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

Sat Jan 16 18:28:38 CET 2010

Thank you Roland. Now, it is working... :)

--
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 Fri, Jan 15, 2010 at 7:03 PM, Roland Schulz <roland at utk.edu> wrote:

> 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
>>>
>>> --
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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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