From: Mariana Graterol (marianagraterol_at_gmail.com)
Date: Sun Aug 26 2012 - 14:07:17 CDT
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 *
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:57 CST