[gmx-users] Problem of mdrun_d in CVS VERSION 3.3_beta_20050823

xu yechun ycxu222 at hotmail.com
Wed Aug 24 17:37:59 CEST 2005

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 
  -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 
-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
         -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 
   -[no]glas   bool     no  Do glass simulation with special long range
 -[no]ionize   bool     no  Do a simulation including the effect of an 
                            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 

"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

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