Re: RE: [gmx-users] g_nmeig_d error: can't allocate region

Thu Mar 4 10:51:13 CET 2010

Hi Berk,
             Thanks for your reply.   What is the correct way to compile gromacs in 64 bit mode? 
I installed fftw-3.0.1. using the following commands
   ./configure
   make
  sudo make install

Then I downloaded the gromacs 4.0.7 source code and installed it using the following 
commands
./configure   
make
sudo make install

I updated the Path.
What else do I need to do to compile gromacs in 64 bit? 
Is it required to use "CPPFLAGS" , "LDFLAGS" etc.?

Thanks in advance
Sarbani

On Tue, 02 Mar 2010 20:01:51 +0530  wrote
>
Hi,

The allocation that causes the error should allocate about 3 GB.
My guess is that you compiled Gromacs in 32bit mode, whereas 64bit mode
is required for allocation of more than 2 GB.

Berk

Date: Tue, 2 Mar 2010 13:35:58 +0000
To: gmx-users at gromacs.org
From: sarbani_c84 at rediffmail.com
Subject: [gmx-users] g_nmeig_d error: can't allocate region

Hi,

  I am trying to do normal mode analysis on a protein having 6398 atoms in vaccum.

I tried to energy minimize the structure using steepest descent, followed by "l-bfgs" 

minimization. the .mdp file I used is

define                   = -DFLEXIBLE

constraints              = none

integrator               = l-bfgs

tinit                    = 0

nsteps                   = 15000

nbfgscorr                = 50

emtol                    = .001

emstep                   = 0.1

gen_vel                  = yes

gen-temp                 = 300

nstcomm                  =  1

; NEIGHBORSEARCHING PARAMETERS

; nblist update frequency

nstlist                  = 0

; ns algorithm (simple or grid)

ns-type                  = simple

; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)

pbc                      = no

; nblist cut-off

rlist                    = 0

domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype              = Cut-Off

rcoulomb-switch          = 0

rcoulomb                 = 0

; Dielectric constant (DC) for cut-off or DC of reaction field

epsilon-r                = 1

; Method for doing Van der Waals

vdw-type                 = Cut-off

; cut-off lengths

rvdw-switch              = 0

rvdw                     = 0

after running the 15000 steps the Fmax was:

Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 10197 steps

Potential Energy  = -8.26391832320506e+04

Maximum force     =  9.37558560558845e-04 on atom 4562

Norm of force     =  2.24887722104890e-04

Again the "l-bfgs" minimization was run using the same .mdp file( with emtol = 0.000001)

the output was'

Low-Memory BFGS Minimizer converged to Fmax < 1e-06 in 4143 steps

Potential Energy  = -8.26391832324998e+04

Maximum force     =  9.67927896882578e-07 on atom 3271

Norm of force     =  1.70637151528245e-07

After this I prepared the "nm.mdp " file for NMA, where I used exactly the same parameters 

as the ones used in lbfgs energy minimization( with integrator = nm)

the commands that were used were:

grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr -zero -p 

../topol.top

nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx &

"nohup.out" had the following message:

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

memory...starting normal mode calculation 'Protein'6398 steps.Maximum force: 9.67928e-

07

The run ended successfully:

Then i used the command 

g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr

I get the following error:

Reading file new_nm.tpr, VERSION 4.0.7 (double precision)

Reading file new_nm.tpr, VERSION 4.0.7 (double precision)

Reading double precision matrix generated by Gromacs VERSION 4.0.7

Full matrix storage format, nrow=19194, ncols=19194

Diagonalizing to find vectors 1 through 50...

g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

I am not being able to understand the problem. the computer  has a 16gb memory

If I use different parameters in the nm.mdp file as

rlist                    = 1.5

domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype              = switch

rcoulomb-switch          = 1

rcoulomb                 = 1.2

; Dielectric constant (DC) for cut-off or DC of reaction field

epsilon-r                = 1

; Method for doing Van der Waals

vdw-type                 = switch

; cut-off lengths

rvdw-switch              = 1

rvdw                     = 1.2

then i get the message :Maximum force: 3.14171e+03

Maximum force probably not small enough to ensure that you are in an

energy well. Be aware that negative eigenvalues may occur when the

resulting matrix is diagonalized.

I am sorry to post such a lengthy  query, but I have no clue about the root of the problem.

Any suggestion  will be of great help.

Thanks in advance,

Sarbani. 

>New Windows 7: Simplify what you do everyday. Find the right PC for you.

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