processor counts FFT and NAMD

From: Bishop, Thomas C (bishop_at_tulane.edu)
Date: Wed Mar 25 2009 - 10:42:43 CDT

Dear NAMD,

Is is typical to have a significantly different processor count for the FFT calls than allocated for hte simulation? How does this affect performance and/or how can I increase FFT proc count?

Here's relevant messages from my namdoutput

grep proc dyn.out
Info: Running on 80 processors.
Info: REMOVING PATCHES FROM PROCESSOR 0
Info: PME using 55 and 55 processors for FFT and reciprocal sum.
LDB: Measuring processor speeds ... Done.

HERe's complete output
more dyn17.out
Charm++> Running on MPI version: 2.0 multi-thread support: MPI_THREAD_SINGLE (max
supported: MPI_THREAD_SINGLE)
Charm warning> Randomization of stack pointer is turned on in Kernel, run 'echo 0
> /proc/sys/kernel/randomize_va_space' as root to disable it. Thread migration may
 not work!
Charm++> cpu topology info is being gathered!
Charm++> 20 unique compute nodes detected!
Info: NAMD 2.7b1 for Linux-x86_64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60100 for mpi-linux-x86_64
Info: Built Tue Mar 24 13:17:48 CDT 2009 by root on admin-02-01
Info: 1 NAMD 2.7b1 Linux-x86_64 80 compute-01-37 bishop
Info: Running on 80 processors.
Info: Charm++/Converse parallel runtime startup completed at 0.419275 s
Info: 4.32088 MB of memory in use based on mallinfo
Info: Configuration file is dyn17.conf
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE dyn16.xsc
Warning: The parameter fullElectFrequency now defaults to nonbondedFreq (1) rather
 than stepsPerCycle.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 500000
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 146.598 0 0
Info: PERIODIC CELL BASIS 2 0 152.346 0
Info: PERIODIC CELL BASIS 3 0 0 91.9832
Info: PERIODIC CELL CENTER 77.2804 81.0183 48.4533
Info: WRAPPING ALL CLUSTERS 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: REMOVING PATCHES FROM PROCESSOR 0
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: VELOCITY FILE dyn16.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 0.83333
Info: DCD FILENAME dyn17.dcd
Info: DCD FREQUENCY 500
Info: DCD FIRST STEP 500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME dyn17.xst
Info: XST FREQUENCY 500
Info: VELOCITY DCD FILENAME dyn17.dvd
Info: VELOCITY DCD FREQUENCY 500
Info: VELOCITY DCD FIRST STEP 500
Info: OUTPUT FILENAME dyn17
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME rst
Info: RESTART FREQUENCY 5000
Info: RESTART FILES WILL NOT BE OVERWRITTEN
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 14
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 2
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 18.5
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: MOMENTUM OUTPUT STEPS 5000
Info: TIMING OUTPUT STEPS 5000
Info: PRESSURE OUTPUT STEPS 5000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN DAMPING COEFFICIENT IS 0.2 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Warning: Option useGroupPressure is being enabled due to pressure control with rig
idBonds.
Info: BERENDSEN PRESSURE COUPLING ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: COMPRESSIBILITY ESTIMATE IS 4.57e-05 BAR^(-1)
Info: RELAXATION TIME IS 5000 FS
Info: APPLIED EVERY 1 STEPS
Info: PRESSURE CONTROL IS GROUP-BASED
Info: CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 164 164 164
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-x86_64.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.7b1_Linux-x86_64.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1237995113
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE sys.parm
Info: AMBER COORDINATE FILE sys.crd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES dyn16.coor
Reading parm file (sys.parm) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: Found 60548 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 68 BONDS
Info: 148 ANGLES
Info: 70 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 231 VDW_PAIRS
Info: TIME FOR READING PDB FILE: 3.8147e-06
Info:
Info: Reading from binary file dyn16.coor
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 206014 ATOMS
Info: 206353 BONDS
Info: 44853 ANGLES
Info: 90335 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 313030 EXCLUSIONS
Info: 192477 RIGID BONDS
Info: 425565 DEGREES OF FREEDOM
Info: 74085 HYDROGEN GROUPS
Info: TOTAL MASS = 1.29427e+06 amu
Info: TOTAL CHARGE = -4.08352e-05 e
Info: *****************************
Info:
Info: Entering startup at 13.9251 s, 38.0429 MB of memory in use
Info: Startup phase 0 took 0.184281 s, 38.0413 MB of memory in use
Info: Startup phase 1 took 38.4269 s, 66.9703 MB of memory in use
Info: Startup phase 2 took 0.194505 s, 68.5459 MB of memory in use
Info: PATCH GRID IS 7 (PERIODIC) BY 8 (PERIODIC) BY 4 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file dyn16.vel
Info: REMOVING COM VELOCITY 0.0122789 -0.0111696 0.019356
Info: LARGEST PATCH (72) HAS 1032 ATOMS
Info: CREATING 15437 COMPUTE OBJECTS
Info: Startup phase 3 took 3.08311 s, 94.4295 MB of memory in use
Info: PME using 55 and 55 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 1 3 5 6 7 9 10 11 13 14 ...
Info: PME TRANS LOCATIONS: 1 2 4 5 6 8 9 10 12 13 ...
Info: Startup phase 4 took 8.62039 s, 94.4324 MB of memory in use
Info: Startup phase 5 took 1.06483 s, 69.9706 MB of memory in use
LDB: Measuring processor speeds ... Done.
Info: Startup phase 6 took 3.06811 s, 69.9777 MB of memory in use
Info: CREATING 15437 COMPUTE OBJECTS
Info: useSync: 0 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: Startup phase 7 took 0.269264 s, 72.2592 MB of memory in use
Info: Startup phase 8 took 0.000176191 s, 72.3853 MB of memory in use
Info: Finished startup at 68.8367 s, 72.3853 MB of memory in use

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