New subject: Build Phenix from Source Code

24 Apr 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  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  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  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  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  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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Re: [phenixbb] Build Phenix from Source Code

Chen Zhao

Tim Gruene

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