Linux dynamic linking problem

[jason.kaelber@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-693.2.2.el7.x86_64-x86_64-with-centos-7.4.1708-Core
ChimeraX Version: 0.9 (2019-06-06)
Description
chimerax-daily [installed November 26 2019], but NOT production build [ucsf-chimerax-0.9-1.el7.x86_64.rpm], fails to launch with this error:

chimerax-daily: relocation error: /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5DBus.so.5: symbol dbus_message_get_allow_interactive_authorization, version LIBDBUS_1_3 not defined in file libdbus-1.so.3 with link time reference

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 384.90
OpenGL renderer: Quadro M4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Greg Couch]

I am very surprised to see that error. What is the output of "rpm -ql dbus-libs"? And assuming /usr/lib/libdbus-1.so.3 is in that output. What is the output of "objdump -p /usr/lib64/libdbus-1.so.3"?

Also, why haven't you updated your system from CentOS 7.4 to 7.7? It shouldn't make a difference, but it could. And there have been lots of security and bug fixes.

[jason.kaelber@…]

The output of "rpm -ql dbus-libs" is:
/lib64/libdbus-1.so.3
/lib64/libdbus-1.so.3.7.4

The output of "objdump -p /usr/lib64/libdbus-1.so.3" is:


/usr/lib64/libdbus-1.so.3:     file format elf64-x86-64

Program Header:
    LOAD off    0x0000000000000000 vaddr 0x0000000000000000 paddr 0x0000000000000000 align 2**21
         filesz 0x00000000000458ac memsz 0x00000000000458ac flags r-x
    LOAD off    0x0000000000046808 vaddr 0x0000000000246808 paddr 0x0000000000246808 align 2**21
         filesz 0x0000000000000efc memsz 0x00000000000011d8 flags rw-
 DYNAMIC off    0x0000000000046dc8 vaddr 0x0000000000246dc8 paddr 0x0000000000246dc8 align 2**3
         filesz 0x00000000000001f0 memsz 0x00000000000001f0 flags rw-
    NOTE off    0x00000000000001c8 vaddr 0x00000000000001c8 paddr 0x00000000000001c8 align 2**2
         filesz 0x0000000000000024 memsz 0x0000000000000024 flags r--
EH_FRAME off    0x0000000000038a50 vaddr 0x0000000000038a50 paddr 0x0000000000038a50 align 2**2
         filesz 0x0000000000001f14 memsz 0x0000000000001f14 flags r--
   STACK off    0x0000000000000000 vaddr 0x0000000000000000 paddr 0x0000000000000000 align 2**4
         filesz 0x0000000000000000 memsz 0x0000000000000000 flags rw-
   RELRO off    0x0000000000046808 vaddr 0x0000000000246808 paddr 0x0000000000246808 align 2**0
         filesz 0x00000000000007f8 memsz 0x00000000000007f8 flags r--

Dynamic Section:
  NEEDED               libpthread.so.0
  NEEDED               librt.so.1
  NEEDED               libc.so.6
  SONAME               libdbus-1.so.3
  INIT                 0x0000000000006a78
  FINI                 0x00000000000317b4
  INIT_ARRAY           0x0000000000246808
  INIT_ARRAYSZ         0x0000000000000008
  FINI_ARRAY           0x0000000000246810
  FINI_ARRAYSZ         0x0000000000000008
  GNU_HASH             0x00000000000001f0
  STRTAB               0x0000000000002b00
  SYMTAB               0x00000000000009b8
  STRSZ                0x0000000000001e29
  SYMENT               0x0000000000000018
  PLTGOT               0x0000000000247000
  PLTRELSZ             0x0000000000001458
  PLTREL               0x0000000000000007
  JMPREL               0x0000000000005620
  RELA                 0x0000000000004cc0
  RELASZ               0x0000000000000960
  RELAENT              0x0000000000000018
  VERNEED              0x0000000000004bf0
  VERNEEDNUM           0x0000000000000003
  VERSYM               0x000000000000492a
  RELACOUNT            0x000000000000005b

Version References:
  required from librt.so.1:
    0x09691a75 0x00 10 GLIBC_2.2.5
  required from libpthread.so.0:
    0x09691973 0x00 11 GLIBC_2.3.3
    0x09691972 0x00 05 GLIBC_2.3.2
    0x09691a75 0x00 04 GLIBC_2.2.5
  required from libc.so.6:
    0x0d696918 0x00 09 GLIBC_2.8
    0x06969194 0x00 08 GLIBC_2.14
    0x06969190 0x00 07 GLIBC_2.10
    0x0d696914 0x00 06 GLIBC_2.4
    0x09691974 0x00 03 GLIBC_2.3.4
    0x09691a75 0x00 02 GLIBC_2.2.5


________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, November 27, 2019 8:14 PM
Cc: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; Jason Kaelber <jason.kaelber@rutgers.edu>
Subject: Re: [ChimeraX] #2622: Linux dynamic linking problem

#2622: Linux dynamic linking problem
--------------------------------------+------------------------
          Reporter:  jason.kaelber@…  |      Owner:  Greg Couch
              Type:  defect           |     Status:  assigned
          Priority:  normal           |  Milestone:
         Component:  Platform         |    Version:
        Resolution:                   |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+------------------------

Comment (by Greg Couch):

 I am very surprised to see that error.  What is the output of "rpm -ql
 dbus-libs"?  And assuming /usr/lib/libdbus-1.so.3 is in that output.  What
 is the output of "objdump -p /usr/lib64/libdbus-1.so.3"?

 Also, why haven't you updated your system from CentOS 7.4 to 7.7?  It
 shouldn't make a difference, but it could.  And there have been lots of
 security and bug fixes.

--
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[Greg Couch]

My output of "objdump -p /usr/lib64/libdbus-1.so.3" is mostly the same. On CentOS 7.7, I see a "Version definitions:" section between the "Dynamic Section:" and the "Version References:" section. And appears to be the crucial missing piece. So either (1) your version got corrupted, and you need to reinstall it, or (2) that version is buggy, and you need to updated it with yum. If you can, I'd recommending doing a "sudo yum update" to get the latest bug and security fixes.