<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Berk,<div class=""><br class=""></div><div class="">Yes I changed the default value from 50 to 3N because I need all the modes for further analyses. And it looks like it’s still taking “forever” to get the 50 first modes diagonalised...</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div style="margin: 0px; font-family: Menlo;" class="">************************************************************</div><div style="margin: 0px; font-family: Menlo;" class="">Adrien Nicolaï / Maître de conférences</div><div style="margin: 0px; font-family: Menlo;" class="">Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS</div><div style="margin: 0px; font-family: Menlo;" class="">Département NANO - Equipe Physique appliquée aux protéines</div><div style="margin: 0px; font-family: Menlo;" class="">Université de Bourgogne Franche-Comté / Faculté des Sciences et Techniques Mirande</div><div style="margin: 0px; font-family: Menlo;" class="">9, Av. Savary - B.P. 47 870 21078. DIJON CEDEX - France</div><div style="margin: 0px; font-family: Menlo;" class="">Email : <a href="mailto:adrien.nicolai@u-bourgogne.fr" class="">adrien.nicolai@u-bourgogne.fr</a></div><div style="margin: 0px; font-family: Menlo;" class="">Tél: 03 80 39 60 93</div><div style="margin: 0px; font-family: Menlo;" class="">URL : <a href="https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html" class="">https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html</a></div><div style="margin: 0px; font-family: Menlo;" class="">************************************************************</div></div></div></div>
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">On 05 Jul 2016, at 14:26, Berk Hess <<a href="mailto:hess@kth.se" class="">hess@kth.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta content="text/html; charset=windows-1252" http-equiv="Content-Type" class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<div class="moz-cite-prefix">This is using the sparse matrix code.
The default value for -last (end) is 50, which should work. I
assume you increased it.<br class="">
<br class="">
We should fix the code by casting the column and row size to
size_t before multiplying them.<br class="">
<br class="">
Cheers,<br class="">
<br class="">
Berk<br class="">
<br class="">
On 2016-07-05 14:21, Erik Lindahl wrote:<br class="">
</div>
<blockquote cite="mid:B8FA0AF1-E3EF-41DA-8053-6206A2B075B7@gmail.com" type="cite" class="">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252" class="">
Seems like a bug - we should use a size_t to calculate the size of
the matrix storage required.
<div class=""><br class="">
</div>
<div class="">However, before you get your hopes up: The reason
why this happens is that you are asking the code to do a full
diagonalization of a matrix that is 63255^2. That will take at
least ~100GB of memory, and probably take several months. I
would recommend that you use some cutoff-based
electrostatics/VdW instead to enable sparse matrix
diagonalization.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
</div>
<div class="">Erik</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 05 Jul 2016, at 14:02, Adrien Nicolaï <<a moz-do-not-send="true" href="mailto:adrien.nicolai@u-bourgogne.fr" class=""></a><a class="moz-txt-link-abbreviated" href="mailto:adrien.nicolai@u-bourgogne.fr">adrien.nicolai@u-bourgogne.fr</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space;" class="">Dear
GROMACS developers,
<div class=""><br class="">
</div>
<div class="">I’m performing a Normal mode analysis
using the GROMACS 5.1 software. The system I study is
a dimer of a protein surrounded by water molecules and
is comprised of 21075 atoms (corresponding to 63225
modes). After a proper minimisation using the L-BFGS
algorithm and a normal mode calculation in double
precision, I tried to diagonalise the entire hessian
matrix using the nmeig command.</div>
<div class=""><br class="">
</div>
<div class="">The use of the gmx_d nmeig command leads
to the following error:</div>
<div class=""><br class="">
</div>
<div class="">
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Reading double precision matrix generated
by GROMACS VERSION 5.1</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);
min-height: 16px;"><br class="">
</div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">-------------------------------------------------------</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Program gmx nmeig, VERSION 5.1</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Source code file:
/tmp3/gromacs-5.1-20150825/gromacs-5.1/src/gromacs/utility/smalloc.c,
line: 182</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);
min-height: 16px;"><br class="">
</div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Fatal error:</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Not enough memory. Failed to calloc
-297566671 elements of size 8 for eigenvectors</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">(called from file
/tmp3/gromacs-5.1-20150825/gromacs-5.1/src/gromacs/gmxana/gmx_nmeig.c,
line 401)</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">For more information and tips for
troubleshooting, please check the GROMACS</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">website at <a moz-do-not-send="true" href="http://www.gromacs.org/Documentation/Errors" class="">http://www.gromacs.org/Documentation/Errors</a></b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">-------------------------------------------------------</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">: Cannot allocate memory</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Using begin = 1 and end = 63225</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Sparse matrix storage format, nrow=63225,
ncols=63225</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Starter(339849): Return code=1</b></div>
<div class="" style="margin: 0px; font-size: 14px;
line-height: normal; font-family: Menlo; color:
rgb(255, 255, 255); background-color: rgb(0, 0, 0);"><b class="">Starter end(339849)</b></div>
</div>
<div class=""><br class="">
</div>
<div class="">Could you help me with the meaning of this
error? Is my system to big for NMA using GROMACS 5.1?</div>
<div class=""><br class="">
</div>
<div class="">Thanks you in advance for your help</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class=""><br class="">
</div>
<div class="">
<div style="letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div class="">
<div style="margin: 0px; font-family: Menlo;" class="">************************************************************</div>
<div style="margin: 0px; font-family: Menlo;" class="">Adrien Nicolaï / Maître de
conférences</div>
<div style="margin: 0px; font-family: Menlo;" class="">Laboratoire Interdisciplinaire Carnot
de Bourgogne, UMR 6303 CNRS</div>
<div style="margin: 0px; font-family: Menlo;" class="">Département NANO - Equipe Physique
appliquée aux protéines</div>
<div style="margin: 0px; font-family: Menlo;" class="">Université de Bourgogne Franche-Comté
/ Faculté des Sciences et Techniques Mirande</div>
<div style="margin: 0px; font-family: Menlo;" class="">9, Av. Savary - B.P. 47 870 21078.
DIJON CEDEX - France</div>
<div style="margin: 0px; font-family: Menlo;" class="">Email : <a moz-do-not-send="true" href="mailto:adrien.nicolai@u-bourgogne.fr" class="">adrien.nicolai@u-bourgogne.fr</a></div>
<div style="margin: 0px; font-family: Menlo;" class="">Tél: 03 80 39 60 93</div>
<div style="margin: 0px; font-family: Menlo;" class="">URL : <a moz-do-not-send="true" href="https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html" class="">https://icb.u-bourgogne.fr/fr/axes-scientifiques/nano/physique-appliquee-aux-proteines.html</a></div>
<div style="margin: 0px; font-family: Menlo;" class="">************************************************************</div>
</div>
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</div>
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<br class="">
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