<div dir="ltr"><br><br><div class="gmail_quote">2012/6/5 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 5/06/2012 9:11 AM, Peter C. Lai wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The quick and dirty way is to post-patch Makefile in src/tools.<br>
<br>
I think patching the appropriate Makefile.in is sufficient for configure to<br>
pick up and automake into Makefile if all you need to do is append a make<br>
target.<br>
<br>
As to your previous question, on our cluster, I use Intel ICC 11.1.056<br>
<br>
both openmpi and fftw3 are also built with icc but root builds those and<br>
exposes their libs/headers through Modules, so I just module load them<br>
and specify the appropriate CPPFLAGS, LDFLAGS, and MPICC to configure<br>
(I'm still on 4.5.4 here).<br>
<br>
Btw: If you are patching 4.6 you should ask for someone else on here to tell<br>
you how to add it to the CMake config, since that's going to be the default<br>
build framework going forward.<br>
</blockquote>
<br></div>
That's easy with CMake - just add your tool to the list in src/tools/CMakeLists.txt and re-make (which I expect will trigger a re-cmake automatically).<span class="HOEnZb"><font color="#888888"><br></font></span></blockquote>
<div>How about in gromacs 4.0.7? Is it as Peter says?Just add it manually to the Makefile in src/tools, or is there an automatic way to generate this make file?<br> <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<span class="HOEnZb"><font color="#888888">
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
On 2012-06-05 01:43:09AM +0300, Shay Teaching wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
One more question: How do I get my new g_whatever analysis to be included<br>
in the compilation?<br>
Simply placing my file in src/tools won't work of course. How to I place it<br>
correctly in the build?<br>
Thanks,<br>
-Shay<br>
<br>
2012/6/5 Justin A. Lemkul<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
On 6/4/12 5:16 PM, Shay Teaching wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
2012/6/4 Justin A. Lemkul<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><mailto:<a href="mailto:jalemkul@vt.edu" target="_blank"><u></u>jalemkul@vt.edu</a>>><br>
<br>
<br>
<br>
<br>
On 6/4/12 2:59 PM, Shay Teaching wrote:<br>
<br>
Dear Gromacs users,<br>
<br>
I want to write new analyses for gromacs and compile it (so I'll<br>
have<br>
g_whatever) as part of the gromacs package.<br>
Per the instructions I found on gromacs website, I installed<br>
kdevelop<br>
and opened<br>
the gromacs as a project using kdevelop. However I have two<br>
questions:<br>
1) When I try to compile gromacs source, through kdevelop, I get a<br>
"permission<br>
denied" error. I think it is because gromacs installation requires<br>
root<br>
privileges. Any suggestions on how to bypass that, so I won't have<br>
to use<br>
kdevelop as root (which is a *really* bad idea)? (e.g., installing<br>
gromacs<br>
without root?)<br>
<br>
<br>
Assuming you're trying to compile template.c in some system-level<br>
directory,<br>
you're certain to run into that problem. Compile in a different<br>
location.<br>
<br>
Actually, I tried installing Gromacs to my home directory, not system<br>
directory.<br>
You're saying that I'm not supposed to encounter this error?<br>
<br>
<br>
</blockquote>
You shouldn't have permission errors in your home directory. I've never<br>
used KDevelop; what happens if you try to compile from a normal command<br>
line?<br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2) Are there any guidelines for writing new g_whatever analyses?<br>
Or any<br>
general<br>
suggestions on how to approach it?<br>
<br>
<br>
Write good code? ;) I don't really know what you're asking here, but<br>
if you<br>
want pointers for writing code, you'll need to at least state what<br>
you're doing.<br>
<br>
Write good code of course :-)<br>
What I mean is: Is there a proper list of gromacs functions used for<br>
'common'<br>
operations? (such as, reading from trajectory, reading index file,<br>
documentation<br>
of types and data structures for dealing with gromacs trajectory: atom,<br>
molecule, their input and output, etc.)<br>
Of course I'll open existing analyses, and see how its done there<br>
(g_mindist,<br>
g_rms..) but it would be useful to have like... a list of methods so I<br>
won't<br>
waste time on stuff that's already been dealt with.<br>
<br>
<br>
</blockquote>
The only related information is probably on the website at<br>
<a href="http://www.gromacs.org/**Developer_Zone/Programming_**Guide" target="_blank">http://www.gromacs.org/**<u></u>Developer_Zone/Programming_**<u></u>Guide</a><<a href="http://www.gromacs.org/Developer_Zone/Programming_Guide" target="_blank">http://www.gromacs.org/<u></u>Developer_Zone/Programming_<u></u>Guide</a>>.<br>
I doubt you'll get a how-to for coding though. The approach of looking at<br>
existing files for these routines is probably as efficient as it gets.<br>
<br>
<br>
-Justin<br>
<br>
--<br>
==============================<u></u>**==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
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