[gmx-developers] Gromacs source-code integrate with Eclipse IDE - Help

[Roland Schulz]

Hi,

sorry for not looking everything up in the first place.

I just tried it and you can use egit with cmake.

Steps:
1) Download Gromacs with egit - but DON'T  click "Import project after
clone"
2) Run Cmake outside of eclipse to generate eclipse project file. Choose
CDT4 project file as generator. And run it directly in the source folder.
3) Import this project file in eclipse
4) Right click project->Team->Share Project to enable egit control of this
project.

Instead of step 2) you can also use ./bootstrap, ./configure. Then you just
also need to add the make targets.

The help for the Cmake Generator is at:
http://www.itk.org/Wiki/Eclipse_CDT4_Generator

For Cmake you currenlty need to manually enable SSE for acceleration and
GMX_IA32_ASM or GMX_X86_64_ASM to get fast kernels.

Roland


On Thu, Jan 14, 2010 at 11:01 AM, Roland Schulz <roland at utk.edu> wrote:

> Hi,
>
> there is one alternative I forgot to mention.
>
> Download git with some other tool (e.g. commandline) as before.
>
> Then use cmake to generate an eclipse project file (don't create a separate
> build directory but use the source as build directory). And then import that
> project file into eclipse.
>
> Then you don't need to generate a project in eclipse and you don't need to
> generate the make targets. Only disadvantage the use of cmake is not yet
> documented.
> Also I don't know how to combine cmake with egit.
>
> Roland
>
>
> On Thu, Jan 14, 2010 at 10:42 AM, Roland Schulz <roland at utk.edu> wrote:
>
>> HI,
>>
>> no you don't need Bioclipse. I'm not sure how to use egit yet. It seems
>> that a Eclipse project file has to be on the git server for it to work.
>> Currently there is none.
>>
>> @all: Does anyone object for me to add a Eclipse project file to the
>> source? It shouldn't affect anyone not using eclipse.
>>
>> I use the command line git to download Gromacs and then import it
>> afterwards into Eclipse. Just do this by
>> File->New->C Project->Makefile project->Empty Project->Linux Gcc Toolchain
>> And just select the folder where you downloaded the code from with git.
>>
>> To compile:
>> First set the compile environment up as usual on the console (e.g.
>> ./bootstrap, ./configure).   (I don't think you can do this within eclipse -
>> let me know if you know how to do it)
>> Then create a build target to build what you want (e.g. all or mdrun).
>>
>> Let me know if you need more detailed steps.
>>
>> Roland
>>
>>
>> On Thu, Jan 14, 2010 at 10:14 AM, Rodrigo faccioli <
>> rodrigo_faccioli at uol.com.br> wrote:
>>
>>> Hi all,
>>>
>>> I've tried to integrate Eclipse IDE and Gromacs source-code because I've
>>> worked with Eclipse in my Python and Java programs. Unfortunately, I can't
>>> do it works fine. I want to do it because I've studied the Gromacs
>>> source-code and now the time to use it in my PhD project came.
>>>
>>> My steps to try realized it was:
>>>
>>>    1. Import C++ project where I chose the Git Repository Option.
>>>    2. I put the link git://git.gromacs.org/gromacs.git which I obtained
>>>    from Gromacs website at
>>>    http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage
>>>    3. I check the option: Import project after clone.
>>>
>>> I get the Gromacs source-code from Git. However, I can't import Gromacs
>>> files in my Eclipse project . I tried to run bootstrap command which did not
>>> work too.
>>>
>>> I searched about it on web and I found the Bioclipse project which tells
>>> about Eclipse and Gromacs work together. However, I did not find
>>> documentation about it enough. So, my question is: I need to install the
>>> Bioclipse or is there other way?
>>>
>>> I appreciate any help.
>>>
>>> Thanks in advance.
>>>
>>> --
>>> Rodrigo Antonio Faccioli
>>> Ph.D Student in Electrical Engineering
>>> University of Sao Paulo - USP
>>> Engineering School of Sao Carlos - EESC
>>> Department of Electrical Engineering - SEL
>>> Intelligent System in Structure Bioinformatics
>>> http://laips.sel.eesc.usp.br
>>> Phone: 55 (16) 3373-9366 Ext 229
>>> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
>>>
>>> --
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>>> gmx-developers at gromacs.org
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>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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