From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Fri Mar 04 2016 - 04:15:01 CST
Dear NMAD users,
I am trying to carry out a metadynamics simulation with collective
variables module, version 2012-03-23 as implemented in NAMD 2.9 for
Linux-x86_64-multicore-CUDA on a 32 core workstation running with centos 7
with an nvidia gtx 750; the simulation immediately stops, or does not even
start, with a segmentation fault message appearing on the command editor.
If I try to start a simulation with the same config file without the colvar
module the simulation seems to proceed fine. Does anybody have any
suggestions?
Reported below are the files of the simulation.
segmentation fault:
"[1]+ segmentation fault (core dumped)
/home/sguglielmo/programmi/NAMD_2.9_Source/Linux-x86_64-g++/namd2 +p32
+idlepoll cdk_8gs_metadyn.conf > log_cdk_8gs_metadyn_50ns"
NAMD config file:
"#############################################################
## JOB DESCRIPTION ##
#############################################################
# Metadynamic simulation of equilibrated cdk2_8GS complex
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure /home/sguglielmo/cdk/cdk_8gS/cdk_8gS_w_ion.psf
coordinates /home/sguglielmo/cdk/cdk_8gS/cdk_8gS_w_ion.pdb
set temperature 310
set outputname cdk_8gS_metadyn_50ns
# Continuing a job from the restart files
if {1} {
set inputname cdk_8gS_dyn_1ns_fin
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.restart.xsc
}
firsttimestep 1107000
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters /home/sguglielmo/cdk/equil/par_all27_prot_lipid_na.inp
parameters /home/sguglielmo/cdk/cdk_8gS/8g_S_gam_aligned.par
#temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 10.0
switching on
switchdist 8.0
pairlistdist 12.0
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Temperature increasing
if {0} {
temperature 10 # starting at 10 K
reassignFreq 100
reassignIncr 0.6
reassignHold 310 # target T: 310 K
numsteps 50000 #
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Gradual temp increase
#run 1000
#for { set TEMP 0 } { $TEMP <= 310 } {incr TEMP 1 } {
#langevinTemp $TEMP
#run 1000
#}
useGroupPressure yes ;# needed for rigid bondsÃ
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 310
# Output
outputName $outputname
binaryoutput yes
restartfreq 500
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
outputTiming 1000
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#extraBonds on
#extraBondsFile extrabond.txt
colvars on
colvarsConfig colvar.txt
if {0} {
constraints on
consexp 2
consref /home/sguglielmo/cdk/cdk_8gS/cdk_8gS_w_ion.pdb
conskfile /home/sguglielmo/cdk/cdk_8gS/cdk_8gS_1.cnst
conskcol B
}
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 14.776220321655273 9.699084281921387 17.676881790161133
sphericalBCr1 53.03223891986549
sphericalBCk1 10
sphericalBCexp1 2
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
if {0} {
minimize 10000
reinitvels $temperature
}
run 37500000 ;# 75 ns"
colvarsconfig:
"colvarsTrajFrequency 100 # output values every 100 steps
colvar {
name DistGloopGlu12
upperWall 30
upperWallConstant 800
distance {
group1 {
atomNumbersRange 4908-4961
}
group2 {
atomNumbersRange 187-201
}
}
}
colvar {
name DistLeu83
width 2
distance {
group1 {
atomNumbers 4914
}
group2 {
atomNumbers 1296
}
}
}
colvar {
name angle
width 22.92
angle {
group1 {
atomNumbers 1296
}
group2 {
atomNumbers 4914
}
group3 {
atomNumbers 4910
}
}
}
metadynamics {
colvars DistLeu83 angle
hillWeight 0.6
newHillFrequency 1000
wellTempered on
biasTemperature 890
hillWidth 1.25
useGrids off
}"
logfile:
"Charm++: standalone mode (not using charmrun)
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 (32-way SMP).
Charm++> cpu topology info is gathered in 0.020 seconds.
Info: NAMD 2.9 for Linux-x86_64-multicore-CUDA
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 multicore-linux64
Info: Built lun 25 gen 2016, 10.22.28, CET by sguglielmo on pcPharm004
Info: 1 NAMD 2.9 Linux-x86_64-multicore-CUDA 32 pcPharm004 sguglielmo
Info: Running on 32 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0805919 s
Pe 18 physical rank 18 will use CUDA device of pe 16
Pe 17 physical rank 17 will use CUDA device of pe 16
Pe 31 physical rank 31 will use CUDA device of pe 16
Pe 4 physical rank 4 will use CUDA device of pe 16
Pe 19 physical rank 19 will use CUDA device of pe 16
Pe 11 physical rank 11 will use CUDA device of pe 16
Pe 29 physical rank 29 will use CUDA device of pe 16
Pe 14 physical rank 14 will use CUDA device of pe 16
Pe 10 physical rank 10 will use CUDA device of pe 16
Pe 1 physical rank 1 will use CUDA device of pe 16
Pe 20 physical rank 20 will use CUDA device of pe 16
Pe 28 physical rank 28 will use CUDA device of pe 16
Pe 8 physical rank 8 will use CUDA device of pe 16
Pe 3 physical rank 3 will use CUDA device of pe 16
Pe 13 physical rank 13 will use CUDA device of pe 16
Pe 6 physical rank 6 will use CUDA device of pe 16
Pe 12 physical rank 12 will use CUDA device of pe 16
Pe 30 physical rank 30 will use CUDA device of pe 16
Pe 23 physical rank 23 will use CUDA device of pe 16
Pe 15 physical rank 15 will use CUDA device of pe 16
Pe 7 physical rank 7 will use CUDA device of pe 16
Pe 2 physical rank 2 will use CUDA device of pe 16
Pe 9 physical rank 9 will use CUDA device of pe 16
Pe 24 physical rank 24 will use CUDA device of pe 16
Pe 25 physical rank 25 will use CUDA device of pe 16
Pe 26 physical rank 26 will use CUDA device of pe 16
Pe 27 physical rank 27 will use CUDA device of pe 16
Pe 5 physical rank 5 will use CUDA device of pe 16
Pe 22 physical rank 22 will use CUDA device of pe 16
Pe 21 physical rank 21 will use CUDA device of pe 16
Pe 16 physical rank 16 binding to CUDA device 0 on pcPharm004: 'GeForce GTX
750' Mem: 2047MB Rev: 5.0
Did not find +devices i,j,k,... argument, using all
Pe 0 physical rank 0 will use CUDA device of pe 16
Info: 19.8633 MB of memory in use based on /proc/self/stat
Info: Configuration file is cdk_8gs_metadyn.conf
Info: Working in the current directory /home/sguglielmo/cdk/cdk_8gS
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE cdk_8gS_dyn_1ns_fin.restart.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 1107000
Info: STEPS PER CYCLE 10
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: MIN ATOMS PER PATCH 40
Info: VELOCITY FILE cdk_8gS_dyn_1ns_fin.restart.vel
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 cdk_8gS_metadyn_50ns.dcd
Info: DCD FREQUENCY 500
Info: DCD FIRST STEP 1107500
Info: XST FILENAME cdk_8gS_metadyn_50ns.xst
Info: XST FREQUENCY 500
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME cdk_8gS_metadyn_50ns
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME cdk_8gS_metadyn_50ns.restart
Info: RESTART FREQUENCY 500
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 10
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 0.435
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 14.935
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: COLLECTIVE VARIABLES CALCULATION REQUESTED
Info: COLLECTIVE VARIABLES CONFIGURATION colvar.txt
Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE
Info: RADIUS #1 53.0322
Info: FORCE CONSTANT #1 10
Info: EXPONENT #1 2
Info: SPHERE BOUNDARY CENTER(14.7762, 9.69908, 17.6769)
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
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 310 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 2.3043e-05 2.3043e-05 2.3043e-05
Info: CELL FLUCTUATION IS ISOTROPIC
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 1457085750
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB /home/sguglielmo/cdk/cdk_8gS/cdk_8gS_w_ion.pdb
Info: STRUCTURE FILE /home/sguglielmo/cdk/cdk_8gS/cdk_8gS_w_ion.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS
/home/sguglielmo/cdk/equil/par_all27_prot_lipid_na.inp
Info: PARAMETERS
/home/sguglielmo/cdk/cdk_8gS/8g_S_gam_aligned.par
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES cdk_8gS_dyn_1ns_fin.restart.coor
Info: FIRST TIMESTEP 1107000
Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES k=130 theta0=107.5 k_ub=0 r_ub=0
USING VALUES k=130 theta0=107 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 320 BONDS
Info: 795 ANGLES
Info: 1305 DIHEDRAL
Info: 94 IMPROPER
Info: 6 CROSSTERM
Info: 201 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 1.13072
Info: TIME FOR READING PDB FILE: 0.183152
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 45442 ATOMS
Info: 31947 BONDS
Info: 22367 ANGLES
Info: 12974 DIHEDRALS
Info: 785 IMPROPERS
Info: 288 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 43075 RIGID BONDS
Info: 93251 DEGREES OF FREEDOM
Info: 15918 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 15918 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 277777 amu
Info: TOTAL CHARGE = 3.53158e-06 e
Info: *****************************
Info: Reading from binary file cdk_8gS_dyn_1ns_fin.restart.coor
Info:
Info: Entering startup at 1.57259 s, 66.4023 MB of memory in use
Info: Startup phase 0 took 0.000515938 s, 66.418 MB of memory in use
Info: Startup phase 1 took 0.0345039 s, 73.5469 MB of memory in use
Info: Startup phase 2 took 0.00378895 s, 86.2305 MB of memory in use
Info: Startup phase 3 took 0.000241041 s, 86.3281 MB of memory in use
Info: PATCH GRID IS 5 BY 5 BY 5
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file cdk_8gS_dyn_1ns_fin.restart.vel
Info: REMOVING COM VELOCITY -0.0205004 0.0237052 -0.0415982
Info: LARGEST PATCH (72) HAS 628 ATOMS
Info: Startup phase 4 took 0.055522 s, 94.0977 MB of memory in use
Info: Startup phase 5 took 0.000322104 s, 94.3203 MB of memory in use
Info: Startup phase 6 took 0.002527 s, 94.3203 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 0.00300598 s, 94.5742 MB of memory in use
Info: CREATING 2292 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 705 POINTS
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 3.30872e-24 AT 10.1458
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 9.64837e-17 AT 10.1458
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 100
colvars: # colvarsRestartFrequency = 500 [default]
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be
"cdk_8gS_metadyn_50ns.restart.colvars.state".
colvars: The final output state file will be
"cdk_8gS_metadyn_50ns.colvars.state".
colvars: The trajectory file will be "cdk_8gS_metadyn_50ns.colvars.traj".
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = DistGloopGlu12
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 54 initialized: total mass =
349.455.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 15 initialized: total mass =
128.107.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 800
colvars: # upperWall = 30
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = DistLeu83
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass =
14.0067.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass =
15.999.
colvars: All components initialized.
colvars: # width = 2
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = angle
colvars: Initializing a new "angle" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass =
15.999.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass =
14.0067.
colvars: Initializing atom group "group3".
colvars: Atom group "group3" defined, 1 initialized: total mass =
12.011.
colvars: # oneSiteSystemForce = off [default]
colvars: All components initialized.
colvars: # width = 22.92
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars:
----------------------------------------------------------------------
colvars: Collective variables initialized, 3 in total.
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "metadynamics" instance.
colvars: # name = "metadynamics1" [default]
colvars: # colvars = { DistLeu83, angle }
colvars: # hillWeight = 0.6
colvars: # newHillFrequency = 1000
colvars: # hillWidth = 1.25
colvars: # useGrids = off
colvars: # multipleReplicas = off [default]
colvars: # writeHillsTrajectory = off [default]
colvars: # wellTempered = on
colvars: # biasTemperature = 890
colvars: Well-tempered metadynamics is used.
colvars: The bias temperature is 890.
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars:
----------------------------------------------------------------------
colvars: Initializing step number as firstTimestep.
Pe 2 hosts 1 local and 1 remote patches for pe 16
Pe 3 hosts 2 local and 1 remote patches for pe 16
Pe 6 hosts 2 local and 2 remote patches for pe 16
Pe 0 hosts 1 local and 1 remote patches for pe 16
Pe 13 hosts 2 local and 1 remote patches for pe 16
Pe 18 hosts 3 local and 2 remote patches for pe 16
Pe 5 hosts 1 local and 1 remote patches for pe 16
Pe 7 hosts 1 local and 1 remote patches for pe 16
Pe 26 hosts 1 local and 2 remote patches for pe 16
Pe 15 hosts 3 local and 3 remote patches for pe 16
Pe 16 hosts 2 local and 2 remote patches for pe 16
Pe 23 hosts 1 local and 2 remote patches for pe 16
Pe 11 hosts 2 local and 2 remote patches for pe 16
Pe 1 hosts 1 local and 2 remote patches for pe 16
Pe 17 hosts 3 local and 3 remote patches for pe 16
Pe 14 hosts 3 local and 3 remote patches for pe 16
Pe 19 hosts 5 local and 5 remote patches for pe 16
Pe 30 hosts 2 local and 1 remote patches for pe 16
Pe 9 hosts 2 local and 1 remote patches for pe 16
Pe 21 hosts 3 local and 2 remote patches for pe 16
Pe 8 hosts 1 local and 2 remote patches for pe 16
Pe 4 hosts 2 local and 2 remote patches for pe 16
Pe 10 hosts 1 local and 2 remote patches for pe 16
Pe 25 hosts 2 local and 2 remote patches for pe 16
Pe 28 hosts 1 local and 2 remote patches for pe 16
Pe 22 hosts 1 local and 1 remote patches for pe 16
Pe 31 hosts 2 local and 1 remote patches for pe 16
Pe 20 hosts 2 local and 3 remote patches for pe 16
Pe 27 hosts 2 local and 1 remote patches for pe 16
Pe 29 hosts 1 local and 2 remote patches for pe 16
Pe 12 hosts 5 local and 5 remote patches for pe 16
Pe 24 hosts 2 local and 1 remote patches for pe 16
Info: useSync: 1 useProxySync: 0
Info: Startup phase 8 took 0.253321 s, 169.598 MB of memory in use
Info: Startup phase 9 took 0.000372171 s, 169.598 MB of memory in use
Info: Startup phase 10 took 0.00199294 s, 169.645 MB of memory in use
Info: Finished startup at 1.9287 s, 169.684 MB of memory in use
TCL: Running for 37500000 steps"
Thanks in advance
-- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707678
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