2012/6/5 Erik Marklund <[email protected]> > > 5 jun 2012 kl. 14.23 skrev Shay Teaching: > > > > 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? > > > Yes, IIRC. > > If this is something that is useful for others, then perhaps you should > aim at a more recent version than 4.0.7 > > Best, > > Erik > > My research group is currently finishing up some projects that started with 4.0.x, but I'll make sure to make it easily passable to the 4.5.x if it seems useful. Thanks, -Shay
> > >> >> 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> >> > > -- > 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 > > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > [email protected] > http://www2.icm.uu.se/molbio/elflab/index.html > > > -- > 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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