Siavoush Dastmalchi wrote:
Hi,
I don't know why I get the following error message when I use more than one
node when I run grompp (e.g., grompp -np 32 .....). From previous emails, I
gathered that I need to reduce the number of nodes. But for me it just works
when I use a single node.
upgrade to newer version 3.3.2, or reduce the number of nodes, maybe 16.
Alternatively use constraints = all-bonds iso constraints = h-bonds.
With so few atoms per processor it will be very slow by the way.
Any suggestions? Cheers, Siavoush
Here is the error:
Walking down the molecule graph to make shake-blocks
There are 556 charge group borders and 1 shake borders
There are 556 total borders
Division over nodes in atoms:
41 41 42 40 42 42 44 41 42
41 42 42 42 41 42 40 43 42 41
41 41 42 40 41 42 40 41 37 42
43 41 42
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: splitter.c, line: 121
Fatal error:
Shake block crossing node boundaries
constraint between atoms (1270,1283)
-------------------------------------------------------
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
