<div dir="ltr">Thanks I'll try that<br><br><div class="gmail_quote">2012/6/5 Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>></span><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>
<div><div class="h5"><br>
On 2012-06-05 01:43:09AM +0300, Shay Teaching wrote:<br>
> 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">jalemkul@vt.edu</a>><br>
><br>
> ><br>
> ><br>
> > On 6/4/12 5:16 PM, Shay Teaching wrote:<br>
> ><br>
> >><br>
> >><br>
> >> 2012/6/4 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu">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>
> > 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>
> >><br>
> >> 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>
> > The only related information is probably on the website at<br>
</div></div>> > <a href="http://www.gromacs.org/**Developer_Zone/Programming_**Guide" target="_blank">http://www.gromacs.org/**Developer_Zone/Programming_**Guide</a><<a href="http://www.gromacs.org/Developer_Zone/Programming_Guide" target="_blank">http://www.gromacs.org/Developer_Zone/Programming_Guide</a>>.<br>
<div class="im">> > 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>
</div>> > ==============================**==========<br>
<div class="im">> ><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">(540) 231-9080</a><br>
</div>> > <a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>**<a href="http://vt.edu/Pages/Personal/justin" target="_blank">vt.edu/Pages/Personal/justin</a><<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>><br>
> ><br>
> > ==============================**==========<br>
<div class="im">> > --<br>
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<br>
</div><span class="HOEnZb"><font color="#888888">--<br>
==================================================================<br>
Peter C. Lai | University of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>
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==================================================================<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
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