From: Siri Søndergaard (siris2501_at_gmail.com)
Date: Sun Dec 16 2012 - 22:53:31 CST
I'm trying to get the adaptive tempering module running but it always
crashes when: OPENING EXTENDED SYSTEM TRAJECTORY FILE
Does anybody have an example conf file that works?
This is the log file (I tried with namd2.8 as well and it can up with the
same log file. However the ADAPTIVE TEMPERING: INITIAL TEMPERATURE was 450
and not 300 as for namd2.9):
Charm++> Running on MPI version: 2.1
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired:
MPI_THREAD_SINGLE)
Charm++> Running on non-SMP mode
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (16-way SMP).
Charm++> cpu topology info is gathered in 0.003 seconds.
Info: NAMD 2.9 for Linux-x86_64-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
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 60400 for mpi-linux-x86_64-icc
Info: Built Mon Jul 30 12:57:28 EST 2012 by aab900 on vayu3
Info: 1 NAMD 2.9 Linux-x86_64-MPI 1 vayu2 sxs810
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0510402 s
Info: 265.77 MB of memory in use based on /proc/self/stat
Info: Configuration file is 2KM3_cy3_system_small_adaptive.conf
Info: Working in the current directory
/short/g15/sxs810/Cy3/DNA/Adaptive_temp
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuration file but will be ignored:
Warning: adaptTempRestartFreq (adaptTempRestartFile)
Warning: fixedAtomsFile (fixedatoms)
Warning: fixedAtomsCol (fixedatoms)
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 49 0 0
Info: PERIODIC CELL BASIS 2 0 55 0
Info: PERIODIC CELL BASIS 3 0 0 47
Info: PERIODIC CELL CENTER 1.1 3 0.9
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME 2KM3_cy3_system_small_adaptive.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME 2KM3_cy3_system_small_adaptive.xst
Info: XST FREQUENCY 1000
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME 2KM3_cy3_system_small_adaptive
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME 2KM3_cy3_system_small_adaptive.restart
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 13.5
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 0.48
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16.48
Info: ENERGY OUTPUT STEPS 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 10000
Info: PRESSURE OUTPUT STEPS 1000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: CELL FLUCTUATION IS ISOTROPIC
Info: ADAPTIVE TEMPERING ACTIVE:
Info: OUTPUT FREQUENCY: 10
Info: TEMPERATURE UPDATE FREQUENCY: 10
Info: ADAPTIVE TEMPERING WILL BE DONE FROM STEP 0
Info: ADAPTIVE TEMPERING COUPLED TO LANGEVIN THERMOSTAT
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 70 70 70
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from system
Info: Attempting to read FFTW data from
FFTW_NAMD_2.9_Linux-x86_64-MPI_FFTW3.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.9_Linux-x86_64-MPI_FFTW3.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
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 1355719673
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB 2KM3_cy3_system_small_mini.pdb
Info: STRUCTURE FILE 2KM3_cy3_system_small.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS /home/810/sxs810/short/toppar/par_cy.prm
Info: PARAMETERS /home/810/sxs810/short/toppar/par_all36_na.prm
Info: PARAMETERS
/home/810/sxs810/short/toppar/par_water_ions_new.prm
Info: PARAMETERS
/home/810/sxs810/short/toppar/par_PHOS_linker.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 116 BONDS
Info: 273 ANGLES
Info: 596 DIHEDRAL
Info: 15 IMPROPER
Info: 0 CROSSTERM
Info: 70 VDW
Info: 2 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.0670121
Info: TIME FOR READING PDB FILE: 0.0421872
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 11490 ATOMS
Info: 7946 BONDS
Info: 5015 ANGLES
Info: 2098 DIHEDRALS
Info: 62 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 34470 DEGREES OF FREEDOM
Info: 4108 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 4108 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 73572.2 amu
Info: TOTAL CHARGE = 1.27405e-06 e
Info: MASS DENSITY = 0.964532 g/cm^3
Info: ATOM DENSITY = 0.0907117 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 0.278854 s, 333.32 MB of memory in use
Info: Startup phase 0 took 0.000148058 s, 333.32 MB of memory in use
Info: Startup phase 1 took 0.00545096 s, 335.109 MB of memory in use
Info: Startup phase 2 took 0.023473 s, 335.305 MB of memory in use
Info: Startup phase 3 took 6.8903e-05 s, 335.305 MB of memory in use
Info: PATCH GRID IS 2 (PERIODIC) BY 3 (PERIODIC) BY 2 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY -0.0228269 -0.148165 0.0493902
Info: LARGEST PATCH (4) HAS 995 ATOMS
Info: Startup phase 4 took 0.00545192 s, 337.523 MB of memory in use
Info: PME using 1 and 1 processors for FFT and reciprocal sum.
Info: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: PME GRID LOCATIONS: 0
Info: PME TRANS LOCATIONS: 0
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Startup phase 5 took 0.0858052 s, 338.871 MB of memory in use
Info: Startup phase 6 took 7.98702e-05 s, 338.871 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 0.000726938 s, 338.871 MB of memory in use
Info: CREATING 234 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: Startup phase 8 took 0.00573301 s, 339.617 MB of memory in use
Info: Startup phase 9 took 7.41482e-05 s, 339.617 MB of memory in use
Info: Startup phase 10 took 0.000185013 s, 341.293 MB of memory in use
Info: Finished startup at 0.406051 s, 341.293 MB of memory in use
TCL: Running for 1000000 steps
Info: INITIALISING ADAPTIVE TEMPERING
Info: ADAPTIVE TEMPERING: TEMPERATURE RANGE: [300,600] KELVIN
Info: ADAPTIVE TEMPERING: NUMBER OF BINS TO STORE POT. ENERGY: 100
Info: ADAPTIVE TEMPERING: ADAPTIVE BIN AVERAGING PARAMETER: 0.1
Info: ADAPTIVE TEMPERING: SCALING CONSTANT FOR LANGEVIN TEMPERATURE
UPDATES: 0.001
Info: ADAPTIVE TEMPERING: INITIAL TEMPERATURE: 300
PRESSURE: 0 -732.126 21.354 233.258 21.354 -1115.98 86.8917 233.258 86.8917
-1170.43
GPRESSURE: 0 -3169 17.4826 211.833 18.619 -3464.96 95.4909 212.217 94.4262
-3558.22
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME
PRESSAVG GPRESSAVG
ENERGY: 0 1775.0743 1422.9898 789.4366 2.0700
-64849.0172 6943.1093 0.0000 0.0000
10238.2921 -43678.0452 298.9349 -53916.3372 -43677.9987
298.9349 -1006.1780 -3397.3917 126665.0000
-1006.1780 -3397.3917
OPENING EXTENDED SYSTEM TRAJECTORY FILE
[0] Stack Traceback:
[0:0] /lib64/libc.so.6 [0x7f456f0a12f0]
[0:1] _ZN10Controller15adaptTempUpdateEii+0x8af [0x88dddf]
[0:2] _ZN10Controller9integrateEv+0x54a [0x88911a]
[0:3] _ZN10Controller9threadRunEPS_+0x6c9 [0x89e179]
[0:4] CthStartThread+0x1c [0xb21adc]
[0:5] /lib64/libc.so.6 [0x7f456f0b2ca0]
Regards and thanks
Siri Sondergaard
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:22 CST