[phenixbb] Error building Amber interface to phenix

Mon Jul 30 12:57:04 PDT 2018

Roger

The script is trying to change the mode of a file in
/opt/phenix-1.13-2998/build
but you don't have that access. Can you get access or get your sys admin to
run the script?

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Fri, Jul 27, 2018 at 2:07 PM Roger Shek <roger.shek at stonybrook.edu>
wrote:

> I am trying to build the amber interface to phenix, but encounter an
> error. Running OpenSUSE15. Anyone have any ideas?
>
> phenix.build_amber_interface
>
>  Phenix modules found : /opt/phenix-1.13-2998/modules/phenix
>
>  $AMBERHOME set : /home/roger/bin/Amber/amber18
>
>  Linking AMBERHOME to Phenix modules
>
>  Not linking $AMBERHOME into Phenix modules directory because there is
>  already a link and it points to the same directory as $AMBERHOME.
>    $AMBERHOME : /home/roger/bin/Amber/amber18
>    Phenix link: /opt/phenix-1.13-2998/modules/amber
>
> Building amber_adaptbx
>
>  ~> libtbx.configure amber
>
> Python: 2.7.14 "/opt/phenix-1.13-2998/base/bin/python2.7"
> Compiler: default
> Build mode: release
> Warning level: 0
> Precompiled Headers: False
> Static libraries: False
> Static exe: False
> Scan Boost headers: False
> Write full flex_fwd.h files: False
> Build Boost.Python extensions: True
> Define BOOST_PYTHON_NO_PY_SIGNATURES: False
> Define BOOST_PYTHON_BOOL_INT_STRICT: True
> Enable OpenMP if possible: False
> Boost threads enabled: False
> Enable CUDA: False
> Use opt_resources if available: False
> Use environment flags: False
> Enable C++11: False
> Python3 migration warning policy: None
> command_version_suffix: 1.13-2998
> Relocatable paths anchored at: /opt/phenix-1.13-2998/build
> Top-down list of all modules involved:
>  prime              "/opt/phenix-1.13-2998/modules/cctbx_project/prime"
>  iota               "/opt/phenix-1.13-2998/modules/cctbx_project/iota"
>  xia2               "/opt/phenix-1.13-2998/modules/xia2"
>  xfel               "/opt/phenix-1.13-2998/modules/cctbx_project/xfel"
>  dials              "/opt/phenix-1.13-2998/modules/dials"
>  simtbx             "/opt/phenix-1.13-2998/modules/cctbx_project/simtbx"
>  cma_es             "/opt/phenix-1.13-2998/modules/cctbx_project/cma_es"
>  labelit            "/opt/phenix-1.13-2998/modules/labelit"
>  rstbx              "/opt/phenix-1.13-2998/modules/cctbx_project/rstbx"
>  spotfinder
>         "/opt/phenix-1.13-2998/modules/cctbx_project/spotfinder"
>  annlib+adaptbx     "/opt/phenix-1.13-2998/modules/annlib"
>                     "/opt/phenix-1.13-2998/modules/annlib_adaptbx"
>  phenix             "/opt/phenix-1.13-2998/modules/phenix"
>  reel               "/opt/phenix-1.13-2998/modules/reel"
>  wxtbx              "/opt/phenix-1.13-2998/modules/cctbx_project/wxtbx"
>  phaser_regression  "/opt/phenix-1.13-2998/modules/phaser_regression"
>  phaser             "/opt/phenix-1.13-2998/modules/phaser"
>  tntbx              "/opt/phenix-1.13-2998/modules/tntbx"
>  solve_resolve      "/opt/phenix-1.13-2998/modules/solve_resolve"
>  muscle             "/opt/phenix-1.13-2998/modules/muscle"
>  ksdssp             "/opt/phenix-1.13-2998/modules/ksdssp"
>  pulchra            "/opt/phenix-1.13-2998/modules/pulchra"
>  phenix_html        "/opt/phenix-1.13-2998/modules/phenix_html"
>  phenix_regression  "/opt/phenix-1.13-2998/modules/phenix_regression"
>  elbow              "/opt/phenix-1.13-2998/modules/elbow"
>  Plex               "/opt/phenix-1.13-2998/modules/Plex"
>  PyQuante           "/opt/phenix-1.13-2998/modules/PyQuante"
>  crys3d             "/opt/phenix-1.13-2998/modules/cctbx_project/crys3d"
>  gltbx              "/opt/phenix-1.13-2998/modules/cctbx_project/gltbx"
>  amber+adaptbx      "/opt/phenix-1.13-2998/modules/amber"
>                     "/opt/phenix-1.13-2998/modules/amber_adaptbx"
>  mmtbx              "/opt/phenix-1.13-2998/modules/cctbx_project/mmtbx"
>  suitename          "/opt/phenix-1.13-2998/modules/suitename"
>  king               "/opt/phenix-1.13-2998/modules/king"
>  probe              "/opt/phenix-1.13-2998/modules/probe"
>  reduce             "/opt/phenix-1.13-2998/modules/reduce"
>  iotbx              "/opt/phenix-1.13-2998/modules/cctbx_project/iotbx"
>  ccp4io+adaptbx     "/opt/phenix-1.13-2998/modules/ccp4io"
>                     "/opt/phenix-1.13-2998/modules/ccp4io_adaptbx"
>  dxtbx              "/opt/phenix-1.13-2998/modules/cctbx_project/dxtbx"
>  cbflib+adaptbx     "/opt/phenix-1.13-2998/modules/cbflib"
>                     "/opt/phenix-1.13-2998/modules/cctbx_project/cbflib_adaptbx"
>
>  smtbx              "/opt/phenix-1.13-2998/modules/cctbx_project/smtbx"
>  ucif               "/opt/phenix-1.13-2998/modules/cctbx_project/ucif"
>  cctbx              "/opt/phenix-1.13-2998/modules/cctbx_project/cctbx"
>  scitbx             "/opt/phenix-1.13-2998/modules/cctbx_project/scitbx"
>  fable              "/opt/phenix-1.13-2998/modules/cctbx_project/fable"
>  omptbx             "/opt/phenix-1.13-2998/modules/cctbx_project/omptbx"
>  boost+adaptbx      "/opt/phenix-1.13-2998/modules/boost"
>                     "/opt/phenix-1.13-2998/modules/cctbx_project/boost_adaptbx"
>
>  tbxx               "/opt/phenix-1.13-2998/modules/cctbx_project/tbxx"
>  chiltbx            "/opt/phenix-1.13-2998/modules/cctbx_project/chiltbx"
>  libtbx             "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx"
> Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_amber.sh"
> Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_phenix.sh"
> Creating files in build directory: "/opt/phenix-1.13-2998/build"
>    dispatcher_include_template.sh
>    dispatcher_head.sh
> Traceback (most recent call last):
>  File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
> line 2462, in <module>
>    warm_start(sys.argv)
>  File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
> line 2456, in warm_start
>    env.refresh()
>  File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
> line 1615, in refresh
>    self.write_lib_dispatcher_head()
>  File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
> line 1248, in write_lib_disp
> atcher_head
>    target_file=self.under_build(target_file,
> return_relocatable_path=True))
>  File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
> line 1146, in write_bin_sh_d
> ispatcher
>    target_file.chmod(0755)
>  File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/path.py", line
> 279, in chmod
>    return os.chmod(abs(self), *args, **kwds)
> OSError: [Errno 1] Operation not permitted:
> '/opt/phenix-1.13-2998/build/dispatcher_head.sh'
>
>
>
> --
> Roger Shek
>
> Stony Brook University
> Graduate Student in Biochemistry and Structural Biology (PhD)
> Stony Brook Integrative Structural Biology Organization
> <http://sbinststrbio.com/>
> Cell: (808) 386-3879
> Website: https://www.rogershek.com
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