Biowerkzeug Wiki - User contributions [en]

Performance

2008-12-08T15:49:51Z

Kaihsu: use <source/>

== Single processor performance ==
As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux):
cd testjobs
time ./calc_testjobs
<ul>
<li>We report the ''user'' time.</li>
<li>CPU properties are found with
<pre>cat /proc/cpuinfo</pre>
and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li>
<li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li>
<li>Note that these tests only utilize a ''single core''.</li>
<li>These results only give a rough idea of the ''relative'' performance of different architectures.</li>
<li>The timings have errorbars of about ±2s</li>
</ul>

Please add your own results.
{| class="wikitable sortable"
|+ Benchmark (single core) and [[#Scaling|scaling]] results on multiple cores/cpus. '''cores''' indicates how many cores are available to the user on this cpu ''or'' the maximum number of cores on the node that were used for benchmarking scaling.
! vendor
! model
! GHz
! cores
! time/min
! binary
! revision
! scaling
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:04
| hippo
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:05
| hippo
| rev35 
| [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]]
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:06
| hippo_p3
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420]
| 2.5
| 8 = 2x4
| 1:16
| hippo
| rev35 
| [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]]
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420]
| 2.5
| 4
| 1:16
| hippo
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:27
| hippo
| rev32
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:31
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850]
| 2.5
| 4
| 1:36
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850]
| 2.5
| 4
| 1:37
| hippo_p3
| rev35 
| [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]]
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248]
| 2.2
| 1
| 2:18
| hippo_p3
| rev32 
|-
| Intel
| Core Duo T2300 (Mac Mini)
| 1.66
| 2
| 2:41
| hippo_p3
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4]
| 2.4
| 1
| 3:03
| hippo_p3
| rev26 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+]
| 1.53
| 1
| 4:30
| hippo_p3
| rev26
|}

<small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from
<source lang="bash">
cat /proc/cpuinfo | \
awk 'BEGIN {FS=":"}; \
/vendor_id/ {vendor=$2}; \
/model name/ {model=$2}; \
/cpu MHz/ {GHz=$2/1000}; \
/siblings/ {cores=$2}; \
END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}'
</source>
into the wiki table and replace ''TIME'' by what you measured.</small>

== Scaling ==
All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]].

In the table below, '''# cpus''' really means how many independent cores are available.
{| class="wikitable sortable"
|+ Scaling of the Hippo WALP test case using OpenMP on single-board machines
! vendor
! # cpus
! walltime and scaling
|-
| Intel
| 4
| [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]]
|-
| Intel
| 8
| [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]]
|-
| AMD
| 4
| [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]]
|}

Help:Editing

2008-12-08T15:46:37Z

Kaihsu: /* Highlighting sourcecode */

This page should tell you how to work with this Wiki – it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting).

==Editing an existing page==
# Select the ''Edit'' link at the top.
# Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button.
# Once it looks sort-of right commit your changes by clicking ''save page''.

The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box.

The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>).

==Editing a new page==
If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it.

==Creating a new page==
To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it.

== Signing your name ==
Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST)

== Categories ==
[http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories.

* You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm
<nowiki>[[Category:Hippo]]</nowiki>
<nowiki>[[Category:Analysis]]</nowiki>
: as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Hippo]].

* The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject.
** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit).
** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page.

* In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>.

== Page maintenance ==
=== Redirection ===
A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command:
<nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki>

==Highlighting sourcecode==
MediaWiki can do syntax highlighting for over a dozen programming languages, including C, Python, Perl, Fortran, and C++. Just surround the code with a <tt>source</tt> tag of the name of the language in the variable <tt>lang</tt>. For example:
<pre>
<source lang="python">
import re

lines = file("ifconf.log").readlines()
l_iter = iter(lines)

nodes = []
for l in l_iter:
if l[:7] == "compute":
node = l.split('.')[0]
temp = l_iter.next().split()
iface, addr = temp[0], temp[4]
nodes.append([node, iface, addr])
</source>
</pre>

Gives you
<source lang="python">
import re

lines = file("ifconf.log").readlines()
l_iter = iter(lines)

nodes = []
for l in l_iter:
if l[:7] == "compute":
node = l.split('.')[0]
temp = l_iter.next().split()
iface, addr = temp[0], temp[4]
nodes.append([node, iface, addr])
</source>

==Inserting Gnuplot graphs==
You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example:
<pre>
<gnuplot>
set output 'func_approx.png'
plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \
'-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3
1 2
2 4
3 8
4 16
e
1 3
2 9
3 27
4 81
e
</gnuplot>
</pre>

Gives you the following:
<gnuplot>
set output 'func_approx.png'
plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \
'-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3
1 2
2 4
3 8
4 16
e
1 3
2 9
3 27
4 81
e
</gnuplot>

== Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) ==
You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference.
Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself.

<pre>
Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>:
===Bibliography===
<biblio>
#jcp2005 pmid=15847458
#proteins2005 pmid=15828005
#jcp2004 pmid=15634036
</biblio>
</pre>

Will give you this:
Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>:

<b>Bibliography</b>

<biblio>
#jcp2005 pmid=15847458
#proteins2005 pmid=15828005
#jcp2004 pmid=15634036
</biblio>

== Images ==

The following shows two methods of how to incorporate an image in a wiki page.

=== Upload ===
The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret)

# first [[Special:Upload|upload]] it (use the link in the toolbox on the left)
# enter a wiki link such as <tt><nowiki>[[Image:Gbim.jpg|200px]]
</nowiki></tt> into the text.

[[Image:Gbim.jpg|200px]]

[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]

An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above).

The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ...
<tt><nowiki>[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]</nowiki></tt>
gives a thumbnail image floating on the right hand side.

== Styles ==
One can directly edit the [http://www.w3.org/Style/CSS/ Cascading Style Sheets] (CSS). The most important one is [[Mediawiki:Common.css]] – be careful, all changes directly affect every user.

See the [http://www.mediawiki.org/wiki/Manual:Interface/Stylesheets Mediawiki Stylesheet Manual] for details and there is also the useful [http://www.mediawiki.org/wiki/Manual:FAQ Mediawiki FAQ] on customizing the Interface. [http://en.wikipedia.org/wiki/Help:User_style Wikipedia's Help:User_style] has a lot of howto information.

== Links ==
If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links:

=== Wikipedia edit help documents ===
* Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia)
* Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs
* Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands

=== MediaWiki documents ===
The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links:
* [http://meta.wikimedia.org/wiki/Help:Contents User's Guide]
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

[[Category:Help]]

Help:Editing

2008-12-08T15:45:30Z

Kaihsu: /* Highlighting sourcecode */

This page should tell you how to work with this Wiki – it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting).

==Editing an existing page==
# Select the ''Edit'' link at the top.
# Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button.
# Once it looks sort-of right commit your changes by clicking ''save page''.

The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box.

The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>).

==Editing a new page==
If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it.

==Creating a new page==
To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it.

== Signing your name ==
Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST)

== Categories ==
[http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories.

* You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm
<nowiki>[[Category:Hippo]]</nowiki>
<nowiki>[[Category:Analysis]]</nowiki>
: as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Hippo]].

* The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject.
** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit).
** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page.

* In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>.

== Page maintenance ==
=== Redirection ===
A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command:
<nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki>

==Highlighting sourcecode==
Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example:
<pre>
<source lang="python">
import re

lines = file("ifconf.log").readlines()
l_iter = iter(lines)

nodes = []
for l in l_iter:
if l[:7] == "compute":
node = l.split('.')[0]
temp = l_iter.next().split()
iface, addr = temp[0], temp[4]
nodes.append([node, iface, addr])
</source>
</pre>

Gives you
<source lang="python">
import re

lines = file("ifconf.log").readlines()
l_iter = iter(lines)

nodes = []
for l in l_iter:
if l[:7] == "compute":
node = l.split('.')[0]
temp = l_iter.next().split()
iface, addr = temp[0], temp[4]
nodes.append([node, iface, addr])
</source>

==Inserting Gnuplot graphs==
You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example:
<pre>
<gnuplot>
set output 'func_approx.png'
plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \
'-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3
1 2
2 4
3 8
4 16
e
1 3
2 9
3 27
4 81
e
</gnuplot>
</pre>

Gives you the following:
<gnuplot>
set output 'func_approx.png'
plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \
'-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3
1 2
2 4
3 8
4 16
e
1 3
2 9
3 27
4 81
e
</gnuplot>

== Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) ==
You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference.
Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself.

<pre>
Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>:
===Bibliography===
<biblio>
#jcp2005 pmid=15847458
#proteins2005 pmid=15828005
#jcp2004 pmid=15634036
</biblio>
</pre>

Will give you this:
Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>:

<b>Bibliography</b>

<biblio>
#jcp2005 pmid=15847458
#proteins2005 pmid=15828005
#jcp2004 pmid=15634036
</biblio>

== Images ==

The following shows two methods of how to incorporate an image in a wiki page.

=== Upload ===
The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret)

# first [[Special:Upload|upload]] it (use the link in the toolbox on the left)
# enter a wiki link such as <tt><nowiki>[[Image:Gbim.jpg|200px]]
</nowiki></tt> into the text.

[[Image:Gbim.jpg|200px]]

[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]

An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above).

The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ...
<tt><nowiki>[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]</nowiki></tt>
gives a thumbnail image floating on the right hand side.

== Styles ==
One can directly edit the [http://www.w3.org/Style/CSS/ Cascading Style Sheets] (CSS). The most important one is [[Mediawiki:Common.css]] – be careful, all changes directly affect every user.

See the [http://www.mediawiki.org/wiki/Manual:Interface/Stylesheets Mediawiki Stylesheet Manual] for details and there is also the useful [http://www.mediawiki.org/wiki/Manual:FAQ Mediawiki FAQ] on customizing the Interface. [http://en.wikipedia.org/wiki/Help:User_style Wikipedia's Help:User_style] has a lot of howto information.

== Links ==
If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links:

=== Wikipedia edit help documents ===
* Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia)
* Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs
* Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands

=== MediaWiki documents ===
The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links:
* [http://meta.wikimedia.org/wiki/Help:Contents User's Guide]
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

[[Category:Help]]

Talk:Performance

2008-12-08T15:44:06Z

Kaihsu: /* Scaling */

== Integration with tests ==
We could write a script that does the benchmark while running the test. It would even be possible to automatically post it (with the user's consent, of course). — [[User:Oliver|Oli]] 16:03, 14 November 2008 (UTC)

== Scaling ==
How to run scaling tests/testing methodology:

Use [[test_scaling.py]] which in turn uses [[calc_testjobs_linux.sh]].
cd testjobs
test_scaling.py ''NSLOTS''
where ''NSLOTS'' is the maximum number of available cpus/cores. Results are the files
scaling.xvg # numbers
scaling.png # graphs
* Only measures ''wall time'', hence must be run on an empty machine.
* Uses <code>date +%s</code> so accuracy is limited to seconds.
* No repeat runs; results may vary slightly.

Manually:
Use updated [[calc_testjobs_linux.sh]]
<source lang="bash">
DATA=scaling.xvg
MAXSLOTS=8
echo -e "# scaling for Hippo\n# numthreads walltime/s" > $DATA
for NSLOTS in `seq $MAXSLOTS`; do
echo "-- NSLOTS = $NSLOTS";
../../calc_testjobs_linux.sh -n $NSLOTS walp_octane_NPT_sp_MD \
| awk '/BENCHMARK/ {print $3, $4}' >> $DATA;
done
</source>
All the above remarks apply here, too.

Test scaling.py

2008-12-08T15:43:01Z

Kaihsu: use <source/>

Python script that uses [[calc_testjobs_linux.sh]] to benchmark scaling using the ''walp_octane_NPT_sp_MD'' test case. See [[Talk:Performance#Scaling]] for details.

<source lang="python">
#!/usr/bin/env python
# $Id: test_scaling.py 2534 2008-12-07 15:59:59Z www-data $
# Testing scaling of hippo
# Copyright (c) 2008 Biowerkzeug
# Oliver Beckstein <orbeckst@gmail.com>

from subprocess import Popen,PIPE
import sys,re

calc_test_jobs = '/home/oliver/Library/Hippo/Benchmark/calc_testjobs_linux.sh'
hippo_test_case = 'walp_octane_NPT_sp_MD'
filename = "scaling.xvg"
figname = "scaling.png"

try:
maxslots = int(sys.argv[1])
except:
print "usage: %s NSLOTS" % sys.argv[0]
sys.exit(1)

slotrange = (1,maxslots+1) # <--- 1-4 !!

benchmark_pattern = re.compile(r'BENCHMARK:\s*(\w+)\s+(?P<NUMTHREADS>[0-9]+)\s+(?P<T_SECONDS>[0-9.]+)')

runtime = {}
out = open(filename,'w')
out.write("# scaling for Hippo\n# numthreads walltime/s scaling\n")
for NSLOTS in xrange(*slotrange):
print "-- running NSLOTS = %(NSLOTS)d" % vars()
p1 = Popen([calc_test_jobs, '-n', str(NSLOTS), hippo_test_case],stdout=PIPE)
p2 = Popen(['grep','BENCHMARK:'],stdin=p1.stdout,stdout=PIPE)
output = p2.communicate()[0]
m = benchmark_pattern.match(output)
print "output: ",output,
if not m:
print "ERROR: no benchmark data found"
continue
numthreads = int(m.group('NUMTHREADS'))
walltime = float(m.group('T_SECONDS'))
runtime[numthreads] = walltime
scaling = runtime[1]/walltime # runtime[1] is known after the first iteration!
out.write("%(numthreads)d %(walltime)f %(scaling)f\n" % vars())
out.close()

# Analysis
import numpy
import pylab
N = numpy.sort(runtime.keys())
T = numpy.array([runtime[n] for n in N],dtype=float)
S = T[0]/T

pylab.clf()

pylab.subplot(211)
pylab.title('Hippo test case: '+hippo_test_case)
pylab.xlabel('cpus')
pylab.ylabel('walltime/s')
pylab.plot(N,T,'ro-')

pylab.subplot(212)
pylab.xlabel('cpus')
pylab.ylabel('scaling')
pylab.plot(N,S,'ro-')
pylab.plot([N[0],N[-1]], [1,N[-1]], 'k--')

pylab.savefig(figname)
print "Saved figure "+figname
</source>

Calc testjobs linux.sh

2008-12-08T15:41:52Z

Kaihsu: try <source/>

This script allows running Hippo benchmarks without having to think too much about finding the correct binary and supplemental files. In addition it gives the total wall time required to run each test case; this can be used for crude benchmarks.

* The testing of the mpi binaries is not tested and probably does not work. However, they are ''only'' needed for replica exchange simulations and there are no test cases for those anyway.
* [http://forums.biowerkzeug.org/viewtopic.php?f=22&t=6&p=15&hilit=OpenMP#p15 Not all tests support multi-threaded runs] (with OpenMP); these tests ignore the NSLOTS argument.

<source lang="bash">#!/bin/bash
# $Id: calc_testjobs_linux.sh 2535 2008-12-07 16:07:19Z www-data $
# Running Hippo tests (Linux)
# Copyright (c) 2008 Biowerkzeug
# Oliver Beckstein <orbeckst@gmail.com>
#set -x

prog=$(basename $0)
CURDIR=${PWD}

# defaults (: can be set in environment)
: ${HIPPO_DIR:="${CURDIR}/.."}
HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD"
RUN_TESTS=${HIPPO_TESTS}
USE_MPI=0

usage="usage $prog [opts] [tests]

Run Hippo tests. By default it runs all of them:
${HIPPO_TESTS}

OPTIONS:
-h help
-n number of threads (not possible for all tests)
-D directory where we look for Hippo executables [${HIPPO_DIR}]
-M use mpi (replica exchange) binaries [${USE_MPI}]

Environment variables:
HIPPO_DIR overrides -D [${HIPPO_DIR}]
"

function die () {
local msg="$1" err=${2:-1}
echo 1>&2 "ERROR: failed in $PWD: ${msg}"
cd ${CURDIR}
exit $err
}

NSLOTS=1
# opt processing
while getopts hn:D:M: opt; do
case $opt in
h) echo "$usage"; exit 0;;
n) NSLOTS=${OPTARG};;
D) HIPPO_DIR=${OPTARG};;
M) USE_MPI=${OPTARG};;
*) die "Unknown option" 1;;
esac
done

#echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*"
shift $((OPTIND - 1))
if [ -n "$*" ]; then
RUN_TESTS="$*"
fi

echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}"

# find working executable
# we'll use the first one that only complain about missing input file
#
if [ ${USE_MPI} = 0 ]; then
echo "Trying standard binaries (with OpenMP)"
_HIPPO_BINARIES="hippo hippo_p3"
else
echo "Testing mpi binaries. Note: these are ONLY needed for replica exchange simulations"
_HIPPO_BINARIES="hippo_mpi hippo_p3_mpi"
fi
HIPPO="not_found"
rm -f hippo_input.txt # clean any input files
for h in ${_HIPPO_BINARIES}; do
exe="${HIPPO_DIR}/${h}"
if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then
HIPPO=${exe}
break
fi
done
if [ "${HIPPO}" = "not_found" ]; then
ARCH=$(uname -m);
OS=$(uname -s);
die "No usable hippo executable found; see if there is one at
http://www.biowerkzeug.com for your architecture ${ARCH} and operating
system ${OS}. "
fi

echo "Using executable ${HIPPO}"

TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat
FF=${HIPPO_DIR}/oplsaa_forcefield.dat

echo "Setting up test directory"
rm -rf test
mkdir test
cd test

topdir="${CURDIR}/test"

function setup_hippo () {
local numthreads=${1:-1}
local input=hippo_input.txt
cp ${HIPPO} ./hippo || return $?
cp ${TOPOLOGY} . || return $?
cp ${FF} . || return $?
test -e $input || die "Missing run input file $input in $PWD"
if [ $NSLOTS -gt 1 ]; then
# adjusting for OpenMP run
sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input
fi
return 0
}

function run_test () {
local testdir="$1" numthreads="${2:-1}"
echo "---------------------------------------------------------"
cd ${testdir} || die "Cannot 'cd ${testdir}'"
setup_hippo ${numthreads} || die "setup_hippo() failed"
echo "Set up all files for NSLOTS=${numthreads}"
echo "Running hippo test case ${testdir}..."
t_start=$(date +%s)
./hippo
t_stop=$(date +%s)
delta_t=$(( t_stop-t_start ))
echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads"
echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}"
cd ${topdir}
}

cp -r ../jobs/* .

for t in ${RUN_TESTS};
do run_test $t ${NSLOTS}
done

echo "Finished running hippo test suite"
</source>

Performance

2008-11-21T14:54:49Z

Kaihsu:

As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux):
cd testjobs
time ./calc_testjobs
<ul>
<li>We report the ''user'' time.</li>
<li>CPU properties are found with
<pre>cat /proc/cpuinfo</pre>
and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li>
<li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li>
<li>Note that these tests only utilize a ''single core''.</li>
<li>These results only give a rough idea of the ''relative'' performance of different architectures.</li>
</ul>

Please add your own results.
{| class="wikitable sortable"
|-
! vendor
! model
! GHz
! cores
! time/min
! binary
! revision
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:04
| hippo
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:06
| hippo_p3
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420]
| 2.5
| 4
| 1:16
| hippo
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:27
| hippo
| rev32
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:31
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850]
| 2.75
| 4
| 1:36
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248]
| 2.2
| 1
| 2:18
| hippo_p3
| rev32 
|-
| Intel
| Core Duo T2300 (Mac Mini)
| 1.66
| 2
| 2:41
| hippo_p3
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4]
| 2.4
| 1
| 3:03
| hippo_p3
| rev26 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+]
| 1.53
| 1
| 4:30
| hippo_p3
| rev26
|}

<small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from
cat /proc/cpuinfo | \
awk 'BEGIN {FS=":"}; \
/vendor_id/ {vendor=$2}; \
/model name/ {model=$2}; \
/cpu MHz/ {GHz=$2/1000}; \
/siblings/ {cores=$2}; \
END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}'
into the wiki table and replace ''TIME'' by what you measured.</small>

Performance

2008-11-21T14:54:26Z

Kaihsu:

As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux):
cd testjobs
time ./calc_testjobs
<ul>
<li>We report the ''user'' time.</li>
<li>CPU properties are found with
<pre>cat /proc/cpuinfo</pre>
and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li>
<li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li>
<li>Note that these tests only utilize a ''single core''.</li>
<li>These results only give a rough idea of the ''relative'' performance of different architectures.</li>
</ul>

Please add your own results.
{| class="wikitable sortable"
|-
! vendor
! model
! GHz
! cores
! time/min
! binary
! revision
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:04
| hippo
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:06
| hippo_p3
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420]
| 2.5
| 4
| 1:16
| hippo
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:27
| hippo
| rev32
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:31
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850]
| 2.75
| 4
| 1:36
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248]
| 2.2
| 1
| 2:18
| hippo_p3
| rev32 
|-
| Intel
| Core Duo T2300 (Mac Mini)
| 1.66
| 2
| 2:41
| hippo_p3
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4]
| 2.4
| 1
| 3:03
| hippo_p3
| rev26 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+]
| 1.53
| 1
| 4:30
| hippo_p3
| rev26
|}

<small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from
cat /proc/cpuinfo | \
awk 'BEGIN {FS=":"}; \
/vendor_id/ {vendor=$2}; \
/model name/ {model=$2}; \
/cpu MHz/ {GHz=$2/1000}; \
/siblings/ {cores=$2}; \
END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}'
into the wiki table and replace ''TIME'' by what you measured.</small>

Performance

2008-11-21T14:51:04Z

Kaihsu: try sortable

As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux):
cd testjobs
time ./calc_testjobs
<ul>
<li>We report the ''user'' time.</li>
<li>CPU properties are found with
<pre>cat /proc/cpuinfo</pre>
and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li>
<li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li>
<li>Note that these tests only utilize a ''single core''.</li>
<li>These results only give a rough idea of the ''relative'' performance of different architectures.</li>
</ul>

Please add your own results.
{| class="wikitable sortable"
|-
! vendor
! model
! GHz
! cores
! time/min
! binary
! revision
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:04
| hippo
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550]
| 2.83
| 4
| 1:06
| hippo_p3
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420]
| 2.5
| 4
| 1:16
| hippo
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:27
| hippo
| rev32
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:31
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850]
| 2.75
| 4
| 1:36
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248]
| 2.2
| 1
| 2:18
| hippo_p3
| rev32 
|-
| Intel
| Core Duo T2300 (Mac Mini)
| 1.66
| 2
| 2:41
| hippo_p3
| rev32 
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4]
| 2.4
| 1
| 3:03
| hippo_p3
| rev26 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+]
| 1.53
| 1
| 4:30
| hippo_p3
| rev26
|}

<small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from
cat /proc/cpuinfo | \
awk 'BEGIN {FS=":"}; \
/vendor_id/ {vendor=$2}; \
/model name/ {model=$2}; \
/cpu MHz/ {GHz=$2/1000}; \
/siblings/ {cores=$2}; \
END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}'
into the wiki table and replace ''TIME'' by what you measured.</small>

Main Page

2008-11-18T15:08:47Z

Kaihsu:

<div id="hauptseite">

{| width="100%" cellspacing="0" cellpadding="0"
| colspan="2" |
This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums].

Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips and tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help→Editing]] to get started on contributing to this community resource.

Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]].

|-
| width="50%" style="vertical-align:top;" |
<div id="Hippo" class="hauptseite-links">
== Hippo ==
<div class="inhalt">
[[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]]
* [[Hippo|Features]]
* [[Download]]
* [[Simulations]]
* [[Analysis]]
* [[Graphical interface]]
* [[Files]]
* [[Performance]]
</div>
</div>

<div id="Methods" class="hauptseite-links">

== Methods ==
<div class="inhalt">
* [[Molecular dynamics]]
* [[Monte Carlo]]
* [[Force fields]]
* [[Algorithms]]
* [[Solvents]]
* [[Membranes]]
</div>
</div>

| width="50%" style="vertical-align:top;" |

<div id="Simulation protocols" class="hauptseite-rechts">
== Simulation protocols ==
<div class="inhalt">
* [[Globular proteins]] in solvent
* [[Membrane proteins]] in membrane and solvent
* [[Free energy calculations]]
* [[Transition path sampling]]
</div>
</div>

<div id="Visualization" class="hauptseite-rechts">
== Visualization ==
<div class="inhalt">
* [[Visualization software|Software]]
* [[Visualization tutorial|tutorial]] with [[VMD]]
* [[Movie tutorial]]
</div>
</div>

<div id="Software" class="hauptseite-rechts">

== Software ==
<div class="inhalt">
* [[Molecular dynamics codes]]
* [[Monte Carlo codes]]
* [[Electrostatics]] and [[Brownian dynamics]]
* [[Model building]]
* [[Visualization software|Visualization]]
* [[Analysis software]]
</div>
</div>

|}
</div>
__NOTOC__

Download

2008-11-17T16:49:00Z

Kaihsu: correct misspelling

Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeug.com download page] for '''Linux''' and '''Windows'''.

Note that by downloading you consent to the the [[Hippo license|license]].

[[Hippo#Installing_the_software|Installation of Hippo]] is trivial because the program comes as a precompiled executable and only requires a few additional data files.

Talk:Hippo license

2008-11-17T16:48:12Z

Kaihsu: New page: Is this a ''sui generis'' licence or is it one of the boilerplate free-software licence? Cheers. – ~~~~

Is this a ''sui generis'' licence or is it one of the boilerplate free-software licence? Cheers. – [[User:Kaihsu|Kaihsu]] 16:48, 17 November 2008 (UTC)

Performance

2008-11-14T14:58:38Z

Kaihsu:

As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux):
cd testjobs
time ./calc_testjobs
We report the ''user'' time. CPU properties are found with
cat /proc/cpuinfo
and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus].

Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.

Note that these tests only utilize a ''single core''.

Please add your own results.
{| class="wikitable"
|-
! vendor
! model
! GHz
! cores
! time/min
! binary
! revision
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:27
| hippo
| rev32
|-
| Intel
| [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410]
| 2.33
| 4
| 1:31
| hippo_p3
| rev32 
|-
| Intel
| Core Duo T2300 (Mac Mini)
| 1.66
| 2
| 2:41
| hippo_p3
| rev32 
|-
| AMD
| [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+]
| 1.53
| 1
| 4:30
| hippo_p3
| rev26
|}

Main Page

2008-11-13T13:50:13Z

Kaihsu: /* Hippo */

<div id="hauptseite">

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This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums].

Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help→Editing]] to get started on contributing to this community resource.

Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]].

|-
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<div id="Hippo" class="hauptseite-links">
== Hippo ==
<div class="inhalt">
[[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]]
* [[Hippo|Features]]
* [[Simulations]]
* [[Analysis]]
* [[Graphical interface]]
* [[Files]]
</div>
</div>

<div id="Methods" class="hauptseite-links">

== Methods ==
<div class="inhalt">
* [[Molecular dynamics]]
* [[Monte Carlo]]
* [[Force fields]]
* [[Algorithms]]
* [[Solvents]]
* [[Membranes]]
</div>
</div>

| width="50%" style="vertical-align:top;" |

<div id="Simulation protocols" class="hauptseite-rechts">
== Simulation protocols ==
<div class="inhalt">
* [[Globular proteins]] in solvent
* [[Membrane proteins]] in membrane and solvent
* [[Free energy calculations]]
* [[Transition path sampling]]
</div>
</div>

<div id="Visualization" class="hauptseite-rechts">
== Visualization ==
<div class="inhalt">
* [[Visualization software|Software]]
* [[Visualization tutorial|tutorial]] with [[VMD]]
* [[Movie tutorial]]
</div>
</div>

<div id="Software" class="hauptseite-rechts">

== Software ==
<div class="inhalt">
* [[Molecular dynamics codes]]
* [[Monte Carlo codes]]
* [[Electrostatics]] and [[Brownian dynamics]]
* [[Model building]]
* [[Visualization software|Visualization]]
* [[Analysis software]]
</div>
</div>

|}
</div>
__NOTOC__

Hippo

2008-11-13T13:49:05Z

Kaihsu: /* Features */

[[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]]
'''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]).

== Features ==
[[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]]
=== Simulation methods ===
* [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles <cite>Proteins2008</cite>
* Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite>
* [[Replica exchange]] with MD and MC <cite>Proteins2007</cite>

=== Force fields ===
* OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite>

=== Solvation models ===
* explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>)
* Generalized Born implicit solvent (GB/SA)
* Generalized Born implicit membrane (GB/IM) <cite>Proteins2008,Proteins2007,BJ2007,Proteins2005</cite>

=== Enhanced productivity ===
A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes:
* seamless restarts
* intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology
* graphical frontend under development (Windows only)

=== Analysis ===
[[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]]
A growing number of analysis tools are built into Hippo, for instance
; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state
; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure
; helicity: degree of helicity of segments along trajectory
; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite>
; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite>
; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane)
; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame.

The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used.

== Installation ==
=== Download ===
Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''.


=== Installing the software ===

Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find
* compiled executables (see below)
** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]]
** <tt>analyse</tt>: the [[#Analysis|analysis program]]
* the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf])
* the [[Hippo license|license]] (to which you consent by downloading)
* the OPLS-AA forcefield file (in Hippo format)
* the readme.txt file
* the <tt>testjobs</tt> directory with example systems

{| class="wikitable" align="right"
|+Hippo executables
!cpu !!Linux !!Windows
|-
|SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt>
|-
|SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt>
|}

The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''.

If in doubt, simply try them out in order; if it will not run you will receive an error message such as
Fatal Error: This program was not built to run on the processor in your system.
The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors
with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support.
In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum].

Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for [[replica exchange simulations]] (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with [http://www.openmp.org/ OpenMP]).

=== Test cases ===
The <tt>testjobs</tt> directory contains a number of testcases.

Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes.

Use the tests in order to get started in running your own systems.

== References ==
<biblio>
#MMB2008 pmid=18428040
#Proteins2007 pmid=17600830
#BJ2007 pmid=17218457
#BJ2006 pmid=16339877
#JPhysChemB2006 pmid=16913813
#Proteins2005 pmid=15723347
#JACS2004 pmid=14871118
#Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d].
#Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760].
#Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985.
#Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981.
#Cordes2002 pmid=12417206
#Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>].
#Proteins2008 Jakob P. Ulmschneider and Martin B. Ulmschneider. ''Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations''. Proteins [http://dx.doi.org/10.1002/prot.22270 10.1002/prot.22270].
</biblio>

[[Category:Hippo]]
[[Category:Software]]

File:Hippopotamus.jpg

2008-11-13T13:48:41Z

Kaihsu:

not this hippo

Licensed under GFDL from [http://commons.wikimedia.org/wiki/Image:Nijlpaard.jpg]; see there for details of licence.

File:Hippopotamus.jpg

2008-11-13T13:47:48Z

Kaihsu: not this hippo

not this hippo

User:Kaihsu

2008-11-12T15:24:08Z

Kaihsu: New page: [http://sbcb.bioch.ox.ac.uk/kaihsu/ Kaihsu Tai]

[http://sbcb.bioch.ox.ac.uk/kaihsu/ Kaihsu Tai]