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Hi,<br><br>Ah, so you have anistropic pressure coupling on.<br>I forgot to put in a check for that when chosing the domain<br>decomposition grid.<br><br>Changing line 200 of src/mdlib/domdec_setup.c from:<br> if (box[j][i] != 0)<br>to<br> if (box[j][i] != 0 || ir->deform[j][i] != 0 ||<br> (ir->epc != epcNO && ir->compress[j][i] != 0))<br>should fix the problem.<br>If will commit this fix for 4.0.3.<br><br>(PS: you can also set -dd nx ny nz by hand, where for anisotropic<br>pressure coupling you should not have nx=1 or ny=1 when ny!=1 or nz!=1)<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] parallelization error? gromacs-4.0.2<br>Date: Thu, 20 Nov 2008 22:05:52 +0100<br><br>
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Hi,<br><br>Do you have anisotropic pressure coupling turned on?<br><br>Could you send me the tpr file?<br><br>Berk<br><br><hr id="EC_stopSpelling">Date: Thu, 20 Nov 2008 14:47:53 +0000<br>From: lastexile7gr@yahoo.de<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] parallelization error? gromacs-4.0.2<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit;" valign="top">Hello,<br><br>I tried from the beginning to test gromacs-4.0.2 with a monoclinic system on 8 processors (one two quad core machine). The skew errors seem to be gone, yet other errors appeared.<br><br>Now after a successful md, taking the output and trying to do annealing I get the following error:<br><br>Fatal error:<br>Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use dom<br>ain decomposition: ncells = 2 1 4, box vector[3] = -1.070924 -0.000007 6.415503<br><br>In my input files I do not have a vector as the bolded one above.<br><br>I tried to run the same input on my server which has two processors and up to know that I'm writing this email the run is running without any errors at all.<br><br>I have compiled gromacs-4.0.2 with fftw-3.2. Any files needed or any other information will be at
your disposal.<br><br>Thank you,<br>Nikos<br><br></td></tr></tbody></table><br><br><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/">MSN Messenger</a><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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