Re: [phenixbb] Build Phenix from Source Code

25 Apr 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:
***************************************************************************************************************
...
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",
...
...
...
...
...
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",
...
...
...
...
...
self.build_cctbx_dependencies() File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
...
...
...
...
...
self.build_imaging() File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
...
...
...
...
...
confirm_import_module="Image") File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
...
...
...
...
...
log=pkg_log) File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
...
...
...
...
...
return call(args, log=log) File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py",
bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_type: No such file or
line 9, in <module>
line 95, in __init__
line 134, in build_cctbx_dependencies
line 349, in build_imaging
line 325, in build_python_module_simple
line 150, in call
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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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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