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

[Rodrigo faccioli]

Firstly, thank you, Roland, for your help.

Actually, it is my first time that I work with cmake and Eclipse. I choose
to work Gromacs, cmake and Eclipse because I want to learn about them :)

I tried to run Roland's last email. The step 1 ran correctly. However, when
I execute the step 2 did not work. Below, I show the command line which I
used and its output.

faccioli at faccioli-laptop:~/workspace/gromacs$ cmake -G"Eclipse CDT4 - Unix
Makefiles"
-- checking for module 'libxml-2.0'
--   package 'libxml-2.0' not found
-- Could NOT find LibXml2  (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
-- Could NOT find FFTW3  (missing:  FFTW3_LIBRARIES FFTW3_INCLUDE_DIR)
CMake Error at CMakeLists.txt:335 (MESSAGE):
  Cannot find fftw3 (with correct precision).  Fix it, choose another FFT
  library, or use the Gromacs built-in fftpack (slower)!


-- Configuring incomplete, errors occurred!

I followed the installation process according to Quick and Dirty
Installation (
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions/Quick_and_Dirty_Installation
)
The difference is I'm working with FFTW 3.2.2 and openmpi 1.3.4.
Furthermore, I installed the libxml2 its version
2.7.3

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


On Thu, Jan 14, 2010 at 2:22 PM, Roland Schulz <roland at utk.edu> wrote:

> 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
>>>>
>>>> --
>>>> gmx-developers mailing list
>>>> gmx-developers at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20100115/e169ba4e/attachment.html>