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).
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]>>
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>
==============================**==========
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