Hi, I had checked and found that gromacs has been compiled in 64 bit mode. However still I am getting this error with "g_nmeig_d " command which says g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12) *** error: can't allocate region
I am running this on a 8 node machine,each with 2GB of RAM ( g_nmeig_d runs on a single node). Is it required to increase the RAM of 1 node to get rid of this error? Any suggestion will be very helpful. Thanking You, 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@gromacs.org > From: sarbani_...@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 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.
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