Discussion:
Problem of mdrun_d in CVS VERSION 3.3_beta_20050823
(too old to reply)
xu yechun
2005-08-24 15:37:59 UTC
Permalink
Dear users,

I installed the CVS version(3.3_beta_20050823) with double precision.
When I use mdrun_d to produce the hessian matrix, the error information
comes like this:

mdrun_d -v -s nm1.tpr -g h.log -mtx h1
:-) G R O M A C S (-:

GROningen Mixture of Alchemy and Childrens' Stories

:-) VERSION 3.3_beta_20050823 (-:


Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) mdrun_d (double precision) (-:

Option Filename Type Description
------------------------------------------------------------
-s nm1.tpr Input Generic run input: tpr tpb tpa xml
-o traj.trr Output Full precision trajectory: trr trj
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-c confout.gro Output Generic structure: gro g96 pdb xml
-e ener.edr Output Generic energy: edr ene
-g h.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
pdb
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-pi pull.ppa Input, Opt. Pull parameters
-po pullout.ppa Output, Opt. Pull parameters
-pd pull.pdo Output, Opt. Pull data output
-pn pull.ndx Input, Opt. Index file
-mtx h1.mtx Output, Opt! Hessian matrix
-dn dipole.ndx Output, Opt. Index file

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-deffnm string Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-np int 1 Number of nodes, must be the same as used for
grompp
-nt int 1 Number of threads to start on each node
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]sepdvdl bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-[no]multi bool no Do multiple simulations in parallel (only with
-np > 1)
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a
seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an
X-Ray
bombardment on your system


Back Off! I just backed up h.log to ./#h.log.2#
Getting Loaded...
Reading file nm1.tpr, VERSION 3.3_beta_20050823 (double precision)
Loaded with Money

Non-cutoff electrostatics used, forcing full Hessian format.
Allocating Hessian memory...

-------------------------------------------------------
Program mdrun_d, VERSION 3.3_beta_20050823
Source code file: smalloc.c, line: 113

Fatal error:
calloc for full_matrix (nelem=269091216, elsize=8, file minimize.c, line
1854)
-------------------------------------------------------

"Everything He Lacks, He Makes Up In Denial" (Offspring)
: No such file or directory



Does someone meet such error before? Any suggestion will be appreciated!


Best regards
Yechun Xu

_________________________________________________________________
??????????????? MSN Hotmail? http://www.hotmail.com
David
2005-08-24 19:33:49 UTC
Permalink
Post by xu yechun
Dear users,
I installed the CVS version(3.3_beta_20050823) with double precision.
When I use mdrun_d to produce the hessian matrix, the error information
message means you need more than 2Gb memory.
Post by xu yechun
-------------------------------------------------------
Program mdrun_d, VERSION 3.3_beta_20050823
Source code file: smalloc.c, line: 113
calloc for full_matrix (nelem=269091216, elsize=8, file minimize.c, line
1854)
-------------------------------------------------------
--
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
xu yechun
2005-08-25 07:21:27 UTC
Permalink
Dear David,

Thank you very much for the answer. But the fact is that there is more
than 2GB memory in the computer(128 CPU, SGI Origin3800). The top
information show that there is about 33GB memory free.

Best regards
Yechun Xu
Post by xu yechun
Dear users,
I installed the CVS version(3.3_beta_20050823) with double precision.
When I use mdrun_d to produce the hessian matrix, the error information
message means you need more than 2Gb memory.
Post by xu yechun
-------------------------------------------------------
Program mdrun_d, VERSION 3.3_beta_20050823
Source code file: smalloc.c, line: 113
calloc for full_matrix (nelem=269091216, elsize=8, file minimize.c, line
1854)
-------------------------------------------------------
--
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
spoel at xray.bmc.uu.se spoel at gromacs.org
http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_________________________________________________________________
??????????????? MSN Hotmail? http://www.hotmail.com
David van der Spoel
2005-08-25 07:28:17 UTC
Permalink
Post by xu yechun
Dear David,
Thank you very much for the answer. But the fact is that there is more
than 2GB memory in the computer(128 CPU, SGI Origin3800). The top
information show that there is about 33GB memory free.
In that case you probably have to compile in 64 bit mode. Make an extra
gromacs installation for that as it will be slower for MD simulations.
Post by xu yechun
Best regards
Yechun Xu
Post by xu yechun
Dear users,
I installed the CVS version(3.3_beta_20050823) with double precision.
When I use mdrun_d to produce the hessian matrix, the error information
message means you need more than 2Gb memory.
Post by xu yechun
-------------------------------------------------------
Program mdrun_d, VERSION 3.3_beta_20050823
Source code file: smalloc.c, line: 113
calloc for full_matrix (nelem=269091216, elsize=8, file minimize.c, line
1854)
-------------------------------------------------------
--
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
xu yechun
2005-08-25 09:03:29 UTC
Permalink
Post by xu yechun
Dear David,
Thank you very much for the answer. But the fact is that there is more
than 2GB memory in the computer(128 CPU, SGI Origin3800). The top
information show that there is about 33GB memory free.
In that case you probably have to compile in 64 bit mode. Make an extra
gromacs installation for that as it will be slower for MD simulations.

Dear David,

Thank you for the suggestion!

Would you please tell me some details(options) for compile 64 bit mode on
SGI machine? I did not find such answer on the mail list. Thansk a lot!

Best regards
Yechun

_________________________________________________________________
???? MSN Explorer: http://explorer.msn.com/lccn
David van der Spoel
2005-08-25 09:11:23 UTC
Permalink
Post by David van der Spoel
Post by xu yechun
Dear David,
Thank you very much for the answer. But the fact is that there is more
than 2GB memory in the computer(128 CPU, SGI Origin3800). The top
information show that there is about 33GB memory free.
In that case you probably have to compile in 64 bit mode. Make an extra
gromacs installation for that as it will be slower for MD simulations.
Dear David,
Thank you for the suggestion!
Would you please tell me some details(options) for compile 64 bit mode on
SGI machine? I did not find such answer on the mail list. Thansk a lot!
You need option -64 for the compiler. Check compiler manuals.
Post by David van der Spoel
Best regards
Yechun
_________________________________________________________________
???? MSN Explorer: http://explorer.msn.com/lccn
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--
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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