OK, thank you for your suggestion! I will do that. But as a perfectionist, I will try to finish with the installation. I later found that the flag is --with-rosetta but not --python-shared... I have to build it again... Crying...
Best,ChenOn Thu, Apr 24, 2014 at 11:06 PM, Meng, Wuyi <wuyi.meng@yale.edu> wrote:
Sbgrid version means the version compiled by sbgrid (on 130.132.25.142 and other cbic Mac Pros). The Mac Pro runs 2x fast than csb and yale hpc computers of same phenix refinement, they have 8 cores too. Rosetta runs usually take days to weeks to finish, it is wise to do it on yale hpc cluster.�
Wuyi,ChenDear Wuyi,Thank you so much again!
Thank you for your warm help as always! But actually SBGrid is not "installed" in this machine (don't laugh, it is my laptop...) Do you mean phenix-1.8.4-1496 when saying the SBGrid version? I did try this version after you mentioned and at least it passed the step that gave me the error before. I will wait and see how the compilation goes. And if this works, hopefully there will be no error when running rosetta.build_phenix_interface. I will try the one on130.132.25.142� if nothing works.
Good night,
On Thu, Apr 24, 2014 at 10:35 PM, Meng, Wuyi <wuyi.meng@yale.edu> wrote:
phenix.rosetta_refine should work on 130.132.25.142 according to following statement from sbgrid:
Linux 64-bit We have installed and configured nightly versions
of Phenix and Rosetta to support the newly announced Phenix-Rosetta refinement mentioned in Nature Methods. These experimental versions are not the default, so you'll need to add version
overrides in your ~/.sbgrid.conf file: P HE N I X _ X = n i g h t l y R O S E T T A _ X = n i g h t l y You can refresh your memory for setting version overrides on our website. These new features are only available on 64-bit Linux at this time. Phenix
generally has very good support for OS X, but Macs
seem to be a second tier platform for the Rosetta
developers.
> Dear all,
>
> I would like to try phenix.rosetta_refine and it is said in the online tutorial that the phenix should be built from source code in linux. However I ran into some errors, and I am too far from a linux export to figure it out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the source installer (phenix-installer-1.9-1683-source.tar) and run the installer as:
>
> # ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from README-DEV that there is no --python-shared flag as described in the online tutorial)
>
> After while, I receive the following error message:
>
> *************************************************************************************************************************
> Installing Imaging...
> � log file is /workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log
> � getting package Imaging-1.1.7.tar.gz...
> � � using /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz
> Traceback (most recent call last):
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", line 9, in <module>
> � � install_cctbx_base.installer(args=sys.argv, log=sys.stdout)
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 95, in __init__
> � � self.build_cctbx_dependencies()
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 134, in build_cctbx_dependencies
> � � self.build_imaging()
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 349, in build_imaging
> � � confirm_import_module="Image")
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 325, in build_python_module_simple
> � � log=pkg_log)
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 150, in call
> � � return call(args, log=log)
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", line 51, in call
> � � raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))
> RuntimeError: Call to '/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python setup.py build ' failed with exit code 1
> FATAL ERROR: aborting installation.
> *************************************************************************************************************************
>
> I looked into Imaging_install_log, and at the end, I have the following errors:
>
> *************************************************************************************************************************
> /usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC
> /usr/local/lib/libpython2.7.a: could not read symbols: Bad value
> collect2: error: ld returned 1 exit status
> error: command 'gcc' failed with exit status 1
> ***************************************************************************************************************************
>
> Could anybody help me out?
>
> Thank you so much,
> Chen
>
> _______________________________________________
> phenixbb mailing list
> phenixbb@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.