO Pin 009 (P3-06): StepGen #0, pin Direction (Output)
[  856.954360] hm2/hm2_5i25.0:     IO Pin 010 (P3-07): Muxed Encoder Select #0, pin Mux Select 0 (Output)
[  856.954368] hm2/hm2_5i25.0:     IO Pin 011 (P3-08): Muxed Encoder #0, pin Muxed A (Input)
[  856.954375] hm2/hm2_5i25.0:     IO Pin 012 (P3-09): Muxed Encoder #0, pin Muxed B (Input)
[  856.954383] hm2/hm2_5i25.0:     IO Pin 013 (P3-10): Muxed Encoder #0, pin Muxed Index (Input)
[  856.954390] hm2/hm2_5i25.0:     IO Pin 014 (P3-11): Muxed Encoder #1, pin Muxed A (Input)
[  856.954398] hm2/hm2_5i25.0:     IO Pin 015 (P3-12): Muxed Encoder #1, pin Muxed B (Input)
[  856.954405] hm2/hm2_5i25.0:     IO Pin 016 (P3-13): Muxed Encoder #1, pin Muxed Index (Input)
[  856.954413] hm2/hm2_5i25.0:     IO Pin 017 (P2-01): StepGen #4, pin Direction (Output)
[  856.954420] hm2/hm2_5i25.0:     IO Pin 018 (P2-14): StepGen #4, pin Step (Output)
[  856.954427] hm2/hm2_5i25.0:     IO Pin 019 (P2-02): StepGen #5, pin Direction (Output)
[  856.954434] hm2/hm2_5i25.0:     IO Pin 020 (P2-15): StepGen #5, pin Step (Output)
[  856.954441] hm2/hm2_5i25.0:     IO Pin 021 (P2-03): StepGen #6, pin Direction (Output)
[  856.954448] hm2/hm2_5i25.0:     IO Pin 022 (P2-16): StepGen #6, pin Step (Output)
[  856.954455] hm2/hm2_5i25.0:     IO Pin 023 (P2-04): StepGen #7, pin Direction (Output)
[  856.954463] hm2/hm2_5i25.0:     IO Pin 024 (P2-17): StepGen #7, pin Step (Output)
[  856.954470] hm2/hm2_5i25.0:     IO Pin 025 (P2-05): PWMGen #0, pin Out0 (PWM or Up) (Output)
[  856.954477] hm2/hm2_5i25.0:     IO Pin 026 (P2-06): PWMGen #0, pin Not-Enable (Output)
[  856.954485] hm2/hm2_5i25.0:     IO Pin 027 (P2-07): PWMGen #0, pin Out1 (Dir or Down) (Output)
[  856.954491] hm2/hm2_5i25.0:     IO Pin 028 (P2-08): IOPort
[  856.954497] hm2/hm2_5i25.0:     IO Pin 029 (P2-09): IOPort
[  856.954503] hm2/hm2_5i25.0:     IO Pin 030 (P2-10): IOPort
[  856.954509] hm2/hm2_5i25.0:     IO Pin 031 (P2-11): Muxed Encoder #2, pin Muxed Index (Input)
[  856.954517] hm2/hm2_5i25.0:     IO Pin 032 (P2-12): Muxed Encoder #2, pin Muxed B (Input)
[  856.954524] hm2/hm2_5i25.0:     IO Pin 033 (P2-13): Muxed Encoder #2, pin Muxed A (Input)
[  856.954673] hm2/hm2_5i25.0: registered
[  856.954679] hm2_5i25.0: initialized AnyIO board at 0000:05:00.0
[  857.629171] hm2_5i25.0: dropping AnyIO board at 0000:05:00.0
[  857.629184] hm2/hm2_5i25.0: unregistered
[  857.629220] hm2_pci 0000:05:00.0: PCI INT A disabled
[  857.629887] hm2_pci: driver unloaded
[  857.634759] hm2: unloading
[  857.708759] RTAI[math]: unloaded.
[  857.729742] SCHED releases registered named ALIEN RTGLBH
[  857.792969] RTAI[malloc]: unloaded.
[  857.892038] RTAI[sched]: unloaded (forced hard/soft/hard transitions: traps 0, syscalls 0).
[  857.896371] I-pipe: Domain RTAI unregistered.
[  857.896517] RTAI[hal]: unmounted.