[phenixbb] Build Phenix from Source Code

Tim Gruene tg at shelx.uni-ac.gwdg.de
Fri Apr 25 01:39:54 PDT 2014


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Dear Chen,

just a guess: If you specify the directory with the source as the
target directory (--prefix), I could imagine this leads to confusion -
I would try something like '--prefix=/usr/local' on the command line,
or any other directory where no conflict with the files from the
source may occur.

Cheers,
Tim

On 04/25/2014 06:17 AM, Chen Zhao wrote:
> I switched to version 1.8.4-1496 and this time the same error
> didn't occur. Also --python-shared/--with-rosetta flag works. But I
> ran it as
> 
> # ./install --prefix=/usr/local/src --nproc=8 --no-gui
> --phython-shared
> 
> then regenerate the dispatchers by running libtbx.refresh as shown
> in the message after installation. However, the installation is not
> complete, and if I source phenix_env.sh, the error message as below
> will show up:
> 
> ***************************************************************************************************************
>
> 
bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_type: No such file or
> directory bash:
> /usr/local/src/phenix-1.8.4-1496/bin/machine_version: No such file
> or directory bash:
> /usr/local/src/phenix-1.8.4-1496/bin/find-installation: No such
> file or directory 
> ***************************************************************************************************************
>
>  What else should I run to complete building phenix?
> 
> PS. Because the first time I didn't append --python-shared flag, I
> build it again after deleting the original directory. I guess there
> might be files elsewhere that are changed, since I didn't have this
> error the first time.
> 
> Thanks a lot, Chen
> 
> 
> On Thu, Apr 24, 2014 at 11:10 PM, Chen Zhao <c.zhao at yale.edu>
> wrote:
> 
>> 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, Chen
>> 
>> 
>> On Thu, Apr 24, 2014 at 11:06 PM, Meng, Wuyi <wuyi.meng at yale.edu>
>> wrote:
>> 
>>> Sbgrid version means the version compiled by sbgrid (on
>>> 130.132.25.142and 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,
>>> 
>>> On Apr 24, 2014, at 10:49 PM, Chen Zhao <c.zhao at yale.edu>
>>> wrote:
>>> 
>>> Dear Wuyi,
>>> 
>>> 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.
>>> 
>>> Thank you so much again!
>>> 
>>> Good night, Chen <130.132.25.142>
>>> 
>>> 
>>> On Thu, Apr 24, 2014 at 10:35 PM, Meng, Wuyi
>>> <wuyi.meng at 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.
>>>> 
>>>> Wuyi,
>>>> 
>>>>> On Apr 24, 2014, at 10:14 PM, Chen Zhao <c.zhao at yale.edu>
>>>>> wrote:
>>>>> 
>>>>> 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 at phenix-online.org 
>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>> 
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>>> 
>> 
> 
> 
> 
> _______________________________________________ phenixbb mailing
> list phenixbb at phenix-online.org 
> http://phenix-online.org/mailman/listinfo/phenixbb
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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