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Opened 5 years ago
Closed 5 years ago
#3556 closed defect (fixed)
A problem starting chimerax on Centos7
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | major | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Hello,
I installed chimreax on Centos7 today (28/07/2020). I downloaded the rpm
package on the website for Latest Production Release for Centos7.
The installation completed, but I had the following error when I try to
start chimerax:
[guest@rosen ~]$ chimerax
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/runpy.py", line 193, in
_run_module_as_main
"__main__", mod_spec)
File "/opt/UCSF/ChimeraX/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py",
line 895, in <module>
exit_code = init(sys.argv)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py",
line 502, in init
sess.ui = ui_class(sess)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 116, in __init__
import PyQt5.QtWebEngineWidgets
ImportError:
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineWidgets.so.5:
symbol _ZN12QQuickWidget18focusNextPrevChildEb, version Qt_5 not defined in
file libQt5QuickWidgets.so.5 with link time reference
I tried that with two computers having centos7, and got exactly the same
error.
Also, I tried the rpm package for centos7 from the Daily Builds and it
gives the same error.
Regards,
Mohamad HARASTANI, PhD candidate
IMPMC, UMR 7590
Sorbonne University
Change History (9)
comment:1 by , 5 years ago
| Component: | Unassigned → Platform |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Priority: | normal → major |
| Project: | → ChimeraX |
| Status: | new → assigned |
comment:2 by , 5 years ago
| Status: | assigned → feedback |
|---|
follow-up: 3 comment:3 by , 5 years ago
Salut Greg,
Thank you very much for your reply. Unfortunately, the workaround "env -u
LD_LIBRARY_PATH" worked. I am using csh as a shell, so I just used
(setenv LD_LIBRARY_PATH " ") and chimerax launched in that session.
Here is the output of objdump:
[guest@rosen ~]$ objdump -p
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineWidgets.so.5
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineWidgets.so.5:
file format elf64-x86-64
Program Header:
LOAD off 0x0000000000000000 vaddr 0x0000000000000000 paddr
0x0000000000000000 align 2**21
filesz 0x000000000003be7c memsz 0x000000000003be7c flags r-x
LOAD off 0x000000000003c980 vaddr 0x000000000023c980 paddr
0x000000000023c980 align 2**21
filesz 0x0000000000002540 memsz 0x00000000000025a0 flags rw-
DYNAMIC off 0x000000000003dab0 vaddr 0x000000000023dab0 paddr
0x000000000023dab0 align 2**3
filesz 0x0000000000000320 memsz 0x0000000000000320 flags rw-
NOTE off 0x00000000000001c8 vaddr 0x00000000000001c8 paddr
0x00000000000001c8 align 2**2
filesz 0x0000000000000024 memsz 0x0000000000000024 flags r--
EH_FRAME off 0x0000000000034a98 vaddr 0x0000000000034a98 paddr
0x0000000000034a98 align 2**2
filesz 0x00000000000013f4 memsz 0x00000000000013f4 flags r--
STACK off 0x0000000000000000 vaddr 0x0000000000000000 paddr
0x0000000000000000 align 2**4
filesz 0x0000000000000000 memsz 0x0000000000000000 flags rw-
RELRO off 0x000000000003c980 vaddr 0x000000000023c980 paddr
0x000000000023c980 align 2**0
filesz 0x0000000000001680 memsz 0x0000000000001680 flags r--
Dynamic Section:
NEEDED libQt5WebEngineCore.so.5
NEEDED libQt5Quick.so.5
NEEDED libQt5PrintSupport.so.5
NEEDED libQt5Widgets.so.5
NEEDED libQt5Gui.so.5
NEEDED libQt5WebChannel.so.5
NEEDED libQt5Qml.so.5
NEEDED libQt5Network.so.5
NEEDED libQt5Positioning.so.5
NEEDED libQt5Core.so.5
NEEDED libpthread.so.0
NEEDED libQt5QuickWidgets.so.5
NEEDED libGL.so.1
NEEDED libstdc++.so.6
NEEDED libm.so.6
NEEDED libgcc_s.so.1
NEEDED libc.so.6
SONAME libQt5WebEngineWidgets.so.5
RUNPATH $ORIGIN
INIT 0x00000000000191b0
FINI 0x000000000002f288
INIT_ARRAY 0x000000000023c980
INIT_ARRAYSZ 0x0000000000000010
FINI_ARRAY 0x000000000023c990
FINI_ARRAYSZ 0x0000000000000008
GNU_HASH 0x00000000000001f0
STRTAB 0x0000000000006f30
SYMTAB 0x0000000000000e88
STRSZ 0x000000000000b59f
SYMENT 0x0000000000000018
PLTGOT 0x000000000023e000
PLTRELSZ 0x0000000000002bf8
PLTREL 0x0000000000000007
JMPREL 0x00000000000165b8
RELA 0x0000000000013078
RELASZ 0x0000000000003540
RELAENT 0x0000000000000018
VERDEF 0x0000000000012ce0
VERDEFNUM 0x0000000000000010
FLAGS 0x0000000000000001
FLAGS_1 0x0000000000000080
VERNEED 0x0000000000012f08
VERNEEDNUM 0x000000000000000a
VERSYM 0x00000000000124d0
RELACOUNT 0x000000000000013b
Version definitions:
1 0x01 0x00d94ed5 libQt5WebEngineWidgets.so.5
2 0x00 0x0dcbd2c9 Qt_5_PRIVATE_API
3 0x00 0x00058a25 Qt_5
4 0x02 0x058a2810 Qt_5.0
Qt_5
5 0x02 0x058a2811 Qt_5.1
Qt_5.0
6 0x02 0x058a2812 Qt_5.2
Qt_5.1
7 0x02 0x058a2813 Qt_5.3
[guest@rosen ~]$ echo $LD_LIBRARY_PATH
/home/guest/xmipp-bundle/xmipp/build/lib:/home/guest/xmipp-bundle/xmipp/build/bindings/python:::/usr/local/cuda:/usr/local/cuda/lib64:/usr/lib64:/usr/lib:/usr/lib64/openmpi3/lib:
Qt_5.2
8 0x02 0x058a2814 Qt_5.4
Qt_5.3
9 0x02 0x058a2815 Qt_5.5
Qt_5.4
10 0x02 0x058a2816 Qt_5.6
Qt_5.5
11 0x02 0x058a2817 Qt_5.7
Qt_5.6
12 0x02 0x058a2818 Qt_5.8
Qt_5.7
13 0x02 0x058a2819 Qt_5.9
Qt_5.8
14 0x02 0x08a28110 Qt_5.10
Qt_5.9
15 0x02 0x08a28111 Qt_5.11
Qt_5.10
16 0x00 0x08a28112 Qt_5.12
Qt_5.11
Version References:
required from libc.so.6:
0x06969194 0x00 28 GLIBC_2.14
0x09691a75 0x00 27 GLIBC_2.2.5
required from libstdc++.so.6:
0x08922974 0x00 26 GLIBCXX_3.4
0x056bafd3 0x00 25 CXXABI_1.3
required from libQt5PrintSupport.so.5:
0x00058a25 0x00 24 Qt_5
required from libQt5Gui.so.5:
0x00058a25 0x00 23 Qt_5
required from libQt5Quick.so.5:
0x00058a25 0x00 22 Qt_5
required from libQt5Widgets.so.5:
0x00058a25 0x00 21 Qt_5
required from libQt5Network.so.5:
0x00058a25 0x00 20 Qt_5
required from libQt5Core.so.5:
0x08a28112 0x00 29 Qt_5.12
0x00058a25 0x00 19 Qt_5
required from libQt5WebEngineCore.so.5:
0x00058a25 0x00 18 Qt_5
required from libQt5QuickWidgets.so.5:
0x00058a25 0x00 17 Qt_5
Here is what the LD_LIBRARY_PATH has:
[guest@rosen ~]$ echo $LD_LIBRARY_PATH
/home/guest/xmipp-bundle/xmipp/build/lib:/home/guest/xmipp-bundle/xmipp/build/bindings/python:::/usr/local/cuda:/usr/local/cuda/lib64:/usr/lib64:/usr/lib:/usr/lib64/openmpi3/lib:
I tested to include the paths in LD_LIBRARY_PATH one at a time and I found
the error caused by (/usr/lib64).
Meaning, when I test:
setenv LD_LIBRARY_PATH
"/home/guest/xmipp-bundle/xmipp/build/lib:/home/guest/xmipp-bundle/xmipp/build/bindings/python:::/usr/local/cuda:/usr/local/cuda/lib64:/usr/lib:/usr/lib64/openmpi3/lib:"
chimerax works.
Best regards,
Mohamad
On Tue, Jul 28, 2020 at 8:14 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
follow-up: 4 comment:4 by , 5 years ago
*fortunatly. On Wed, Jul 29, 2020 at 2:57 PM Mohamad HARASTANI <mohamad.harastani@upmc.fr> wrote:
comment:5 by , 5 years ago
Good to hear that we've identified the problem. I've put a fix into the daily build, so the next daily build should not need the workaround. Please try a daily build dated 2020-07-30 or newer (so starting tomorrow) and tell if it is actually fixed or not.
comment:6 by , 5 years ago
Salut Mohamad,
Have you had a chance to check out today's ChimeraX daily build? I think it should run without changing LD_LIBRARY_PATH.
-- Greg
follow-up: 7 comment:7 by , 5 years ago
Salut Greg, Unfortunately, today is a very hot day in Paris and I am working from home, I will be back to the lab on Monday and I promise to follow it up. After your hint in the previous email, I removed from LD_LIBRARY_PATH what was conflicting with ChimeraX, and things worked, and I got busy solving other issues. Thank you very much for your collaboration, it is the second time I report a bug and I get a solution in no time. I respect and appreciate that. Regards Mohamad On Fri, Jul 31, 2020 at 9:08 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
follow-up: 8 comment:8 by , 5 years ago
Dear Greg, I tested the chimera-daily version 2020.08.03 on Centos and Ububtu. Both start well without the need of manipulating LD_LIBRARY_PATH. Best Regards, Mohamad On Fri, Jul 31, 2020 at 11:53 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
comment:9 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
My apologies for not closing this sooner. Thank you for confirming that the daily build fixed the issue.
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Salut Mohamad,
That is a bizarre error. If you run "objdump -p /opt/UCSF/ChimeraX/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineWidgets.so.5", you'll see in the "Version definitions:" section that "Qt_5" is defined. If you don't, please send me the objdump output, so I can review it.
By googling, I see this is sometimes happens with anaconda setups. Try running "env -u LD_LIBRARY_PATH chimerax" and let me know if that works around the problem for you. "env -u LD_LIBRARY_PATH" temporarily removes the LD_LIBRARY_PATH environment variable, so it won't interfere with chimerax.