Firstly, thank you, Roland, for your help.<br><br>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 :)<br><br>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.<br>
<br>faccioli@faccioli-laptop:~/workspace/gromacs$ cmake -G"Eclipse CDT4 - Unix Makefiles" <br>-- checking for module 'libxml-2.0'<br>-- package 'libxml-2.0' not found<br>-- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)<br>
-- Could NOT find FFTW3 (missing: FFTW3_LIBRARIES FFTW3_INCLUDE_DIR)<br>CMake Error at CMakeLists.txt:335 (MESSAGE):<br> Cannot find fftw3 (with correct precision). Fix it, choose another FFT<br> library, or use the Gromacs built-in fftpack (slower)!<br>
<br><br>-- Configuring incomplete, errors occurred!<br><br>I followed the installation process according to Quick and Dirty Installation (<a href="http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions/Quick_and_Dirty_Installation">http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions/Quick_and_Dirty_Installation</a>)<br>
The difference is I'm working with FFTW 3.2.2 and openmpi 1.3.4. Furthermore, I installed the libxml2 its version <br>2.7.3<br><br>I appreciate any help. <br><br>Thanks in advance.<br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>
Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br">http://laips.sel.eesc.usp.br</a><br>
Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218">http://lattes.cnpq.br/1025157978990218</a><br>
<br><br><div class="gmail_quote">On Thu, Jan 14, 2010 at 2:22 PM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu">roland@utk.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br><br>sorry for not looking everything up in the first place.<br><br>I just tried it and you can use egit with cmake.<br><br>Steps: <br>1) Download Gromacs with egit - but DON'T click "Import project after clone"<br>
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.<br>3) Import this project file in eclipse<br>4) Right click project->Team->Share Project to enable egit control of this project.<br>
<br>Instead of step 2) you can also use ./bootstrap, ./configure. Then you just also need to add the make targets. <br><br>The help for the Cmake Generator is at:<br><a href="http://www.itk.org/Wiki/Eclipse_CDT4_Generator" target="_blank">http://www.itk.org/Wiki/Eclipse_CDT4_Generator</a><br>
<br>For Cmake you currenlty need to manually enable SSE for acceleration and GMX_IA32_ASM or GMX_X86_64_ASM to get fast kernels.<br><font color="#888888"><br>Roland</font><div><div></div><div class="h5"><br><br><br><div class="gmail_quote">
On Thu, Jan 14, 2010 at 11:01 AM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br><br>there is one alternative I forgot to mention.<br><br>Download git with some other tool (e.g. commandline) as before.<br>
<br>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.<br>
<br>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. <br>Also I don't know how to combine cmake with egit. <br>
<font color="#888888">
<br>Roland</font><div><div></div><div><br><br><div class="gmail_quote">On Thu, Jan 14, 2010 at 10:42 AM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
HI,<br><br>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.<br><br>@all: Does anyone object for me to add a Eclipse project file to the source? It shouldn't affect anyone not using eclipse.<br>
<br>I use the command line git to download Gromacs and then import it afterwards into Eclipse. Just do this by <br>File->New->C Project->Makefile project->Empty Project->Linux Gcc Toolchain<br>And just select the folder where you downloaded the code from with git.<br>
<br>To compile:<br>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)<br>Then create a build target to build what you want (e.g. all or mdrun).<br>
<br>Let me know if you need more detailed steps.<br><br>Roland<br>
<br><br><div class="gmail_quote"><div><div></div><div>On Thu, Jan 14, 2010 at 10:14 AM, Rodrigo faccioli <span dir="ltr"><<a href="mailto:rodrigo_faccioli@uol.com.br" target="_blank">rodrigo_faccioli@uol.com.br</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div>
Hi all,<br><br>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. <br>
<br>My steps to try realized it was:<br><ol><li>Import C++ project where I chose the Git Repository Option. </li><li>I put the link git://<a href="http://git.gromacs.org/gromacs.git" target="_blank">git.gromacs.org/gromacs.git</a> which I obtained from Gromacs website at <a href="http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage" target="_blank">http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage</a></li>
<li>I check the option: Import project after clone.</li></ol>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.<br>
<br>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?<br>
<br>I appreciate any help.<br><br>Thanks in advance.<br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>
Department of Electrical Engineering - SEL<br>Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a><br>Phone: 55 (16) 3373-9366 Ext 229<br>
Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a><br>
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