<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Yes, it will still take very long.<br>
<br>
Supporting more than 2^31 total eigenvector elements requires code
changes through all our matrix and I/O routines. I don't think
this is worth the effort with the current diagonalization times.
If we add OpenMP parallelization, we can reconsider doing this.<br>
For now I will add checks that ensure we don't ask for more than
2^31 matrix or eigenvector elements.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2016-07-05 14:36, Adrien Nicolaï wrote:<br>
</div>
<blockquote
cite="mid:14190B95-5A50-4EFE-97AE-29B9879099D0@u-bourgogne.fr"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
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 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>
</div>
</div>
</div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 05 Jul 2016, at 14:26, Berk Hess <<a
moz-do-not-send="true" href="mailto:hess@kth.se"
class=""><a class="moz-txt-link-abbreviated" href="mailto:hess@kth.se">hess@kth.se</a></a>> wrote:</div>
<br class="Apple-interchange-newline">
<div 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=""> 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"
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=""><a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></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>
</div>
</div>
</div>
<br class="">
</div>
-- <br class="">
Gromacs Developers mailing list<br class="">
<br class="">
* Please search the archive at <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List"
class=""><a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a></a>
before posting!<br class="">
<br class="">
* Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists" class="">http://www.gromacs.org/Support/Mailing_Lists</a><br
class="">
<br class="">
* For (un)subscribe requests visit<br class="">
<a moz-do-not-send="true"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers"
class="">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a>
or send a mail to <a moz-do-not-send="true"
href="mailto:gmx-developers-request@gromacs.org"
class="">gmx-developers-request@gromacs.org</a>.</div>
</blockquote>
</div>
<br class="">
</div>
<br class="">
<fieldset class="mimeAttachmentHeader"></fieldset>
<br class="">
</blockquote>
<br class="">
</div>
-- <br class="">
Gromacs Developers mailing list<br class="">
<br class="">
* Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List"
class="">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a>
before posting!<br class="">
<br class="">
* Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
class="">http://www.gromacs.org/Support/Mailing_Lists</a><br
class="">
<br class="">
* For (un)subscribe requests visit<br class="">
<a moz-do-not-send="true"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers"
class="">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a>
or send a mail to <a moz-do-not-send="true"
href="mailto:gmx-developers-request@gromacs.org"
class="">gmx-developers-request@gromacs.org</a>.</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>