From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Aug 28 2012 - 02:00:12 CDT
Hi
First of all, you should check a newer version as namd already reached 2.9.
Furthermore, check where namd got this huge box dimensions from, maybe a xsc
file?
Or could it be that you measured the box dimensions from a unwrapped
coor/dcd file?
Could you post your namd infile of the crashed run, and the one before that
you try to restart from?
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von subbarao kanchi
Gesendet: Montag, 27. August 2012 20:59
An: Suranga Edirisinghe
Cc: Mariana Graterol; namd-l_at_ks.uiuc.edu; namd_at_ks.uiuc.edu; Prof. Marķa
Luisa Serrano
Betreff: Re: namd-l: Please read: fatal error namd 2.7b1 for Win32 Memory
allocation failed on processor > 0
hi all
what ever the water number, If You give little more box size and run
only in NVT with out doing NPT equilibration it will form the babbles.the
box size should should optimise according to your system size.
subbarao kanchi
IISc bangalore.
On Mon, Aug 27, 2012 at 10:58 PM, Suranga Edirisinghe <nerangedi_at_gmail.com>
wrote:
Hi
127011 ATOMS
Is this atom numbers includes water. if so I would check this values
PERIODIC CELL BASIS 1 1015.77 0 0
PERIODIC CELL BASIS 2 0 1432.08 0
PERIODIC CELL BASIS 3 0 0 1354.43
As you have water bubble (as you mentioned in other post) in your
simulation, this values may be wrong.
Thanks
Suranga
On Sun, Aug 26, 2012 at 12:07 PM, Mariana Graterol
<marianagraterol_at_gmail.com> wrote:
Hi namd's support team:
I work with NAMD 2.7b1 for Win32 in a personal computer with
6 AMD FX(tm)-6100 Six-Core Processor and 8 Gb of ram memory.
I were doing an equilbration run of my protein system, with pbc, in NPT
ensamble; then, when I reached constante pressure, total energy, temp. etc,
and when I want to switch to an NVT ensamble, I can't begin the calculation
with restart option because it appears a fatal error with the number of
processors (at the end of this post I describe briefly).
I checked the output files of my NPT run, I guess not having a constant
volume cell size changes, as expected, but it increases from aprox. 120 x
120 x120 until 1100 x 1100 x 1100 AA, which is huge to PME calculation, as
reflected in the size of the grid that is needed for.
How can I fix this bug? or how can I restart the calculation with my new
conditions - constant pressure, no cell volume constant-?
Thank you to anyone who read this message...
Mariana
***************************************************************
Info: Based on Charm++/Converse 60100 for multicore-win32
Info: Built Mon Mar 23 10:43:08 CDT 2009 by jcphill on honor
Info: Running on 6 processors.
Info: Charm++/Converse parallel runtime startup completed at 0 s
Info: 0 MB of memory in use based on nothing
***TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 400000
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 1015.77 0 0
Info: PERIODIC CELL BASIS 2 0 1432.08 0
Info: PERIODIC CELL BASIS 3 0 0 1354.43
Info: PERIODIC CELL CENTER 1.5e-005 -3.8e-005 -4.6e-005
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 20
Info: MAX PAIR PARTITIONS 8
Info: SELF PARTITION ATOMS 154
Info: SELF2 PARTITION ATOMS 154
Info: PAIR PARTITION ATOMS 318
Info: PAIR2 PARTITION ATOMS 637
Info: MIN ATOMS PER PATCH 100
***
Info: SWITCHING ON 8
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 12
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 14.5
Info: ENERGY OUTPUT STEPS 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 10000
Info: HARMONIC CONSTRAINTS ACTIVE
Info: HARMONIC CONS EXP 2
Info: INTERACTIVE MD ACTIVE
Info: INTERACTIVE MD PORT 3000
Info: INTERACTIVE MD FREQ 20
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-006
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 1024 1440 1440
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Win32.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.7b1_Win32.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED 12345
Info: USE HYDROGEN BONDS? NO
***
Info: SUMMARY OF PARAMETERS:
Info: 1051 BONDS
Info: 4379 ANGLES
Info: 612 DIHEDRAL
Info: 399 IMPROPER
Info: 0 CROSSTERM
Info: 108 VDW
Info: 14 VDW_PAIRS
Warning: VDW TYPE NAME NP MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME NC MATCHES PARAMETER TYPE NAME N*
Warning: VDW TYPE NAME ST MATCHES PARAMETER TYPE NAME S*
Warning: Residue 1 out of order in segment MOL, lookup for additional
residues in this segment disabled.
***
Info: TIME FOR READING PSF FILE: 2.698
Warning: Man, tiny Elvis, that number is huge!
Warning: We don't know how X-Plor represents over Z999 residues
Warning: And you just tried - so we'll fake it as -55000
Warning: This is reversible, but only inside this program.
Info: TIME FOR READING PDB FILE: 0.437
Info:
Info: Reading from binary file C:\nombre.coor
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 127011 ATOMS
Info: 89678 BONDS
Info: 64131 ANGLES
Info: 38854 DIHEDRALS
Info: 7038 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 4742 CONSTRAINTS
Info: 381033 DEGREES OF FREEDOM
Info: 44771 HYDROGEN GROUPS
Info: TOTAL MASS = 779157 amu
Info: TOTAL CHARGE = -0.000231652 e
Info: *****************************
Info:
Info: Entering startup at 483.71 s, 0 MB of memory in use
Info: Startup phase 0 took 0 s, 0 MB of memory in use
Info: Startup phase 1 took 0.171 s, 0 MB of memory in use
Info: Startup phase 2 took 0 s, 0 MB of memory in use
Info: PATCH GRID IS 8 (PERIODIC) BY 12 (PERIODIC) BY 11 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: nombre.vel
Info: REMOVING COM VELOCITY 0.016296 -0.00786343 -0.00547567
Info: LARGEST PATCH (523) HAS 5267 ATOMS
Info: CREATING 21412 COMPUTE OBJECTS
Info: Startup phase 3 took 0.0940001 s, 0 MB of memory in use
Info: PME using 6 and 6 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0 1 2 3 4 5
Info: PME TRANS LOCATIONS: 0 1 2 3 4 5
FATAL ERROR: Memory allocation failed on processor 4.
This application has requested the Runtime to terminate it in an unusual
way.
Please contact the application's support team for more information.
FATAL ERROR: Memory allocation failed on processor 5.
Program finished.
FATAL ERROR: Memory allocation failed on processor 2.
------------- Processor 4 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Memory allocation failed on processor 4.
-- * mari *
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