<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Message: 4<br>
Date: Wed, 26 Jan 2011 12:53:17 -0500<br>
From: Justin Kat <<a href="mailto:justin.kat@mail.mcgill.ca">justin.kat@mail.mcgill.ca</a>><br>
Subject: Re: [gmx-users] mdrun_mpi executable not found<br>
To: "<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>, Discussion list for GROMACS<br>
users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<AANLkTinJXi=<a href="mailto:7zN80eBnj01VkGggv6tzKst33qkTVy_P9@mail.gmail.com">7zN80eBnj01VkGggv6tzKst33qkTVy_P9@mail.gmail.com</a>><br>
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<br>
Thank you, I have been to that page probably a good 100 times by now.<br>
<br>
Was the 'No.' response with regards to my primary question? Or to the<br>
one within the parentheses?<br>
<br>
Suppose I remove my existing installation and reinstall, I am hoping<br>
to figure out when/where exactly should I specify<br>
--program-suffix=_mpi so as to not overwrite the pre-existing serial<br>
mdrun as I have mistakenly done so with my current installation.<br>
<br>
<br>
*./configure --enable-mpi --program-suffix=_mpi<br>
**make mdrun<br>
**make install-mdrun<br>
**make links*<br>
<br>
Lastly, if the above set of commands are incorrect, or will not carry<br>
out what I intend (to build a separate mdrun_mpi executable apart from<br>
the existing mdrun after a normal build), I am kindly requesting for a<br>
suitable revision.<br>
<br></blockquote><div>Have you tried<br> ./configure --help<br> to find out where the installation is?<br>by default gromacs will be installed at /usr/local/gromacs (according to ./configure --help).<br>If it's not installed there, do you have a openmpi or mpich compiler in your path?<br>
if not, then specify ./configure --enable-mpi --program-suffix=_mpi MPICC=<your own mpi compiler><br><br>Xiaohu<br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
Thanks,<br>
Justin<br>
<br>
<br>
On 26/01/2011 8:50 AM, Justin Kat wrote:<br>
>* Alright. So meaning I should have instead issued:<br>
*>*<br>
*>* ./configure --enable-mpi --program-suffix=_mpi<br>
<br>
<br>
*>* make mdrun<br>
*>* make install-mdrun<br>
*>* make links<br>
*>*<br>
*>* to have installed an MPI-enabled executable called mdrun_mpi apart<br>
*>* from the existing mdrun executable? (Would I also need to append the<br>
<br>
<br>
*>* _mpi suffix when issuing the first two make and make install commands<br>
*>* above?<br>
*<br>
No. See <a href="http://www.gromacs.org/Downloads/Installation_Instructions" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions</a><br>
<br>
<br>
<br>
Mark<br>
<br>
>*<br>
*>* Thanks,<br>
*>* Justin<br>
*>*<br>
*>* On Mon, Jan 24, 2011 at 8:08 PM, Justin A. Lemkul <jalemkul at<br>
<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>><br>
<br>
<br>
*<br>
- Show quoted text -<br>
>* <mailto:<a href="mailto:jalemkul">jalemkul</a> at <a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>>>> wrote:<br>
*>*<br>
*>*<br>
*>*<br>
*>* Justin Kat wrote:<br>
<br>
*>* > Thank you for the reply!<br>
<br>
*>* ><br>
*>* > hmm mdrun_mpi does not appear in the list of executables in<br>
*>* > /usr/local/gromacs/bin (and well therefore not in /usr/local/bin).<br>
*>* ><br>
<br>
<br>
*>* > Which set of installation commands that I used should have<br>
*>* compiled the<br>
*>* > mdrun_mpi executable? And how should I go about getting the<br>
*>* mdrun_mpi<br>
<br>
<br>
*>* > executable at this point?<br>
*>* ><br>
*>*<br>
*>* I see it now. When you configured with --enable-mpi, you didn't<br>
*>* specify<br>
*>* --program-suffix=_mpi, so the installation procedure over-wrote<br>
<br>
<br>
*>* your existing<br>
*>* (serial) mdrun with an MPI-enabled one simply called "mdrun." The<br>
*>* configure<br>
*>* output should have warned you about this. You could, in theory,<br>
<br>
<br>
*>* simply re-name<br>
*>* your existing executable "mdrun_mpi" and then re-install a serial<br>
*>* mdrun, if you<br>
*>* need it.<br>
*>*<br>
*>* -Justin<br>
<br>
<br>
*>*<br>
*>* --<br>
*>* ========================================<br>
*>*<br>
*>* Justin A. Lemkul<br>
*>* Ph.D. Candidate<br>
*>* ICTAS Doctoral Scholar<br>
<br>
<br>
*>* MILES-IGERT Trainee<br>
*>* Department of Biochemistry<br>
*>* Virginia Tech<br>
*>* Blacksburg, VA<br>
*<br>
>* jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
<br>
<br>
*<br>
>* <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
*>*<br>
*>* ========================================<br>
<br>
<br>
*>* --<br>
*<br>
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