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

Fri Jan 15 22:03:40 CET 2010

Hi,

On Fri, Jan 15, 2010 at 1:40 PM, Rodrigo faccioli <
rodrigo_faccioli at uol.com.br> wrote:

> 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

The FFTW version and libxml version should be fine. Where did you install
them? By default it probably only finds it in the  system locations (e.g.
/usr/lib). In case you installed it in non standard locations you need to
set FFTW_INCLUDE_DIR FFTW_LIBRARIES and equivalent for libxml.

Roland

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