<div dir="ltr"><div><div><div><div>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 <br><br># ./install --prefix=/usr/local/src --nproc=8 --no-gui --phython-shared<br>
<br></div>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:<br>
<br>***************************************************************************************************************<br>bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_type: No such file or directory<br>bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_version: No such file or directory<br>
bash: /usr/local/src/phenix-1.8.4-1496/bin/find-installation: No such file or directory<br>***************************************************************************************************************<br><br></div>What else should I run to complete building phenix?<br>
<br></div><div>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.<br>
</div><div><br></div>Thanks a lot,<br></div>Chen<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 24, 2014 at 11:10 PM, Chen Zhao <span dir="ltr"><<a href="mailto:c.zhao@yale.edu" target="_blank">c.zhao@yale.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>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...<br>
<br></div><div>Best,<br></div><div>Chen<br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 24, 2014 at 11:06 PM, Meng, Wuyi <span dir="ltr"><<a href="mailto:wuyi.meng@yale.edu" target="_blank">wuyi.meng@yale.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="auto">
<div>Sbgrid version means the version compiled by sbgrid (on <a href="tel:130.132.25.142" value="+13013225142" target="_blank">130.132.25.142</a> 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.�<span><font color="#888888"><br>
<br>
Wuyi,</font></span></div><div>
<div><br>
On Apr 24, 2014, at 10:49 PM, Chen Zhao <<a href="mailto:c.zhao@yale.edu" target="_blank">c.zhao@yale.edu</a>> wrote:<br>
<br>
</div>
</div><blockquote type="cite">
<div><div>
<div dir="ltr">
<div>
<div>Dear Wuyi,<br>
<br>
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 on<a href="tel:130.132.25.142" value="+13013225142" target="_blank">130.132.25.142</a>�
if nothing works. <br>
<br>
</div>
Thank you so much again!<br>
<br>
Good night,<br>
</div>
Chen<br>
<div>
<div>
<div><a href="tel:130.132.25.142" value="+13013225142" target="_blank"><span><span style="background-color:rgb(0,0,0)"></span></span></a></div>
</div>
</div>
</div>
</div><div class="gmail_extra"><br>
<br>
<div class="gmail_quote"><div>On Thu, Apr 24, 2014 at 10:35 PM, Meng, Wuyi <span dir="ltr">
<<a href="mailto:wuyi.meng@yale.edu" target="_blank">wuyi.meng@yale.edu</a>></span> wrote:<br>
</div><div><div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
phenix.rosetta_refine should work on <a href="tel:130.132.25.142" value="+13013225142" target="_blank">
130.132.25.142</a> according to following statement from sbgrid:<br>
<br>
Linux 64-bit We have installed and configured nightly versions<br>
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<br>
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<br>
generally has very good support for OS X, but Macs<br>
seem to be a second tier platform for the Rosetta<br>
developers.<br>
<div><br>
Wuyi,<br>
<br>
> On Apr 24, 2014, at 10:14 PM, Chen Zhao <<a href="mailto:c.zhao@yale.edu" target="_blank">c.zhao@yale.edu</a>> wrote:<br>
><br>
</div>
<div>
<div>> Dear all,<br>
><br>
> 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:<br>
><br>
> # ./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)<br>
><br>
> After while, I receive the following error message:<br>
><br>
> *************************************************************************************************************************<br>
> Installing Imaging...<br>
> � 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<br>
> � getting package Imaging-1.1.7.tar.gz...<br>
> � � using /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz<br>
> Traceback (most recent call last):<br>
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", line 9, in <module><br>
> � � install_cctbx_base.installer(args=sys.argv, log=sys.stdout)<br>
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 95, in __init__<br>
> � � self.build_cctbx_dependencies()<br>
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 134, in build_cctbx_dependencies<br>
> � � self.build_imaging()<br>
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 349, in build_imaging<br>
> � � confirm_import_module="Image")<br>
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 325, in build_python_module_simple<br>
> � � log=pkg_log)<br>
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 150, in call<br>
> � � return call(args, log=log)<br>
> � File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", line 51, in call<br>
> � � raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<br>
> 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<br>
> FATAL ERROR: aborting installation.<br>
> *************************************************************************************************************************<br>
><br>
> I looked into Imaging_install_log, and at the end, I have the following errors:<br>
><br>
> *************************************************************************************************************************<br>
> /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<br>
> /usr/local/lib/libpython2.7.a: could not read symbols: Bad value<br>
> collect2: error: ld returned 1 exit status<br>
> error: command 'gcc' failed with exit status 1<br>
> ***************************************************************************************************************************<br>
><br>
> Could anybody help me out?<br>
><br>
> Thank you so much,<br>
> Chen<br>
><br>
</div>
</div>
<div>
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</blockquote>
</div></div></div>
<br>
</div>
</div>
</blockquote>
</div>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>