Thanks I'll try that 2012/6/5 Peter C. Lai <[email protected]>
> The quick and dirty way is to post-patch Makefile in src/tools. > > I think patching the appropriate Makefile.in is sufficient for configure to > pick up and automake into Makefile if all you need to do is append a make > target. > > As to your previous question, on our cluster, I use Intel ICC 11.1.056 > > both openmpi and fftw3 are also built with icc but root builds those and > exposes their libs/headers through Modules, so I just module load them > and specify the appropriate CPPFLAGS, LDFLAGS, and MPICC to configure > (I'm still on 4.5.4 here). > > Btw: If you are patching 4.6 you should ask for someone else on here to > tell > you how to add it to the CMake config, since that's going to be the default > build framework going forward. > > On 2012-06-05 01:43:09AM +0300, Shay Teaching wrote: > > One more question: How do I get my new g_whatever analysis to be included > > in the compilation? > > Simply placing my file in src/tools won't work of course. How to I place > it > > correctly in the build? > > Thanks, > > -Shay > > > > 2012/6/5 Justin A. Lemkul <[email protected]> > > > > > > > > > > > On 6/4/12 5:16 PM, Shay Teaching wrote: > > > > > >> > > >> > > >> 2012/6/4 Justin A. Lemkul <[email protected] <mailto:[email protected]>> > > >> > > >> > > >> > > >> > > >> On 6/4/12 2:59 PM, Shay Teaching wrote: > > >> > > >> Dear Gromacs users, > > >> > > >> I want to write new analyses for gromacs and compile it (so > I'll > > >> have > > >> g_whatever) as part of the gromacs package. > > >> Per the instructions I found on gromacs website, I installed > > >> kdevelop > > >> and opened > > >> the gromacs as a project using kdevelop. However I have two > > >> questions: > > >> 1) When I try to compile gromacs source, through kdevelop, I > get a > > >> "permission > > >> denied" error. I think it is because gromacs installation > requires > > >> root > > >> privileges. Any suggestions on how to bypass that, so I won't > have > > >> to use > > >> kdevelop as root (which is a *really* bad idea)? (e.g., > installing > > >> gromacs > > >> without root?) > > >> > > >> > > >> Assuming you're trying to compile template.c in some system-level > > >> directory, > > >> you're certain to run into that problem. Compile in a different > > >> location. > > >> > > >> Actually, I tried installing Gromacs to my home directory, not system > > >> directory. > > >> You're saying that I'm not supposed to encounter this error? > > >> > > >> > > > You shouldn't have permission errors in your home directory. I've > never > > > used KDevelop; what happens if you try to compile from a normal command > > > line? > > > > > > > > > > > >> > > >> 2) Are there any guidelines for writing new g_whatever > analyses? > > >> Or any > > >> general > > >> suggestions on how to approach it? > > >> > > >> > > >> Write good code? ;) I don't really know what you're asking here, > but > > >> if you > > >> want pointers for writing code, you'll need to at least state what > > >> you're doing. > > >> > > >> Write good code of course :-) > > >> What I mean is: Is there a proper list of gromacs functions used for > > >> 'common' > > >> operations? (such as, reading from trajectory, reading index file, > > >> documentation > > >> of types and data structures for dealing with gromacs trajectory: > atom, > > >> molecule, their input and output, etc.) > > >> Of course I'll open existing analyses, and see how its done there > > >> (g_mindist, > > >> g_rms..) but it would be useful to have like... a list of methods so I > > >> won't > > >> waste time on stuff that's already been dealt with. > > >> > > >> > > > The only related information is probably on the website at > > > http://www.gromacs.org/**Developer_Zone/Programming_**Guide< > http://www.gromacs.org/Developer_Zone/Programming_Guide>. > > > I doubt you'll get a how-to for coding though. The approach of > looking at > > > existing files for these routines is probably as efficient as it gets. > > > > > > > > > -Justin > > > > > > -- > > > ==============================**========== > > > > > > Justin A. Lemkul, Ph.D. > > > Research Scientist > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > > > ==============================**========== > > > -- > > > gmx-users mailing list [email protected] > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > > Please search the archive at http://www.gromacs.org/** > > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > > Please don't post (un)subscribe requests to the list. Use the www > > > interface or send it to [email protected]. > > > Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > [email protected] | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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