# Can't start Slicer on Linux on one machine
**URL:** https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175
**Category:** Support
**Created:** [August 26, 2019, 7:12am UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175 "2019-08-26T07:12:06Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 26, 2019, 7:12am UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/1 "2019-08-26T07:12:06Z")
I get the following message when launching Slicer :
> $ ./Slicer
> error: [/home/user/programs/Slicer-4.11.0-2019-08-22-linux-amd64/bin/SlicerApp-real] exit abnormally -
> Report the problem.
This happens on my desktop machine only, it launches normally on my laptop. It happens with both home built Slicher unchanged and with packages from your repository.
Unfortunately, there are no hints in the console message. This started after the major ITK/CTK updates.
I suspect a system library problem, but can’t get to it. But could be another root cause.
Using Qt 5.13.0 on both machines. I’ll provide other useful information you may need to resolve this. I fear it will be a lengthy process without error messages.
Regards.
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [August 26, 2019, 12:49pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/2 "2019-08-26T12:49:02Z")
Can you get a call stack?
If you build Slicer with debug information and run it in a debugger then you get detailed information about what goes wrong.
---
### Author:  [@pieper](https://discourse.slicer.org/u/pieper)
#### Post date: [August 26, 2019, 2:33pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/3 "2019-08-26T14:33:11Z")
Another debugging approach (works with the binary download or local build):
First create a shell with Slicer’s environment:
```auto
./Slicer --launch xterm
```
Then in the new window:
```auto
strace ./bin/SlicerApp-real
```
This will give you a log of system calls and typically the last operations will indicate what was going on at the time of the crash (e.g. what file or library was being loaded).
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 26, 2019, 3:05pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/4 "2019-08-26T15:05:37Z")
> [@pieper](#):
>
> log of system calls and typically the last operations
> [@pieper](#):
>
> what file or library was being loaded
> $ LC\_ALL=C LANG=C strace ./bin/SlicerApp-real
> execve(“./bin/SlicerApp-real”, [“./bin/SlicerApp-real”], 0x7ffef0915fc0 /\* 86 vars _/) = 0
> brk(NULL) = 0x5615e14c0000
> arch\_prctl(0x3001 /_ ARCH\_??? \*/, 0x7fff7595d240) = -1 EINVAL (Invalid argument)
> access(“/etc/ld.so.preload”, R\_OK) = -1 ENOENT (No such file or directory)
> openat(AT\_FDCWD, “/etc/ld.so.cache”, O\_RDONLY|O\_CLOEXEC) = 3
> fstat(3, {st\_mode=S\_IFREG|0644, st\_size=336853, …}) = 0
> mmap(NULL, 336853, PROT\_READ, MAP\_PRIVATE, 3, 0) = 0x7fb626511000
> close(3) = 0
> openat(AT\_FDCWD, “/usr/lib/tls/x86\_64/x86\_64/libqSlicerApp.so”, O\_RDONLY|O\_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat(“/usr/lib/tls/x86\_64/x86\_64”, 0x7fff7595c480) = -1 ENOENT (No such file or directory)
> openat(AT\_FDCWD, “/usr/lib/tls/x86\_64/libqSlicerApp.so”, O\_RDONLY|O\_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat(“/usr/lib/tls/x86\_64”, 0x7fff7595c480) = -1 ENOENT (No such file or directory)
> openat(AT\_FDCWD, “/usr/lib/tls/x86\_64/libqSlicerApp.so”, O\_RDONLY|O\_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat(“/usr/lib/tls/x86\_64”, 0x7fff7595c480) = -1 ENOENT (No such file or directory)
> openat(AT\_FDCWD, “/usr/lib/tls/libqSlicerApp.so”, O\_RDONLY|O\_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat(“/usr/lib/tls”, 0x7fff7595c480) = -1 ENOENT (No such file or directory)
> openat(AT\_FDCWD, “/usr/lib/x86\_64/x86\_64/libqSlicerApp.so”, O\_RDONLY|O\_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat(“/usr/lib/x86\_64/x86\_64”, 0x7fff7595c480) = -1 ENOENT (No such file or directory)
> openat(AT\_FDCWD, “/usr/lib/x86\_64/libqSlicerApp.so”, O\_RDONLY|O\_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat(“/usr/lib/x86\_64”, 0x7fff7595c480) = -1 ENOENT (No such file or directory)
> openat(AT\_FDCWD, “/usr/lib/x86\_64/libqSlicerApp.so”, O\_RDONLY|O\_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat(“/usr/lib/x86\_64”, 0x7fff7595c480) = -1 ENOENT (No such file or directory)
> openat(AT\_FDCWD, “/usr/lib/libqSlicerApp.so”, O\_RDONLY|O\_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat(“/usr/lib”, {st\_mode=S\_IFDIR|0755, st\_size=299008, …}) = 0
> writev(2, [{iov\_base=“./bin/SlicerApp-real”, iov\_len=20}, {iov\_base=“: “, iov\_len=2}, {iov\_base=“error while loading shared libra”…, iov\_len=36}, {iov\_base=”: “, iov\_len=2}, {iov\_base
> =“libqSlicerApp.so”, iov\_len=16}, {iov\_base=”: “, iov\_len=2}, {iov\_base=“cannot open shared object file”, iov\_len=30}, {iov\_base=”: “, iov\_len=2}, {iov\_base=“No such file or directory”,
> iov\_len=25}, {iov\_base=”\n”, iov\_len=1}], 10./bin/SlicerApp-real: error while loading shared libraries: libqSlicerApp.so: cannot open shared object file: No such file or directory
> ) = 136
> exit\_group(127) = ?
> +++ exited with 127 +++
It seems it could not find libqSlicerApp.so, file that is present of course.
If I set LD\_LIBRARY\_PATH to ./lib/Slicer-4.11, it outputs similar results but for every library it tries to load.
Now I don’t have any kind of special setup on that particular machine.
I’m ready to try with a debug build, but won’t be able to do it before a few days.
Thanks.
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [August 26, 2019, 3:20pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/5 "2019-08-26T15:20:00Z")
Have you executed `strace ./bin/SlicerApp-real` in a terminal created by `./Slicer --launch (your-terminal-executable-here)`?
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 26, 2019, 3:59pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/6 "2019-08-26T15:59:46Z")
> [@lassoan](#):
>
> Have you executed `strace ./bin/SlicerApp-real`
Yes, the result is just [one post above](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/4).
---
### Author:  [@pieper](https://discourse.slicer.org/u/pieper)
#### Post date: [August 26, 2019, 4:50pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/7 "2019-08-26T16:50:18Z")
It looks like something is interfering with Slicer’s paths. Does your environment have any special variables set (e.g. `LD_PRELOAD`?)
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [August 26, 2019, 5:22pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/8 "2019-08-26T17:22:51Z")
Could you copy-paste here the value of environment variables you have in the terminal where you attempted to run SlicerApp-real?
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 26, 2019, 6:27pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/9 "2019-08-26T18:27:53Z")
I’ll post the env variables when I get back to work. Thanks.
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 27, 2019, 6:02am UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/10 "2019-08-27T06:02:45Z")
> [@lassoan](#):
>
> opy-paste here the value of environment variables
> [@pieper](#):
>
> any special variables
Here are the environment variables in the relevant terminal. All variables are in this sorted list, though some values have been masked.
> \_=/bin/env
> COLORFGBG=15;0
> COLORTERM=truecolor
> DBUS\_SESSION\_BUS\_ADDRESS=unix:path=/run/user/1001/bus
> DESKTOP\_SESSION=/usr/share/xsessions/plasma
> DISPLAY=:0
> EDITOR=/usr/bin/vim
> GS\_LIB=/home/user/.fonts
> GTK2\_RC\_FILES=/etc/gtk-2.0/gtkrc:/home/user/.gtkrc-2.0:/home/user/.config/gtkrc-2.0
> GTK\_MODULES=canberra-gtk-module
> GTK\_RC\_FILES=/etc/gtk/gtkrc:/home/user/.gtkrc:/home/user/.config/gtkrc
> HISTCONTROL=ignoreboth:erasedups
> HOME=/home/user
> KDE\_FULL\_SESSION=true
> KDE\_SESSION\_UID=1001
> KDE\_SESSION\_VERSION=5
> KONSOLE\_DBUS\_SERVICE=:1.31
> KONSOLE\_DBUS\_SESSION=/Sessions/7
> KONSOLE\_PROFILE\_NAME=Shell
> KONSOLE\_VERSION=190403
> LANG=fr\_FR.UTF-8
> LANGUAGE=fr
> LC\_ADDRESS=fr\_FR.UTF-8
> LC\_COLLATE=fr\_FR.UTF-8
> LC\_CTYPE=fr\_FR.UTF-8
> LC\_IDENTIFICATION=fr\_FR.UTF-8
> LC\_MEASUREMENT=fr\_FR.UTF-8
> LC\_MESSAGES=fr\_FR.UTF-8
> LC\_MONETARY=fr\_FR.UTF-8
> LC\_NAME=fr\_FR.UTF-8
> LC\_NUMERIC=fr\_FR.UTF-8
> LC\_PAPER=fr\_FR.UTF-8
> LC\_TELEPHONE=fr\_FR.UTF-8
> LC\_TIME=fr\_FR.UTF-8
> LL\_HP=%eth0
> LL\_SEC1L=%eth0
> LL\_SEC1=%eth0
> LL\_SEC2L=%eth0
> LL\_SEC2=%eth0
> LL\_U2=%eth0
> LL\_U3=%eth0
> LL\_VASC1=%eth0
> LL\_VASC2=%eth0
> LL\_Z2P=%eth0
> LOGNAME=user
> MAC\_SEC1=
> MAC\_SEC2=
> MAC\_U2=
> MAC\_U3=
> MAC\_VASC1=
> MAC\_VASC2=
> MAIL=/var/spool/mail/user
> MOZ\_PLUGIN\_PATH=/usr/lib/mozilla/plugins
> OLDPWD=/home/user
> PAM\_KWALLET5\_LOGIN=/run/user/1001/kwallet5.socket
> PATH=/home/user/.bin:/bin:/usr/bin:/usr/local/bin:/usr/local/sbin:/usr/lib/jvm/default/bin:/usr/bin/site\_perl:/usr/bin/vendor\_perl:/usr/bin/core\_perl
> PROFILEHOME=
> PS1=#[\u@\h \W][\033[01;32m][${PIPESTATUS[@]}][\033[00m]$
> PWD=/home/user/programs/Slicer-4.11.0-2019-08-22-linux-amd64
> QT\_AUTO\_SCREEN\_SCALE\_FACTOR=0
> QT\_SCREEN\_SCALE\_FACTORS=DisplayPort-0=1;DisplayPort-1=1;DisplayPort-2=1;HDMI-A-0=1;DVI-D-0=1;
> SESSION\_MANAGER=local/vasc2.chirvasc-60.pro:@/tmp/.ICE-unix/819,unix/vasc2.chirvasc-60.pro:/tmp/.ICE-unix/819
> SHELL=/bin/bash
> SHELL\_SESSION\_ID=7659513d5ce046b9b392de66453524a6
> SHLVL=2
> SSH\_AGENT\_PID=707
> SSH\_AUTH\_SOCK=/tmp/ssh-vEy99OqlN3Qy/agent.706
> TERM=xterm-256color
> USER=user
> WINDOWID=50331655
> XAUTHORITY=/tmp/xauth-1001-\_0
> XCURSOR\_THEME=breeze\_cursors
> XDG\_CONFIG\_HOME=/home/user/.config
> XDG\_CURRENT\_DESKTOP=KDE
> XDG\_DATA\_DIRS=/usr/share:/usr/share:/usr/local/share
> XDG\_RUNTIME\_DIR=/run/user/1001
> XDG\_SEAT\_PATH=/org/freedesktop/DisplayManager/Seat0
> XDG\_SEAT=seat0
> XDG\_SESSION\_CLASS=user
> XDG\_SESSION\_DESKTOP=KDE
> XDG\_SESSION\_ID=c1
> XDG\_SESSION\_PATH=/org/freedesktop/DisplayManager/Session0
> XDG\_SESSION\_TYPE=x11
> XDG\_VTNR=1
> XZ\_DEFAULTS=-T0
---
### Author:  [@pieper](https://discourse.slicer.org/u/pieper)
#### Post date: [August 27, 2019, 12:33pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/11 "2019-08-27T12:33:29Z")
Is this the shell where you try to run Slicer? You should be seeing a lot of Slicer-related environment variables when you start with the launcher. Like custom PATH and LD\_LIBRARY\_PATH and APPLAUNCHER variables.
E.g. if you run this command:
```auto
./Downloads/Slicer-4.11.0-2019-08-22-linux-amd64/Slicer --launch env
```
Maybe there’s something resetting your environment.
If that’s not the issue you might compare `/etc/ld.so.conf` and `/etc/ld.so.conf.d` contents across systems.
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 27, 2019, 4:19pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/12 "2019-08-27T16:19:21Z")
> [@pieper](#):
>
> This will give you a log of system calls and typically the last operations will indicate what was going on at the time of the crash
Well, the program ‘xterm’ was not installed on my machine ! Hence all logs I posted above are irrelevant.
Please find the new log data [here](https://yadi.sk/d/RyqvqQyZewFgZQ).
Sorry for the inconvenience.
---
### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [August 27, 2019, 5:12pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/13 "2019-08-27T17:12:05Z")
Could you post strace output and environment that you get on the computer where Slicer starts correctly?
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 27, 2019, 7:47pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/14 "2019-08-27T19:47:23Z")
[Here](https://yadi.sk/d/RyqvqQyZewFgZQ) is the console output for strace and env, on my laptop, where the same Slicer build works fine.
Thanks.
---
### Author:  [@pieper](https://discourse.slicer.org/u/pieper)
#### Post date: [August 27, 2019, 8:00pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/15 "2019-08-27T20:00:47Z")
Looks like the same zipfile link twice?
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 27, 2019, 8:43pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/16 "2019-08-27T20:43:43Z")
Oops ! Here’s the right [zip](https://yadi.sk/d/6RaeOS9pcxce2A) file (tiresome day), sorry.
---
### Author:  [@pieper](https://discourse.slicer.org/u/pieper)
#### Post date: [August 27, 2019, 9:14pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/17 "2019-08-27T21:14:43Z")
No worries 😄
Unfortunately I don’t see anything definitive in the traces - maybe something to do with gnutls, which is being accessed right before the crash. Could be some kind of incompatibility. Unless you see something probably it makes sense to create a debug build.
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [August 28, 2019, 6:52am UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/18 "2019-08-28T06:52:55Z")
> [@pieper](#):
>
> probably it makes sense to create a debug build
I’ll end up doing the debug build, ASAP. For now, I found this in dmesg, everytime I run the problematic build :
> [21639.829126] traps: SlicerApp-real[15453] trap invalid opcode ip:7f8aa07fa1c8 sp:7ffce616fca8 error:0 in libitkgdcmcharls-5.0.so.1[7f8aa07e4000+84000]
It points out at least one library. ldd on this file does not reveal missing dependency.
---
### Author:  [@pieper](https://discourse.slicer.org/u/pieper)
#### Post date: [August 28, 2019, 6:51pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/19 "2019-08-28T18:51:30Z")
Maybe the file is corrupted? `invalid opcode` indicates something pretty low level is going on.
---
### Author:  [@chir.set](https://discourse.slicer.org/u/chir.set)
#### Post date: [September 1, 2019, 3:40pm UTC](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175/20 "2019-09-01T15:40:22Z")
Hi,
I built Slicer in debug mode and it does not crash surprisingly.
Then I built with RelWithDebInfo and this one does not start. I next ran
> ./Slicer --launch xterm
and in the new terminal
> gdb ./bin/SlicerApp-real
> Fatal Python error: initsite: Failed to import the site module
> Traceback (most recent call last):
> File “/home/user/programs/Test/Slicer-4.11.0-2019-08-22-linux-amd64-RelWithDebInfo-O2/bin/…/lib/Python/lib/python3.6/site.py”, line 553, in
> main()
> File “/home/user/programs/Test/Slicer-4.11.0-2019-08-22-linux-amd64-RelWithDebInfo-O2/bin/…/lib/Python/lib/python3.6/site.py”, line 539, in main
> known\_paths = addusersitepackages(known\_paths)
> File “/home/user/programs/Test/Slicer-4.11.0-2019-08-22-linux-amd64-RelWithDebInfo-O2/bin/…/lib/Python/lib/python3.6/site.py”, line 282, in addusersitepackages
> user\_site = getusersitepackages()
> File “/home/user/programs/Test/Slicer-4.11.0-2019-08-22-linux-amd64-RelWithDebInfo-O2/bin/…/lib/Python/lib/python3.6/site.py”, line 258, in getusersitepackages
> user\_base = getuserbase() # this will also set USER\_BASE
> File “/home/user/programs/Test/Slicer-4.11.0-2019-08-22-linux-amd64-RelWithDebInfo-O2/bin/…/lib/Python/lib/python3.6/site.py”, line 248, in getuserbase
> USER\_BASE = get\_config\_var(‘userbase’)
> File “/home/user/programs/Test/Slicer-4.11.0-2019-08-22-linux-amd64-RelWithDebInfo-O2/lib/Python/lib/python3.6/sysconfig.py”, line 601, in get\_config\_var
> return get\_config\_vars().get(name)
> File “/home/user/programs/Test/Slicer-4.11.0-2019-08-22-linux-amd64-RelWithDebInfo-O2/lib/Python/lib/python3.6/sysconfig.py”, line 550, in get\_config\_vars
> \_init\_posix(\_CONFIG\_VARS)
> File “/home/user/programs/Test/Slicer-4.11.0-2019-08-22-linux-amd64-RelWithDebInfo-O2/lib/Python/lib/python3.6/sysconfig.py”, line 421, in \_init\_posix
> \_temp = **import** (name, globals(), locals(), [‘build\_time\_vars’], 0)
> ModuleNotFoundError: No module named ‘\_sysconfigdata\_m\_linux\_x86\_64-linux-gnu’
It seems that Python in the Slicer tree is looking for an unknown module in non-debug builds. On this single machine at least.
I’ll be using the debug build, and hope for a fix.
Regards.
[Next page](https://discourse.slicer.org/t/cant-start-slicer-on-linux-on-one-machine/8175.md?page=2)