Ha14 installation - Revision history

Aaron: Aaron moved page Installation to Ha14 installation: deprecated installation instructions

2018-11-06T23:13:49Z

Aaron moved page Installation to Ha14 installation: deprecated installation instructions

← Older revision	Revision as of 23:13, 6 November 2018
(No difference)

Aaron: /* Finish up the build */

2017-03-31T22:45:56Z

Finish up the build

← Older revision		Revision as of 22:45, 31 March 2017
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	After downloading the sources, you need to be sure you have the appropriate compilers before executing the next command. At SLAC, that means you need to ssh to one of the psana nodes, as the pslogin nodes do not have the requisite compilers. When ready, configure and compile thusly:		After downloading the sources, you need to be sure you have the appropriate compilers before executing the next command. At SLAC, that means you need to ssh to one of the psana nodes, as the pslogin nodes do not have the requisite compilers. When ready, configure and compile thusly:

	python bootstrap.py build --builder=xfel --with-python=`which python` --nproc=<# cores available for compile>l		python bootstrap.py build --builder=xfel --with-python=`which python` --nproc=<# cores available for compile>

	On SLAC's interactive nodes, this takes just over 6 minutes. To avoid problems with run-time dynamic linking of Python extensions, the Python interpreter required for the above command must be the one provided by the PSDM software distribution. That interpreter can be located using find, <i>e.g.</i>		On SLAC's interactive nodes, this takes just over 6 minutes. To avoid problems with run-time dynamic linking of Python extensions, the Python interpreter required for the above command must be the one provided by the PSDM software distribution. That interpreter can be located using find, <i>e.g.</i>

Nicksauter: /* Finish up the build */

2017-03-31T18:43:31Z

Finish up the build

← Older revision		Revision as of 18:43, 31 March 2017
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	After downloading the sources, you need to be sure you have the appropriate compilers before executing the next command. At SLAC, that means you need to ssh to one of the psana nodes, as the pslogin nodes do not have the requisite compilers. When ready, configure and compile thusly:		After downloading the sources, you need to be sure you have the appropriate compilers before executing the next command. At SLAC, that means you need to ssh to one of the psana nodes, as the pslogin nodes do not have the requisite compilers. When ready, configure and compile thusly:

	python bootstrap.py build --builder=xfel --with-python=`which python`		python bootstrap.py build --builder=xfel --with-python=`which python` --nproc=<# cores available for compile>l

	On SLAC's interactive nodes, this takes just over 6 minutes. To avoid problems with run-time dynamic linking of Python extensions, the Python interpreter required for the above command must be the one provided by the PSDM software distribution. That interpreter can be located using find, <i>e.g.</i>		On SLAC's interactive nodes, this takes just over 6 minutes. To avoid problems with run-time dynamic linking of Python extensions, the Python interpreter required for the above command must be the one provided by the PSDM software distribution. That interpreter can be located using find, <i>e.g.</i>

Nicksauter: /* Alternate instructions for non-LBNL developers */

2017-03-31T18:32:51Z

Alternate instructions for non-LBNL developers

← Older revision		Revision as of 18:32, 31 March 2017
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	python bootstrap.py hot --builder=xfel --sfuser=<githubusername> # download the static packages		python bootstrap.py hot --builder=xfel --sfuser=<githubusername> # download the static packages
	python bootstrap.py update --builder=dials --sfuser=<githubusername> # download the github code for dials & cctbx		python bootstrap.py update --builder=dials --sfuser=<githubusername> # download the github code for dials & cctbx
			mkdir modules/cxi_xdr_xes # create a stub directory for experiment-specific python code

	Then download phenix from http://phenix-online.org and untar the package. Locate the modules directory in the phenix directory tree, and copy-paste the labelit subdirectory into the modules directory of your current working area.		Then download phenix from http://phenix-online.org and untar the package. Locate the modules directory in the phenix directory tree, and copy-paste the labelit subdirectory into the modules directory of your current working area.

Nicksauter: /* Alternate instructions for non-LBNL developers */

2017-03-31T18:21:23Z

Alternate instructions for non-LBNL developers

← Older revision		Revision as of 18:21, 31 March 2017
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	python bootstrap.py update --builder=dials --sfuser=<githubusername> # download the github code for dials & cctbx		python bootstrap.py update --builder=dials --sfuser=<githubusername> # download the github code for dials & cctbx

	Then download phenix from http://phenix-online.org and untar the package. Locate the modules directory in the phenix directory tree, and copy-paste the ~~labelit_sources~~ subdirectory into the modules directory of your current working area.		Then download phenix from http://phenix-online.org and untar the package. Locate the modules directory in the phenix directory tree, and copy-paste the labelit subdirectory into the modules directory of your current working area.

	===Finish up the build===		===Finish up the build===

Nicksauter: /* Standard installation using PSDM */

2017-03-31T18:09:10Z

Standard installation using PSDM

← Older revision		Revision as of 18:09, 31 March 2017
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	== Standard installation using PSDM ==		== Standard installation using PSDM ==
			===Quick start===
	This step has to be performed on a host with Internet access. Not all hosts at SLAC have that, but the members of <i>e.g.</i> pslogin pool do. Make and change to a working directory to contain the new source code and build (this directory should be accessible from any computing nodes ''cctbx.xfel'' will be run. Then download these bootstrap modules:		This step has to be performed on a host with Internet access. Not all hosts at SLAC have that, but the members of <i>e.g.</i> pslogin pool do. Make and change to a working directory to contain the new source code and build (this directory should be accessible from any computing nodes ''cctbx.xfel'' will be run. Then download these bootstrap modules:

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	This command instructs bootstrap.py to download static packages required for ''cctbx.xfel'' (hot), and then to checkout the rest of the sources from cci.lbl.gov and github (update), using the user accounts specified by the cciuser and sfuser parameters, respectively.		This command instructs bootstrap.py to download static packages required for ''cctbx.xfel'' (hot), and then to checkout the rest of the sources from cci.lbl.gov and github (update), using the user accounts specified by the cciuser and sfuser parameters, respectively.

			===Alternate instructions for non-LBNL developers===
			Our non-LBNL colleagues will now realize that the "python bootstrap" step does not work without cci username credentials, needed to obtain source code for the program LABELIT. Developers are instructed to use the following alternate procedure:

			python bootstrap.py hot --builder=xfel --sfuser=<githubusername> # download the static packages
			python bootstrap.py update --builder=dials --sfuser=<githubusername> # download the github code for dials & cctbx

			Then download phenix from http://phenix-online.org and untar the package. Locate the modules directory in the phenix directory tree, and copy-paste the labelit_sources subdirectory into the modules directory of your current working area.

			===Finish up the build===
	After downloading the sources, you need to be sure you have the appropriate compilers before executing the next command. At SLAC, that means you need to ssh to one of the psana nodes, as the pslogin nodes do not have the requisite compilers. When ready, configure and compile thusly:		After downloading the sources, you need to be sure you have the appropriate compilers before executing the next command. At SLAC, that means you need to ssh to one of the psana nodes, as the pslogin nodes do not have the requisite compilers. When ready, configure and compile thusly:

Artem: /* Installation on a non-PSDM system */

2017-03-06T20:23:52Z

Installation on a non-PSDM system

← Older revision		Revision as of 20:23, 6 March 2017
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	Please contact the authors if with any issues. Some gotchas:		Please contact the authors if with any issues. Some gotchas:

	1) On a Mac, you will need to make sure you have the latest version of xcode installed. Consider the command xcode-select --install.		1) On a Mac, you will need to make sure you have the latest version of xcode installed. Consider the command xcode-select --install. [NOTE: Xcode v. 8.2.1. for Mac OS 10.12 (Sierra) does not include a gFortran compiler. You will need to install gFortran separately if you need scipy.]

	2) On linux you will likely need to install some dependencies, including gFortran. [Note: gFortran is needed only for the scipy installation, not for the core build based on cctbx. Therefore, only install gFortran if you need scipy.]		2) On linux you will likely need to install some dependencies, including gFortran. [Note: gFortran is needed only for the scipy installation, not for the core build based on cctbx. Therefore, only install gFortran if you need scipy.]

Nicksauter at 19:52, 6 January 2017

2017-01-06T19:52:42Z

← Older revision		Revision as of 19:52, 6 January 2017
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	1) On a Mac, you will need to make sure you have the latest version of xcode installed. Consider the command xcode-select --install.		1) On a Mac, you will need to make sure you have the latest version of xcode installed. Consider the command xcode-select --install.

	2) On linux you will likely need to install some dependencies, including gFortran.		2) On linux you will likely need to install some dependencies, including gFortran. [Note: gFortran is needed only for the scipy installation, not for the core build based on cctbx. Therefore, only install gFortran if you need scipy.]

	== External links ==		== External links ==

Nicksauter at 02:01, 9 December 2016

2016-12-09T02:01:39Z

← Older revision		Revision as of 02:01, 9 December 2016
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	If you find yourself on a machine without PSDM and won't be dealing with XTC directly, for example if you have your own data collected as stills from a non-XFEL source, you can use the below commands in a new directory (again assuming you have a cci user account):		If you find yourself on a machine without PSDM and won't be dealing with XTC directly, for example if you have your own data collected as stills from a non-XFEL source, you can use the below commands in a new directory (again assuming you have a cci user account):

	~~svn export svn~~://~~svn~~.~~code~~.sf.~~net~~/p/cctbx/~~code~~/~~trunk~~/libtbx/auto_build/bootstrap.py		# On Linux:
			wget https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py
			# On MacOSX:
			curl https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py > bootstrap.py

	python bootstrap.py hot update base build --builder=xfel --cciuser=<cciusername> --sfuser=<sourceforgeusername>		python bootstrap.py hot update base build --builder=xfel --cciuser=<cciusername> --sfuser=<sourceforgeusername>

Nicksauter at 01:19, 9 December 2016

2016-12-09T01:19:27Z

← Older revision		Revision as of 01:19, 9 December 2016
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	python bootstrap.py hot update --builder=xfel --cciuser=<cciusername> --sfuser=<githubusername>		python bootstrap.py hot update --builder=xfel --cciuser=<cciusername> --sfuser=<githubusername>

	This command instructs bootstrap.py to download static packages required for ''cctbx.xfel'' (hot), and then to checkout the rest of the sources from cci.lbl.gov and ~~sourceforge.net~~ (update), using the user accounts specified by the cciuser and sfuser parameters, respectively.		This command instructs bootstrap.py to download static packages required for ''cctbx.xfel'' (hot), and then to checkout the rest of the sources from cci.lbl.gov and github (update), using the user accounts specified by the cciuser and sfuser parameters, respectively.

	After downloading the sources, you need to be sure you have the appropriate compilers before executing the next command. At SLAC, that means you need to ssh to one of the psana nodes, as the pslogin nodes do not have the requisite compilers. When ready, configure and compile thusly:		After downloading the sources, you need to be sure you have the appropriate compilers before executing the next command. At SLAC, that means you need to ssh to one of the psana nodes, as the pslogin nodes do not have the requisite compilers. When ready, configure and compile thusly: