5 jun 2012 kl. 14.23 skrev Shay Teaching: > > > 2012/6/5 Mark Abraham <mark.abra...@anu.edu.au> > 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 > > > 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<jalem...@vt.edu> > > > On 6/4/12 5:16 PM, Shay Teaching wrote: > > > 2012/6/4 Justin A. Lemkul<jalem...@vt.edu<mailto:jalem...@vt.edu>> > > > > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists