[phenixbb] PHENIX installation errors with CentOS 6

Tue Sep 30 10:11:07 PDT 2014

Hello,

I am getting install errors with several phenix installations after
upgrading to CentOS 6.

I started with the nightly-build

==========================================================================
                        PHENIX Installation

                        version: dev
                    release tag: 1807
                   machine type: intel-linux-2.6-x86_64
                     OS version: 2.6.32-431.29.2.el6.x86_64
                     user shell: /bin/tcsh
                    destination: /usr/local

=========================================================================

Warning: /usr/local/phenix-dev-1807 already exists, will be overwritten
removing existing temporary directory... ok
finding existing installations...
Removing out-of-date lib directory... ok
Removing out-of-date base software directory... ok
Installing new binary package... ok
Configuring PHENIX components... 
********************************************************************************
configuration step incomplete!  See the log file for detailed error
messages.
********************************************************************************

The log contains only a list of files ending with
(./docutils/._MANIFEST.in) and no error messages.

Then I went back to the latest stable version, which was installed on my
server when it ran CentOS 5.  Both my server and WS now produce the same
error (CentOS 6).

==========================================================================
                      PHENIX Installation

                      version: 1.9
                  release tag: 1692
                 machine type: intel-linux-2.6-x86_64
          source machine type: intel-linux-2.6-x86_64
                   OS version: redhat-e6.5
                   user shell: /bin/tcsh
                  destination: /usr/local
=========================================================================

==========================================================================
                     Installing from binary bundle
==========================================================================

bundle file:
  bundle-1.9-1692-intel-linux-2.6-x86_64.tar.gz
PHENIX installation source directory set to: 
  /home/white/downloads/phenix-installer-1.9-1692
PHENIX installation target directory <PHENIX_LOC > set to: 
  /usr/local/phenix-1.9-1692
PHENIX installation build directory set to: 
  <PHENIX_LOC > /build/intel-linux-2.6-x86_64
PHENIX temporary build directory set to: 
  build-binary/intel-linux-2.6-x86_64/marvin/tmp
PHENIX installation log directory set to: 
  build-binary/intel-linux-2.6-x86_64/marvin/log

==== warning: "/usr/local/phenix-1.9-1692" already exists ====
==== warning: cannot determine installation time-stamp, proceeding ====

installing binary components

removing existing files in
build-binary/intel-linux-2.6-x86_64/marvin/tmp/binary
finding installed versions
finding binary versions
binary components up-to-date
the binary package will not be installed

setting environment

configuring PHENIX components

/home/white/downloads/phenix-installer-1.9-1692/bin/install-from-binary:
line 361: 19688 Segmentation fault      $PHENIX_BUILD/base/bin/python
$PHENIX_LOC/cctbx_project/libtbx/configure.py
--current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS
$CONFIG_OPTS >> $PHENIX_LOG/binary.log 2>&1
Error configuring:
see /home/white/downloads/phenix-installer-1.9-1692/build-binary/intel-linux-2.6-x86_64/marvin/log/binary.log for details

The log contains only a list of files ending with
(./docutils/._MANIFEST.in) and no error messages.

Then I tried installing phenix-dev-1810 from source:

Installing cairo...
  log file
is /home/white/downloads/phenix-installer-dev-1810/install_tmp/intel-linux-2.6-x86_64/marvin/cairo_install_log
  getting package cairo-1.8.10.tar.gz...

using /home/white/downloads/phenix-installer-dev-1810/gui/cairo-1.8.10.tar.gz
Traceback (most recent call last):
  File "./bin/install.py", line 815, in <module>
    run(sys.argv[1:])
  File "./bin/install.py", line 72, in __init__
    self.install_from_source()
  File "./bin/install.py", line 292, in install_from_source
    log=out)
  File
"/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 113, in __init__
    self.build_cctbx_dependencies()
  File
"/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 168, in build_cctbx_dependencies
    self.build_wxpython_dependencies()
  File
"/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 425, in build_wxpython_dependencies
    self.build_wxpython_dependencies_linux()
  File
"/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 504, in build_wxpython_dependencies_linux
    self.build_compiled_package_simple(pkg_name=pkg,
pkg_name_label=name)
  File
"/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 377, in build_compiled_package_simple
    log=pkg_log)
  File
"/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 196, in configure_and_build
    self.call("make -j %d %s" % (self.nproc, " ".join(list(make_args))),
log=log)
  File
"/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 192, in call
    return call(args, log=log)
  File
"/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/installer_utils.py", line 53, in call
    raise RuntimeError("Call to '%s' failed with exit code %d" % (args,
rc))
RuntimeError: Call to 'make -j 8 ' failed with exit code 2

I would like to install the latest developmental version.  Any idea what
could be going wrong?  I have the latest updates installed.

-- 
Yours sincerely, 

Mark A. White, Ph.D. 
Associate Professor of Biochemistry and Molecular Biology, 
Manager, Sealy Center for Structural Biology and Molecular Biophysics 
Macromolecular X-ray Laboratory, 
Basic Science Building, Room 6.630 
University of Texas Medical Branch 
Galveston, TX 77555-0647 
Tel. (409) 747-4747 
Fax. (409) 747-1404 
mailto://[email protected] 
http://xray.utmb.edu 

QQ: "Life is no brief candle to me. It is a sort of splendid torch which
I have got a hold of for the moment, and I want to make it burn as
brightly as possible before handing it on to future generations. " 
- George Bernard Shaw
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