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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>In the CVS version the fourier grid is no longer required to be divisible by the number of processors.<br>But in the other mail you had fourier_nz set to zero, which is complete nonsens.<br>I guess you should do some reading.<br><br>Berk.<br></div><br><br><hr id="EC_stopSpelling">From: regafan@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] invalid number of nodes<br>Date: Wed, 13 Aug 2008 14:12:04 +0000<br><br>
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Thanks a lot for your suggestion.<br>
What I was refering was to this post:<br>
<br><a href="http://www.gromacs.org/pipermail/gmx-developers/2008-February/002378.html" target="_blank">http://www.gromacs.org/pipermail/gmx-developers/2008-February/002378.html</a><br>
<br>
"OR use the 3.3 grompp to produce the mdp files since it will automatically set the fourier grid to fit the number of processors."<br>
<br>
Sorry for not explaining it better. <br>
<br>
Anyway, in the new version of Gromacs, the -np option of grompp does not work, does it?<br>
<br>
I am new in Gromacs, and I am using a version installed in a common cluster. I don´t know if I could install your modificated version myself.<br>
<br>
If I use grompp from the my new version, and I only change fourier_nx and fourier_ny in the input .mdp file, would it be enough to create a correct mdp.out file that works.<br>
<br>
Best wishes,<br>
<br>
Rebeca García Fandiño<br>
Parc Cientific de Barcelona<br>
<br>
<br> <br>
<hr>
<br>
From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] invalid number of nodes<br>Date: Wed, 13 Aug 2008 14:52:30 +0200<br><br><br>
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<div style="text-align: left;">Hi,<br><br>I don't understand your remark about the mdp file.<br>Where on the wiki does it say something like this?<br>The number of processors is never present in the mdp file.<br><br>Just use the new version of grompp.<br>A week ago I have committed large changes to the CVS<br>which make the tpr files much smaller and large simulations a bit more efficient.<br></div><br>Berk.<br><br>
<hr id="EC_EC_EC_stopSpelling">
From: regafan@hotmail.com<br>To: gmx-users@gromacs.org<br>Date: Wed, 13 Aug 2008 11:51:56 +0000<br>Subject: [gmx-users] invalid number of nodes<br><br>
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<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Hello,</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">I want to simulate a membrane+proteína system (more than 700.000 atoms) with Gromacs 4 and I would like to use 512 proc.</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">I am creating the mdp file with Gromacs 3, since I have read in the wiki that it was a good way to include the number or processors ins the mdp file for the new version.</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">For grompp with Gromacs 3.3 I amincluding this options <span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">in the input mdp file:</font></font></font></span></font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman"><font color="#000000" face="Times New Roman" size="3"> </font></font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">fourierspacing<span> </span>= 0.12</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">fourier_nx<span> </span>= 1024</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">fourier_ny<span> </span>= 1024</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">fourier_nz<span> </span>= 0</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"></font></span></p><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">but when I execute:</font></font></font></span><br>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="PT-BR"><font size="3"><font color="#000000"><font face="Times New Roman">grompp -f equilibrado2.mdp -c equilibrado.gro -p para_equilibrado.top -o equilibrado2.tpr -n index.ndx -np 512</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="PT-BR"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="PT-BR"><font size="3"><font color="#000000"><font face="Times New Roman">I receive this error:</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="PT-BR"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">-------------------------------------------------------</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Program grompp, VERSION 3.3.3</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Source code file: grompp.c, line: 1021</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Fatal error:</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">invalid number of nodes 512</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="PT-BR"><font size="3"><font color="#000000"><font face="Times New Roman">-------------------------------------------------------</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="PT-BR"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="PT-BR"><font color="#000000" face="Times New Roman" size="3"></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">When I had tried the same with 256 proc, using fourier_nx= fourier_ny=512, the correspondent error did not appear.</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Is there a limit of processors in Gromacs for grompp or which could be the problem?</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Thank you very much for your help in advance,</font></font></font></span></p>
<p class="EC_EC_EC_MsoNormal"><span lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_EC_EC_MsoNormal"><font color="#000000" face="Times New Roman" size="3">Rebeca García Fandiño</font></p>
<p class="EC_EC_EC_MsoNormal"><font color="#000000" face="Times New Roman" size="3">Parc Cientific of Barcelona</font></p><br>
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