Opened 7 years ago

Closed 7 years ago

#1256 closed defect (fixed)

Module can't find shared lib

Reported by: Elaine Meng Owned by: Conrad Huang
Priority: normal Milestone:
Component: Build System Version:
Keywords: Cc: lpravda@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-08-15)
Description
Command "hbonds" gives error on any structure. 

Log:
UCSF ChimeraX version: 0.8 (2018-08-15)  
How to cite UCSF ChimeraX  

open 1zik

1zik title:  
GCN4-leucine zipper core mutant ASN16LYS in the dimeric state
[more&nbspinfo...;]  
  
Chain information for 1zik #1  
---  
Chain | Description  
A B | general control protein GCN4  
  
  

hbonds reveal true

Traceback (most recent call last):  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/cmd.py", line 83, in cmd_hbonds  
    result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/hbonds/hbond.py", line 465, in find_hbonds  
    from chimerax.atomic.search import AtomSearchTree  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/search/__init__.py", line 14, in <module>  
    from .ast import AtomSearchTree  
ImportError:
dlopen(/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/search/ast.cpython-36m-darwin.so, 2): Library not
loaded: @loader_path/libatom_search.dylib  
  Referenced from:
/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/search/ast.cpython-36m-darwin.so  
  Reason: image not found  
  

ImportError:
dlopen(/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/search/ast.cpython-36m-darwin.so, 2): Library not
loaded: @loader_path/libatom_search.dylib  
Referenced from:
/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/search/ast.cpython-36m-darwin.so  
Reason: image not found  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/search/__init__.py", line 14, in  
from .ast import AtomSearchTree  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Attachments (1)

bundle_builder.py​ (28.1 KB ) - added by Tristan Croll 7 years ago.
Alternate bundle_builder.py

Download all attachments as: .zip

Change History (8)

comment:1 by pett, 7 years ago

Component: Unassigned → Build System
Owner: set to Conrad Huang
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Module can't find shared lib

comment:2 by pett, 7 years ago

Cc: lpravda@… added

comment:3 by Tristan Croll, 7 years ago

AddH is also broken in Linux for the same reason. libatom_search.so is there, but not being found. Possibly for two reasons. On the Mac, looks like it's just because it's set as @loader_path/libatom_search.dylib when it should be @loader_path/lib/libatom_search.dylib. In Linux, there's an extra issue: line 541 of bundle_builder.py should read:

            extra_link_args.append("-Wl,-rpath,\$ORIGIN")

not

            extra_link_args.append("-Wl,-rpath,$ORIGIN")

(see #1190).

comment:4 by Conrad Huang, 7 years ago

Status: assigned → accepted

The Mac problem should be fixed in the daily builds. I'm still looking into the Linux problem.

The issue is that not all shared objects/DLLs are in the main bundle package directory. For example, the .so/.dll files are placed in a lib subdirectory for the Atom_Search bundle (site-packages/chimerax/atomic/search/lib). I've been updating the bundle_builder code to put in the appropriate linker arguments and Linux still needs work.

by Tristan Croll, 7 years ago

Attachment: bundle_builder.py​ added

Alternate bundle_builder.py

comment:5 by Tristan Croll, 7 years ago

I've been replacing bundle_builder.py with this version to build Clipper and ISOLDE for over a month now. Tested and working on Linux and Mac, and I haven't made any changes that should impact Windows. If any of it is helpful, feel free.

in reply to:  7 comment:6 by lpravda@…, 7 years ago 

Hi there,

Just tested the latest build of chimerax (0.8 (2018-08-31)). The missing library issue has been resolved for Mac, but I'm still getting this error on Red Hat Enterprise Linux Server release 7.3 (Maipo). See log for details. I'm not getting this error on the same machine for the 0.7 release though.
---
./bin/ChimeraX --nogui
0.00% done: Initializing core
50.00% done: Initializing bundles
100.00% done: Finished initialization
UCSF ChimeraX version: 0.8 (2018-08-31)
cmd> open /homes/lpravda/ChimeraX/3d12.cif
Executing: open /homes/lpravda/ChimeraX/3d12.cif
Summary of feedback from opening /homes/lpravda/ChimeraX/3d12.cif
---
_warning_ |  Missing entity_poly_seq table. Inferring polymer connectivity.


Chain information for 3d12.cif #1
---
Chain | Description
[A](cxcmd:sequence chain #1/A "Show sequence") [D-2](cxcmd:sequence chain
#1/D-2 "Show sequence") | [Hemagglutinin-neuraminidase](cxcmd:sequence chain
#1/A#1/D-2 "Show sequence")
[B](cxcmd:sequence chain #1/B "Show sequence") [E-2](cxcmd:sequence chain
#1/E-2 "Show sequence") | [Ephrin-B3](cxcmd:sequence chain #1/B#1/E-2 "Show
sequence")


cmd> add hbond true
Executing: addh hbond true
Adding hydrogens
Termini for 3d12.cif (#1) chain A determined from SEQRES records
Termini for 3d12.cif (#1) chain D-2 determined from SEQRES records
Termini for 3d12.cif (#1) chain E-2 determined from SEQRES records
Termini for 3d12.cif (#1) chain B determined from SEQRES records
Chain-initial residues that are actual N termini: /A GLU 176, /D-2 GLU 176, /E-2 SER 29, /B SER 29
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ALA 603, /D-2 ALA 603, /E-2 GLN 169, /B GLN 169
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /E-2 GLN 169
Missing OXT added to C-terminal residue /B GLN 169

Unexpected exception, save your work and exit:

Traceback (most recent call last):
  File "/homes/lpravda/ChimeraX/chimerax/lib/python3.6/site-packages/chimerax/core/nogui.py", line 211, in execute
    self._cmd.run(text)
  File "/homes/lpravda/ChimeraX/chimerax/lib/python3.6/site-packages/chimerax/core/commands/cli.py", line 2561, in run
    result = ci.function(session, **kw_args)
  File "/homes/lpravda/ChimeraX/chimerax/lib/python3.6/site-packages/chimerax/atomic/addh/cmd.py", line 52, in cmd_addh
    add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)
  File "/homes/lpravda/ChimeraX/chimerax/lib/python3.6/site-packages/chimerax/atomic/addh/cmd.py", line 158, in hbond_add_hydrogens
    _make_shared_data(session, structures, in_isolation)
  File "/homes/lpravda/ChimeraX/chimerax/lib/python3.6/site-packages/chimerax/atomic/addh/cmd.py", line 336, in _make_shared_data
    from chimerax.atomic.search import AtomSearchTree
  File "/homes/lpravda/ChimeraX/chimerax/lib/python3.6/site-packages/chimerax/atomic/search/__init__.py", line 14, in <module>
    from .ast import AtomSearchTree
ImportError: libatom_search.so: cannot open shared object file: No such file or directory
--- 

Best,
Lukas

On 20/08/2018, 20:26, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #1256: Module can't find shared lib
    -----------------------------------+----------------------
              Reporter:  meng          |      Owner:  conrad
                  Type:  defect        |     Status:  accepted
              Priority:  normal        |  Milestone:
             Component:  Build System  |    Version:
            Resolution:                |   Keywords:
            Blocked By:                |   Blocking:
    Notify when closed:                |   Platform:  all
               Project:  ChimeraX      |
    -----------------------------------+----------------------
    
    Comment (by tic20):
    
     I've been replacing bundle_builder.py with this version to build Clipper
     and ISOLDE for over a month now. Tested and working on Linux and Mac, and
     I haven't made any changes that should impact Windows. If any of it is
     helpful, feel free.
    
    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1256#comment:5>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:7 by Conrad Huang, 7 years ago

Resolution: → fixed
Status: accepted → closed

Appears to be fixed (after many iterations of bundle_builder.py).

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