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<channel>
	<title>Comments on: Nature&#8217;s Statistical Checklist for Authors</title>
	<atom:link href="http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/feed/" rel="self" type="application/rss+xml" />
	<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/</link>
	<description>by Steve McIntyre</description>
	<lastBuildDate>Sun, 19 May 2013 07:46:52 +0000</lastBuildDate>
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	<item>
		<title>By: Troy Baer</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47710</link>
		<dc:creator><![CDATA[Troy Baer]]></dc:creator>
		<pubDate>Sat, 08 Apr 2006 12:22:06 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47710</guid>
		<description><![CDATA[&lt;blockquote&gt;What can Fortran do with multidimensional arrays that C can&#039;t ?&lt;/blockquote&gt;

Three things I can think of off the top of my head:

&lt;code&gt;ALLOCATE(foo(imax,jmax,kmax))&lt;/code&gt;

&lt;code&gt;a=b+c&lt;/code&gt; # where a, b, and c are arrays of the same dimensionality and size

&lt;code&gt;a=MATMUL(b,x)+c&lt;/code&gt;

These are all things built into the Fortran 90 language, BTW.  Admittedly most of these are just conveniences, but being able to to do multidimensional array operations without having to think too hard about &quot;Did I vectorize that correctly?&quot; is a big win IMHO.]]></description>
		<content:encoded><![CDATA[<blockquote><p>What can Fortran do with multidimensional arrays that C can&#8217;t ?</p></blockquote>
<p>Three things I can think of off the top of my head:</p>
<p><code>ALLOCATE(foo(imax,jmax,kmax))</code></p>
<p><code>a=b+c</code> # where a, b, and c are arrays of the same dimensionality and size</p>
<p><code>a=MATMUL(b,x)+c</code></p>
<p>These are all things built into the Fortran 90 language, BTW.  Admittedly most of these are just conveniences, but being able to to do multidimensional array operations without having to think too hard about &#8220;Did I vectorize that correctly?&#8221; is a big win IMHO.</p>
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	<item>
		<title>By: fFreddy</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47709</link>
		<dc:creator><![CDATA[fFreddy]]></dc:creator>
		<pubDate>Sat, 08 Apr 2006 11:04:54 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47709</guid>
		<description><![CDATA[What has everyone got against C for multidimensional arrays ? The C compiler I was using nearly twenty years ago let you declare them just fine, and it would have been implementing them with direct pointer arithmetic, so I can&#039;t imagine they were slow.
Sure, if you wanted to redimension them at run-time, you would have to write some get and put functions, and they would not be so fast, but I can&#039;t see how any other language would do it better.
What can Fortran do with multidimensional arrays that C can&#039;t ?]]></description>
		<content:encoded><![CDATA[<p>What has everyone got against C for multidimensional arrays ? The C compiler I was using nearly twenty years ago let you declare them just fine, and it would have been implementing them with direct pointer arithmetic, so I can&#8217;t imagine they were slow.<br />
Sure, if you wanted to redimension them at run-time, you would have to write some get and put functions, and they would not be so fast, but I can&#8217;t see how any other language would do it better.<br />
What can Fortran do with multidimensional arrays that C can&#8217;t ?</p>
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	<item>
		<title>By: TCO</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47708</link>
		<dc:creator><![CDATA[TCO]]></dc:creator>
		<pubDate>Fri, 07 Apr 2006 20:40:04 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47708</guid>
		<description><![CDATA[Basic8 is the shiznet!]]></description>
		<content:encoded><![CDATA[<p>Basic8 is the shiznet!</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Troy Baer</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47707</link>
		<dc:creator><![CDATA[Troy Baer]]></dc:creator>
		<pubDate>Fri, 07 Apr 2006 20:31:41 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47707</guid>
		<description><![CDATA[Re: #28

I&#039;ve worked in user support at a supercomputer center for a little over 8 years, and IMHO many scientists who switch from Fortran to C probably shouldn&#039;t.  There&#039;s an old saw about how a good Fortran programmer is able to write Fortran in any language; unfortunately, this also holds true for virtually all naive and/or bad Fortran programmers as well, and C isn&#039;t nearly as forgiving as Fortran.  Working with multidimensional arrays in C can be actively painful, and the ways to shoot yourself in the foot with &lt;code&gt;malloc()&lt;/code&gt; are many and varied.

A humorous anecdote about C++ vs. Fortran:  One user I worked with had a huge molecular dynamics program that he&#039;d written in C++...  but the routine that was the innermost loop of the calculation, the one where most of the time was spent, was written in Fortran.  I once asked him why he didn&#039;t implement that routine in C++ too, because he went to heroic efforts to link this one Fortran routine with his C++ app.  His response was something to the effect of &quot;I tried that once, and the code slowed down by a factor of two.&quot;]]></description>
		<content:encoded><![CDATA[<p>Re: #28</p>
<p>I&#8217;ve worked in user support at a supercomputer center for a little over 8 years, and IMHO many scientists who switch from Fortran to C probably shouldn&#8217;t.  There&#8217;s an old saw about how a good Fortran programmer is able to write Fortran in any language; unfortunately, this also holds true for virtually all naive and/or bad Fortran programmers as well, and C isn&#8217;t nearly as forgiving as Fortran.  Working with multidimensional arrays in C can be actively painful, and the ways to shoot yourself in the foot with <code>malloc()</code> are many and varied.</p>
<p>A humorous anecdote about C++ vs. Fortran:  One user I worked with had a huge molecular dynamics program that he&#8217;d written in C++&#8230;  but the routine that was the innermost loop of the calculation, the one where most of the time was spent, was written in Fortran.  I once asked him why he didn&#8217;t implement that routine in C++ too, because he went to heroic efforts to link this one Fortran routine with his C++ app.  His response was something to the effect of &#8220;I tried that once, and the code slowed down by a factor of two.&#8221;</p>
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	<item>
		<title>By: Gerald Machnee</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47706</link>
		<dc:creator><![CDATA[Gerald Machnee]]></dc:creator>
		<pubDate>Fri, 07 Apr 2006 18:09:27 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47706</guid>
		<description><![CDATA[There was an article in the news here about March 16 about ethics in medical research. I have enclosed the site and the atart of the article.

http://www.canada.com/national/nationalpost/news/cnspolitics/story.html?id=a320fffa-9ff7-48b6-b975-86cdef0b4228

Here is the start of the article:

Medical researchers caught faking it
Federal grant recipients

Margaret Munro, CanWest News Service
Published: Thursday, March 16, 2006
More than a dozen scientists and doctors, several of them recipients of sizable federal grants, have been faking research, destroying data, plagiarizing or conducting experiments on people without necessary ethics approvals, the country&#039;s lead research agencies report.

One medical researcher, who was awarded $1,347,445 for various projects, fabricated and falsified data and was permanently barred last year from receiving more federal money, according to documents obtained by CanWest News Service.]]></description>
		<content:encoded><![CDATA[<p>There was an article in the news here about March 16 about ethics in medical research. I have enclosed the site and the atart of the article.</p>
<p><a href="http://www.canada.com/national/nationalpost/news/cnspolitics/story.html?id=a320fffa-9ff7-48b6-b975-86cdef0b4228" rel="nofollow">http://www.canada.com/national/nationalpost/news/cnspolitics/story.html?id=a320fffa-9ff7-48b6-b975-86cdef0b4228</a></p>
<p>Here is the start of the article:</p>
<p>Medical researchers caught faking it<br />
Federal grant recipients</p>
<p>Margaret Munro, CanWest News Service<br />
Published: Thursday, March 16, 2006<br />
More than a dozen scientists and doctors, several of them recipients of sizable federal grants, have been faking research, destroying data, plagiarizing or conducting experiments on people without necessary ethics approvals, the country&#8217;s lead research agencies report.</p>
<p>One medical researcher, who was awarded $1,347,445 for various projects, fabricated and falsified data and was permanently barred last year from receiving more federal money, according to documents obtained by CanWest News Service.</p>
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	<item>
		<title>By: Tim</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47705</link>
		<dc:creator><![CDATA[Tim]]></dc:creator>
		<pubDate>Fri, 07 Apr 2006 14:57:43 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47705</guid>
		<description><![CDATA[http://www.userfriendly.org/

Check out the April 7th cartoon. It&#039;s like deja&#039;vu all over again :)]]></description>
		<content:encoded><![CDATA[<p><a href="http://www.userfriendly.org/" rel="nofollow">http://www.userfriendly.org/</a></p>
<p>Check out the April 7th cartoon. It&#8217;s like deja&#8217;vu all over again <img src='http://s0.wp.com/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
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	</item>
	<item>
		<title>By: kim</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47704</link>
		<dc:creator><![CDATA[kim]]></dc:creator>
		<pubDate>Thu, 06 Apr 2006 00:24:29 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47704</guid>
		<description><![CDATA[Must&#039;ve been a magnetic flux.
==================]]></description>
		<content:encoded><![CDATA[<p>Must&#8217;ve been a magnetic flux.<br />
==================</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: kim</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47703</link>
		<dc:creator><![CDATA[kim]]></dc:creator>
		<pubDate>Wed, 05 Apr 2006 17:45:25 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47703</guid>
		<description><![CDATA[Much gracious, all, I&#039;m edified.  Thanks also, DD, for the clue about CO2 and infrared several weeks ago.  That helped.
=============================]]></description>
		<content:encoded><![CDATA[<p>Much gracious, all, I&#8217;m edified.  Thanks also, DD, for the clue about CO2 and infrared several weeks ago.  That helped.<br />
=============================</p>
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	<item>
		<title>By: Nicholas</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47702</link>
		<dc:creator><![CDATA[Nicholas]]></dc:creator>
		<pubDate>Tue, 04 Apr 2006 23:51:06 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47702</guid>
		<description><![CDATA[&quot;It makes little difference if the code takes 20 times longer to run if your talking 1 second in opposition to 20 seconds&quot;

True, with big caveats. As I was pointing out, my friend operates supercomputers (and clusters), and the run time of software is typically on the order of days or weeks, during which time it might hog hundreds of nodes and/or some big machines. There&#039;s often a queue of programs waiting to run. So, performance can be an issue :)

As you point out, climate models can be of even greater magnitude. There can be whole cluster or clusters dedicated to a single model for long run periods. Additionally, the models are not all that mathematically complex (as I understand it), rather deal with a large grid of data. I suspect in that circumstance C will be best, as it&#039;s good for light things with many repetitions. Of course, some of my assumptions about how the modeling works could be wrong.]]></description>
		<content:encoded><![CDATA[<p>&#8220;It makes little difference if the code takes 20 times longer to run if your talking 1 second in opposition to 20 seconds&#8221;</p>
<p>True, with big caveats. As I was pointing out, my friend operates supercomputers (and clusters), and the run time of software is typically on the order of days or weeks, during which time it might hog hundreds of nodes and/or some big machines. There&#8217;s often a queue of programs waiting to run. So, performance can be an issue <img src='http://s0.wp.com/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
<p>As you point out, climate models can be of even greater magnitude. There can be whole cluster or clusters dedicated to a single model for long run periods. Additionally, the models are not all that mathematically complex (as I understand it), rather deal with a large grid of data. I suspect in that circumstance C will be best, as it&#8217;s good for light things with many repetitions. Of course, some of my assumptions about how the modeling works could be wrong.</p>
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	<item>
		<title>By: Nicholas</title>
		<link>http://climateaudit.org/2006/04/01/natures-statistical-checklist-for-authors/#comment-47701</link>
		<dc:creator><![CDATA[Nicholas]]></dc:creator>
		<pubDate>Tue, 04 Apr 2006 23:46:33 +0000</pubDate>
		<guid isPermaLink="false">http://www.climateaudit.org/?p=616#comment-47701</guid>
		<description><![CDATA[Actually, I suppose Fortran might be easier for mathematicians to learn. But I remember my friend saying he ended up converting some Fortran programs some mathematicians had written into C for various reasons (possibly performance-related). So it would obviously be less of a pain for him if they could write them in C in the first place :)]]></description>
		<content:encoded><![CDATA[<p>Actually, I suppose Fortran might be easier for mathematicians to learn. But I remember my friend saying he ended up converting some Fortran programs some mathematicians had written into C for various reasons (possibly performance-related). So it would obviously be less of a pain for him if they could write them in C in the first place <img src='http://s0.wp.com/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
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