[phenixbb] exit code 126

Billy Poon BKPoon at lbl.gov
Wed Mar 18 09:56:07 PDT 2020


Hi Wim,

Sorry for the late reply, I must have lost track of this one.

With the official release, 1.17.1-3660, or the latest 1.18 release
candidate, there should be log files from the installation In the
"base_tmp" directory. Can you send those to me? They would have more
detailed information about the nature of the failure. Also, which linux
distribution and version are you using?

Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org


On Fri, Feb 21, 2020 at 9:11 AM Wim Burmeister <Wim.Burmeister at ibs.fr>
wrote:

> Hello,
>
> I am trying to install phenix on a Debian 9 linux machine, but I get
> systematically an error message from install :
>
> # ./install --prefix=/home/wpb/phenix/
>
>
> ==========================================================================
>                           Phenix Installation
>
>                           version: 1.12-2829
>                      machine type: intel-linux-2.6-x86_64
>                        OS version: 4.9.0-12-amd64
>                       destination: /home/wpb/phenix/phenix-1.12-2829
>                   # of processors: 8
>
> =========================================================================
> Configuring Phenix components.
> Traceback (most recent call last):
>   File "./bin/install.py", line 275, in <module>
>     installer(sys.argv[1:]).install()
>   File
> "/home/wpb/mounts/ibs-equipe-burmeister/phenix/phenix-installer-1.12-2829-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py",
> line 197, in install
>     self.install_from_binary()
>   File
> "/home/wpb/mounts/ibs-equipe-burmeister/phenix/phenix-installer-1.12-2829-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py",
> line 319, in install_from_binary
>     self.reconfigure(log=log)
>   File
> "/home/wpb/mounts/ibs-equipe-burmeister/phenix/phenix-installer-1.12-2829-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py",
> line 485, in reconfigure
>     call(args=args, log=log, verbose=self.options.verbose)
>   File
> "/home/wpb/mounts/ibs-equipe-burmeister/phenix/phenix-installer-1.12-2829-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py",
> line 81, in call
>     raise RuntimeError("Call to '%s' failed with exit code %d" % (args,
> rc))
> RuntimeError: Call to '/home/wpb/phenix/phenix-1.12-2829/base/bin/python
> /home/wpb/phenix/phenix-1.12-2829/modules/cctbx_project/libtbx/configure.py
> --current_working_directory /home/wpb/phenix/phenix-1.12-2829/build
> --command_version_suffix 1.12-2829 phenix phaser solve_resolve labelit
> dials xia2 iota prime' failed with exit code 126
>
> Does this ring a bell for somebody ?
> There is an old post (2016) with the same problem, but without an answer.
> I tried to install the most recent version of phenix or an older one (down
> to v10), also chosing directories with shorter paths, but the problem is
> always the same.
> Best regards
> Wim
>
>
> --
> Wim Burmeister
>
> Professeur
> Institut de Biologie Structurale (IBS) CIBB
> 71 avenue des Martyrs / CS 20192
> 38044 Grenoble Cedex 9, FRANCE
> E-mail: wim.burmeister at ibs.fr
> Tel:    +33 (0) 457 42 87 41       Fax: +33 (0) 476 20 94 00
> website
> <http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/>
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