Installing DOCK 6 - Revision history

Frodo: asdf

2024-05-24T01:22:03Z

asdf

Khtang at 19:52, 10 January 2019

2019-01-10T19:52:17Z

← Older revision		Revision as of 19:52, 10 January 2019
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	file (install/config.h) that is created by configure,		file (install/config.h) that is created by configure,
	and execute make -n for a dry run.		and execute make -n for a dry run.
	Consult the [[FAQ]].		Consult the [[DOCK6 FAQ \| FAQ]].
	Search the [[DOCK-Fans]] mailing list archive.		Search the [[DOCK-Fans]] mailing list archive.

Khtang at 19:50, 10 January 2019

2019-01-10T19:50:29Z

← Older revision		Revision as of 19:50, 10 January 2019
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	All steps below should be performed		All steps below should be performed
	using Cygwin or another Unix emulator for Windows.		using Cygwin or another Unix emulator for Windows.
	See also the [[DOCK on cygwin DOCK \| wiki entry for Cygwin]].		See also the [[DOCK on cygwin \| DOCK wiki entry for Cygwin]].

Khtang at 19:50, 10 January 2019

2019-01-10T19:50:01Z

← Older revision		Revision as of 19:50, 10 January 2019
Line 40:		Line 40:
	All steps below should be performed		All steps below should be performed
	using Cygwin or another Unix emulator for Windows.		using Cygwin or another Unix emulator for Windows.
	See also the [[DOCK on cygwin DOCK wiki entry for Cygwin]].		See also the [[DOCK on cygwin DOCK \| wiki entry for Cygwin]].

Khtang at 19:49, 10 January 2019

2019-01-10T19:49:29Z

← Older revision		Revision as of 19:49, 10 January 2019
Line 40:		Line 40:
	All steps below should be performed		All steps below should be performed
	using Cygwin or another Unix emulator for Windows.		using Cygwin or another Unix emulator for Windows.
	See also the [[DOCK wiki entry for Cygwin]].		See also the [[DOCK on cygwin DOCK wiki entry for Cygwin]].

Sudipto at 23:10, 23 March 2016

2016-03-23T23:10:14Z

← Older revision		Revision as of 23:10, 23 March 2016
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	for parallel, pbsa, etc; see step 6.		for parallel, pbsa, etc; see step 6.
	(Here is a quick start for an example gnu serial and parallel installation:		(Here is a quick start for an example gnu serial and parallel installation:
	cd install; ./configure gnu; make install;		cd install; ./configure gnu; make install;
	make dockclean; ./configure gnu parallel;		make dockclean; ./configure gnu parallel;
	setenv MPICH_HOME /bla; make dock; make test;).		setenv MPICH_HOME /bla; make dock; make test;).


	If problems occur then read the diagnostics carefully and apply the		If problems occur then read the diagnostics carefully and apply the
	[[scientific method]].		[[scientific method]].
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	using the following command:		using the following command:

	~~<blockquote>~~		[user@dock ~] tar -zxvf dock.6.7.tar.gz
	[user@dock ~]
	tar -zxvf dock.6.7.tar.gz

	~~</blockquote>~~
	(2) Enter the installation directory:		(2) Enter the installation directory:

	~~<blockquote>~~		[user@dock ~] cd dock6/install
	[user@dock ~] cd dock6/install

	~~</blockquote>~~
	(3) Configure the Makefile for the		(3) Configure the Makefile for the
	appropriate operating system:		appropriate operating system:

	~~<blockquote>~~		[user@dock ~] ./configure [configuration file]
	[user@dock ~] ./configure
	[configuration file]


	AUTHOR: Scott Brozell		AUTHOR: Scott Brozell


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


	OPTIONS: Notable ones are listed below;		OPTIONS: Notable ones are listed below;
	for a complete list see the configure -help output.<br> '''-help''' #emit the usage statement<br> '''configuration file''' #input file		for a complete list see the configure -help output.<br> '''-help''' #emit the usage statement<br> '''configuration file''' #input file

Sudipto at 23:08, 23 March 2016

2016-03-23T23:08:05Z

← Older revision		Revision as of 23:08, 23 March 2016
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	The simple configuration scheme of DOCK is based on plain text files.		The simple configuration scheme of DOCK is based on plain text files.
	Building and testing employ the		Building and testing employ the
	[[make]]		make
	command.		command.
	DOCK installation is so simple and transparent that users		DOCK installation is so simple and transparent that users
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	{\| ~~border~~="1"		{\| class="wikitable"
	\|-		\|-
	\|'''Configuration Files '''		\|'''Configuration Files '''
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	\|-		\|-
	\|gnu.acml		\|gnu.acml
	\|recent GNU compilers and		\|recent GNU compilers and [[ACML]]
	[[ACML]]
	\|-		\|-
	\|gnu.parallel		\|gnu.parallel
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	\|-		\|-
	\|intel.mkl		\|intel.mkl
	\|Intel compilers and		\|Intel compilers and [[MKL]]
	[[MKL]]
	\|-		\|-
	\|pgi		\|pgi
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	\|SGI native compilers		\|SGI native compilers
	\|}		\|}
	~~DESCRIPTION:<br>~~
			= Description =

	Create the DOCK configuration file, config.h, by copying an existing		Create the DOCK configuration file, config.h, by copying an existing
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	to use alternatives.		to use alternatives.

	~~</blockquote>~~		Build the desired DOCK executable(s) via
	~~(4)~~ Build the desired DOCK executable(s) via
	one of the following commands:		one of the following commands:

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

	[user@dock ~] make dock # builds only the dock program<br>

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

	~~</blockquote>~~
	~~(5)~~
	Test the built executable(s) via these commands:		Test the built executable(s) via these commands:

	~~<blockquote>~~		[user@dock ~] cd test; make test; make check
	[user@dock ~] cd test; make test; make check


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	[[here.]]		[[here.]]

	~~</blockquote>~~
	(6) OPTIONAL: Alternate executables.		(6) OPTIONAL: Alternate executables.

	~~<blockquote>~~
	(i) DOCK with parallel processing functionality		(i) DOCK with parallel processing functionality
	requires a Message Passing Interface (MPI) library.		requires a Message Passing Interface (MPI) library.
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	The MPI library must be installed and running on the system if the		The MPI library must be installed and running on the system if the
	parallel features of DOCK are to be used.		parallel features of DOCK are to be used.
	~~<br>~~

	Currently, the DOCK installation mechanism only directly supports		Currently, the DOCK installation mechanism only directly supports
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	for execution information.		for execution information.


	WARNING: The parallel configuration files have been		WARNING: The parallel configuration files have been
	tailored to a typical MPICH2 build.		tailored to a typical MPICH2 build.
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	in general, the LIBS should contain those link flags in the same order.		in general, the LIBS should contain those link flags in the same order.


	(ii) DOCK with PB/SA scoring requires OpenEye Toolkits.		(ii) DOCK with PB/SA scoring requires OpenEye Toolkits.
	In particular, DOCK uses the APIs as in OEChem TK 1.7.0 and Zap TK 2.1.1.		In particular, DOCK uses the APIs as in OEChem TK 1.7.0 and Zap TK 2.1.1.
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	(Here is a quick start for an example gnu pbsa installation after		(Here is a quick start for an example gnu pbsa installation after
	already building and testing a serial gnu installation:		already building and testing a serial gnu installation:
	~~cd install; ./configure gnu.pbsa;~~
	~~setenv ZAP_HOME /openeye/toolkits/1.7.0-3/redhat-RHEL5-g++4.1-x64/;~~
	~~setenv OE_LICENSE /openeye/oe_license.txt;~~
	~~make dockclean; make dock; make testpbsa;).~~

	</~~blockquote>~~		cd install; ./configure gnu.pbsa;
			setenv ZAP_HOME /openeye/toolkits/1.7.0-3/redhat-RHEL5-g++4.1-x64/;
			setenv OE_LICENSE /openeye/oe_license.txt;
			make dockclean; make dock; make testpbsa;).

			[[Category:DOCK]]
			[[Category:DOCK 6]]
			[[Category:Software]]
			[[Category:Freecom]]

Sudipto: Created page with " DOCK is Unix based scientific software and follows a common installation recipe: download, unpack, configure, build, and test. The simple configuration scheme of DOCK is..."

2016-03-23T22:45:06Z

Created page with " DOCK is Unix based scientific software and follows a common installation recipe: download, unpack, configure, build, and test. The simple configuration scheme of DOCK is..."

New page

DOCK is [[Unix]]
based scientific software and
follows a common installation recipe:
download, unpack, configure, build, and test.
The simple configuration scheme of DOCK is based on plain text files.
Building and testing employ the
[[make]]
command.
DOCK installation is so simple and transparent that users
have a reasonable chance of correcting problems themselves.

Start with a plain serial installation.
Follow the detailed steps (1. through 5.) enumerated below.
The appropriate configuration option is likely gnu; see step 3.
Subsequently, additional executables can be installed
for parallel, pbsa, etc; see step 6.
(Here is a quick start for an example gnu serial and parallel installation:
cd install; ./configure gnu; make install;
make dockclean; ./configure gnu parallel;
setenv MPICH_HOME /bla; make dock; make test;).

If problems occur then read the diagnostics carefully and apply the
[[scientific method]].
To observe what's under the hood, view the configuration
file (install/config.h) that is created by configure,
and execute make -n for a dry run.
Consult the [[FAQ]].
Search the [[DOCK-Fans]] mailing list archive.

NOTE FOR WINDOWS
USERS: DOCK and its accessories must be run using a Unix-like
environment such as Cygwin
( [[http://www.cygwin.com/]] ).
We recommend a full Unix installation.
In particular, 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 Unix emulator for Windows.
See also the [[DOCK wiki entry for Cygwin]].

(1) Unpack the distribution
using the following command:

<blockquote>
[user@dock ~]
tar -zxvf dock.6.7.tar.gz

</blockquote>
(2) Enter the installation directory:

<blockquote>
[user@dock ~] cd dock6/install

</blockquote>
(3) Configure the Makefile for the
appropriate operating system:

<blockquote>
[user@dock ~] ./configure
[configuration file]

AUTHOR: Scott Brozell

USAGE: configure [-help]
[configuration file]

OPTIONS: Notable ones are listed below;
for a complete list see the configure -help output. '''-help''' #emit the usage statement '''configuration file''' #input file
containing operating system appropriate variables

{| border="1"
|-
|'''Configuration Files '''
|'''Target'''
|-
|gnu
|GNU compilers
|-
|gnu.acml
|recent GNU compilers and
[[ACML]]
|-
|gnu.parallel
|GNU compilers with parallel processing capability
|-
|gnu.pbsa
|GNU compilers with PB/SA (ZAP library) capability
|-
|gnu.parallel.pbsa
|GNU compilers with parallel processing and PB/SA (ZAP library) capabilities
|-
|ibmaix
|IBM AIX and native compilers
|-
|intel
|Intel compilers
|-
|intel.mkl
|Intel compilers and
[[MKL]]
|-
|pgi
|PGI compilers
|-
|sgi
|SGI native compilers
|}
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.
Note that as of version 6.6 gfortran is the default Fortran compiler in
the gnu config files (replacing g77).
But other Fortran compilers may be used; simply hand edit install/config.h
to use alternatives.

</blockquote>
(4) Build the desired DOCK executable(s) via
one of the following commands:

<blockquote>
[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

</blockquote>
(5)
Test the built executable(s) via these commands:

<blockquote>
[user@dock ~] cd test; make test; make check

The test 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; five minutes is typical.
Un-passed tests should be examined to determine their significance.
The make check command executed from the test directory emits all
the differences uncovered during testing.
The make clean command executed from the test directory removes all files
produced during testing; this command is automatically
executed by the main make test command above; however, to run tests from
a subdirectory of the test directory, one should explicitly execute make clean.

NOTE: Some failures are not significant.
For example, differences in the tails of floating point numbers may not
be significant. The sources of such differences are frequently
platform dependencies from computer hardware, operating systems,
and compilers that impact arithmetic precision and
random number generators.
In addition, the reference outputs as of version 6.4 are from a 64 bit
platform and as of version 6.6 use gfortran gcc version 4.4.5,
and this can cause false positives on 32 bit platforms or with other compilers;
in particular, differing numbers of Orientations or
Conformations and different Contact or Grid scores.
We are working on increasing the QC suite's resilience to these issues.
For now, apply common sense and good judgment to determine
the significance of a possible failure.
Note that some number of failures is
rarely an indication of real problems, but if almost
every test fails then something is amiss.

Some features of DOCK
([[DOCK3.5 Score]] aka ChemGrid Score)
require an electrostatic potential map which is usually generated by DelPhi.
Testing of these features requires that the environment variable
DELPHI_PATH be defined to the full path of the DelPhi executable.
[[DelPhi]]
is not distributed with DOCK; see also
[[here.]]

</blockquote>
(6) OPTIONAL: Alternate executables.

<blockquote>
(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.
(But other MPI implementations can be accommodated probably
with the only extra effort of editing the config.h file.)
The MPICH2 library is freely available from Argonne National Labs
([[http://www.mcs.anl.gov/research/projects/mpi/]]).
Once MPI is installed, define the environment variable MPICH_HOME
to the top level MPICH2 directory.
MPICH_HOME will be referenced by all stages of the build procedure -
from configuration through testing.
See the
[[Parallel DOCK section]]
for execution information.

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 OpenEye Toolkits.
In particular, DOCK uses the APIs as in OEChem TK 1.7.0 and Zap TK 2.1.1.
These can be obtained from OpenEye
([[http://www.eyesopen.com/]]).
Once they are installed, define the environment variable ZAP_HOME to the
directory that contains the ZAP library. ZAP_HOME is used during
installation and testing. For execution the environment variable
OE_LICENSE must also be defined to the full path of the license file.
(Here is a quick start for an example gnu pbsa installation after
already building and testing a serial gnu installation:
cd install; ./configure gnu.pbsa;
setenv ZAP_HOME /openeye/toolkits/1.7.0-3/redhat-RHEL5-g++4.1-x64/;
setenv OE_LICENSE /openeye/oe_license.txt;
make dockclean; make dock; make testpbsa;).

</blockquote>

← Older revision		Revision as of 01:22, 24 May 2024
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	USERS: DOCK and its accessories must be run using a Unix-like		USERS: DOCK and its accessories must be run using a Unix-like
	environment such as Cygwin		environment such as Cygwin
	( [[~~http~~://www.cygwin.com/]] ).		( [[https://www.cygwin.com/]] ).
	We recommend a full Unix installation.		We recommend a full Unix installation.
	In particular, when you install your emulator,		In particular, when you install your emulator,
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	with the only extra effort of editing the config.h file.)		with the only extra effort of editing the config.h file.)
	The MPICH2 library is freely available from Argonne National Labs		The MPICH2 library is freely available from Argonne National Labs
	([[~~http~~://www.mcs.anl.gov/research/projects/mpi/]]).		([[https://www.mcs.anl.gov/research/projects/mpi/]]).
	Once MPI is installed, define the environment variable MPICH_HOME		Once MPI is installed, define the environment variable MPICH_HOME
	to the top level MPICH2 directory.		to the top level MPICH2 directory.
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	In particular, DOCK uses the APIs as in OEChem TK 1.7.0 and Zap TK 2.1.1.		In particular, DOCK uses the APIs as in OEChem TK 1.7.0 and Zap TK 2.1.1.
	These can be obtained from OpenEye		These can be obtained from OpenEye
	([[~~http~~://www.eyesopen.com/]]).		([[https://www.eyesopen.com/]]).
	Once they are installed, define the environment variable ZAP_HOME to the		Once they are installed, define the environment variable ZAP_HOME to the
	directory that contains the ZAP library. ZAP_HOME is used during		directory that contains the ZAP library. ZAP_HOME is used during