Re: Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0

From: subbarao kanchi (ksubbu85_at_gmail.com)
Date: Mon Aug 27 2012 - 13:59:03 CDT

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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