2012/6/5 Mark Abraham <[email protected]> > On 5/06/2012 9:11 AM, Peter C. Lai wrote: > >> 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. >> > > 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). > 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?
> > Mark > > > >> 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]<[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> >>>> <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://vt.edu/Pages/Personal/justin> >>>> <h**ttp://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> >>>> <htt**p://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<h**ttp://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> >>>> <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<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<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> >
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