[phenixbb] PHENIX installation errors with CentOS 6
Tim Gruene
tg at shelx.uni-ac.gwdg.de
Tue Sep 30 11:14:22 PDT 2014
Hi Mark,
you have the warning
"Warning: /usr/local/phenix-dev-1807 already exists, will be overwritten"
I would remove the entire directory before installation. Old files with
old time stamps might confuse the installation procedure.
for the older version: Do you have executable permission in /home? A
cautious installer might mount /home without executable permission.
Just two guesses.
Best,
Tim
On 09/30/2014 07:11 PM, Mark A. White wrote:
> 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 Removing out-of-date lib directory...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 Removing out-of-date base software directory...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.
>
>
>
>
>
>
> _______________________________________________
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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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