[phenixbb] Build Phenix from Source Code
Chen Zhao
c.zhao at yale.edu
Thu Apr 24 21:17:01 PDT 2014
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
>>> >
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