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Removing out-of-date lib directory...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Removing out-of-date base software directory...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
