Install DOCK 6 - Revision history

Frodo: asdf

2020-09-02T01:28:22Z

asdf

← Older revision		Revision as of 01:28, 2 September 2020
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	NOTE: Due to differences in the random number generator and precision keeping in various operating systems, you may find differences in the exact numbers resulting in failure. We are working on increasing DOCK's resilience to these issues. For now, please ignore these failures.		NOTE: Due to differences in the random number generator and precision keeping in various operating systems, you may find differences in the exact numbers resulting in failure. We are working on increasing DOCK's resilience to these issues. For now, please ignore these failures.

	If you have problems with any of the steps above, please contact us at ~~dock_bugs@dock~~.~~compbio~~.~~ucsf~~.~~edu~~ with a full description of your problem.		If you have problems with any of the steps above, please contact us at ... with a full description of your problem.

	[[Category:DOCK 6]]		[[Category:DOCK 6]]
	[[Category:Sysadmin]]		[[Category:Sysadmin]]

Frodo at 06:42, 13 March 2014

2014-03-13T06:42:06Z

← Older revision		Revision as of 06:42, 13 March 2014
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	If you have problems with any of the steps above, please contact us at dock_bugs@dock.compbio.ucsf.edu with a full description of your problem.		If you have problems with any of the steps above, please contact us at dock_bugs@dock.compbio.ucsf.edu with a full description of your problem.

	[[Category:DOCK ~~manual~~]		[[Category:DOCK 6]]
	[[Category:~~Install~~]]		[[Category:Sysadmin]]

Frodo: Frodo moved page Installation to Install DOCK 6

2014-03-12T18:19:11Z

Frodo moved page Installation to Install DOCK 6

← Older revision	Revision as of 18:19, 12 March 2014
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Frodo at 20:03, 31 October 2013

2013-10-31T20:03:49Z

← Older revision		Revision as of 20:03, 31 October 2013
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	[[Category:DOCK manual]		[[Category:DOCK manual]
			[[Category:Install]]

Therese: 2 revisions

2012-10-08T20:27:50Z

2 revisions

← Older revision	Revision as of 20:27, 8 October 2012
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JohnIrwin at 19:44, 20 September 2007

2007-09-20T19:44:05Z

← Older revision		Revision as of 19:44, 20 September 2007
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			NOTE FOR WINDOWS USERS: DOCK and its accessories must be run using a Linux-like environment like Cygwin ( http://www.cygwin.com/ ). When you install your emulator, make sure to also install compilers, unix shells, and perl ( Devel for Cygwin ). All steps below should be performed using Cygwin or another Windows-based Linux emulator.

	~~NOTE FOR WINDOWS USERS: DOCK and its accessories must be run using a Linux-like environment like Cygwin~~ ( ~~http://www.cygwin.com/~~ )~~. When you install your emulator, make sure to also install compilers, unix shells,~~ and ~~perl ( Devel for Cygwin ). All steps below should be performed~~ using ~~Cygwin or another Windows-based Linux emulator.~~		(1) Decompress and extract folders using the following commands:

	~~(1) Decompress and extract folders using the following commands:~~		[user@dock ~] tar -zxvf dock.6.0.tar.gz

	~~[user@dock ~] tar -zxvf dock.6.0.tar.gz~~		(2) Enter the installation directory

	~~(2) Enter the installation directory~~		[user@dock ~] cd dock6/install

	~~[user@dock ~] cd dock6/install~~		(3) Configure the Makefile for the appropriate operating system

	~~(3) Configure the Makefile for the appropriate operating system~~		[user@dock ~] ./configure [configuration file]

	~~[user@dock ~] ./configure [configuration file]~~		AUTHOR: Scott Brozell

	~~AUTHOR~~: ~~Scott Brozell~~		USAGE: configure [-help] [configuration file]

	~~USAGE: configure [-help] [configuration file]~~		OPTIONS

	OPTIONS
	-help #emit the usage statement		-help #emit the usage statement
	configuration file #input file containing operating system appropriate variables		configuration file #input file containing operating system appropriate variables
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	(4) OPTIONAL: Define environment variables.		(4) OPTIONAL: Define environment variables.

	(i) DOCK with parallel processing functionality requires a Message Passing Interface (MPI) library. Because of the vagaries of MPI libraries, building parallel DOCK has more pitfalls than installing the serial version. The MPI library must be installed and running on the system if the parallel features of DOCK are to be used.		(i) DOCK with parallel processing functionality requires a Message Passing Interface (MPI) library. Because of the vagaries of MPI libraries, building parallel DOCK has more pitfalls than installing the serial version. The MPI library must be installed and running on the system if the parallel features of DOCK are to be used.
	Currently, the DOCK installation mechanism only directly supports the MPICH2 and MPICH implementations. The MPICH2 library is freely available from Argonne National Labs ( http://www-unix.mcs.anl.gov/mpi/mpich/ ). Once MPI is installed, define the environment variable MPICH_HOME to the top level MPICH2 directory.		Currently, the DOCK installation mechanism only directly supports the MPICH2 and MPICH implementations. The MPICH2 library is freely available from Argonne National Labs ( http://www-unix.mcs.anl.gov/mpi/mpich/ ). Once MPI is installed, define the environment variable MPICH_HOME to the top level MPICH2 directory.

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	If you have problems with any of the steps above, please contact us at dock_bugs@dock.compbio.ucsf.edu with a full description of your problem.		If you have problems with any of the steps above, please contact us at dock_bugs@dock.compbio.ucsf.edu with a full description of your problem.

			[[Category:DOCK manual]

JohnIrwin at 22:29, 19 September 2006

2006-09-19T22:29:05Z

New page

NOTE FOR WINDOWS USERS: DOCK and its accessories must be run using a Linux-like environment like Cygwin ( http://www.cygwin.com/ ). When you install your emulator, make sure to also install compilers, unix shells, and perl ( Devel for Cygwin ). All steps below should be performed using Cygwin or another Windows-based Linux emulator.

(1) Decompress and extract folders using the following commands:

[user@dock ~] tar -zxvf dock.6.0.tar.gz

(2) Enter the installation directory

[user@dock ~] cd dock6/install

(3) Configure the Makefile for the appropriate operating system

[user@dock ~] ./configure [configuration file]

AUTHOR: Scott Brozell

USAGE: configure [-help] [configuration file]

OPTIONS
-help #emit the usage statement
configuration file #input file containing operating system appropriate variables
Configuration Files Target
gnu gnu-style compiler
gnu.parallel gnu-style compiler with parallel processing library capability
gnu.pbsa gnu-style compiler with PB/SA (ZAP library) capability
gnu.parallel.pbsa gnu-style compiler with parallel processing library and PB/SA (ZAP library) capabilities
sgi sgi-style compiler
sgi.parallel sgi-style compiler with parallel processing library capability

DESCRIPTION:
Create the DOCK configuration file, config.h, by copying an existing configuration file that is selected using the arguments. When invoked without arguments, print this usage statement and if the configuration file exists then print its creation stamp. Some configuration files require that environment variables be defined; these requirements are listed in the files and emitted by configure.

(4) OPTIONAL: Define environment variables.

(i) DOCK with parallel processing functionality requires a Message Passing Interface (MPI) library. Because of the vagaries of MPI libraries, building parallel DOCK has more pitfalls than installing the serial version. The MPI library must be installed and running on the system if the parallel features of DOCK are to be used.
Currently, the DOCK installation mechanism only directly supports the MPICH2 and MPICH implementations. The MPICH2 library is freely available from Argonne National Labs ( http://www-unix.mcs.anl.gov/mpi/mpich/ ). Once MPI is installed, define the environment variable MPICH_HOME to the top level MPICH2 directory.

WARNING: The parallel configuration files have been tailored to a typical MPICH2 build. Linking problems, such as undefined references and cannot find libbla_bla, can occur due to idiosyncrasies in the MPI installation. One corrective approach is to use manual linking; add to the LIBS definition in config.h the link flags (-L and -l) from the command: $MPICH_HOME/mpicc -show; in general, the LIBS should contain those link flags in the same order.
(ii) DOCK with PB/SA scoring requires the OpenEye ZAP library. The ZAP library can be obtained from OpenEye (http://www.eyesopen.com/). Once ZAP is installed, define the environment variable ZAP_HOME to the directory that contains the ZAP library.

(5) Build the desired DOCK executable(s)

[user@dock ~] make all # builds all the DOCK programs
[user@dock ~] make dock # builds only the dock program
[user@dock ~] make utils # builds only the accessory programs

(6) Test the built executable(s)

[user@dock ~] cd test
[user@dock ~] make clean
[user@dock ~] make test

This directory contains the DOCK quality control (QC) suite. It produces pass/fail results via fast regression tests. The suite should complete in less than ten minutes; un-passed tests should be examined to determine their significance.

If failures occur, examine problems using the command

[user@dock ~] make check

NOTE: Due to differences in the random number generator and precision keeping in various operating systems, you may find differences in the exact numbers resulting in failure. We are working on increasing DOCK's resilience to these issues. For now, please ignore these failures.

If you have problems with any of the steps above, please contact us at dock_bugs@dock.compbio.ucsf.edu with a full description of your problem.