Re: segmentation error

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Mar 04 2016 - 10:54:29 CST

Hello Stefano, the first things that come to mind are:
1) try running with only one thread
2) try with the latest version, 2.11; since you are running the
multicore-CUDA version, you should be able to download the precompiled
binary and run it instead of 2.9

Giacomo

On Fri, Mar 4, 2016 at 5:15 AM, Stefano Guglielmo <
stefano.guglielmo_at_unito.it> wrote:

> 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--089e0122aaeeb63405052d3bf9e4--

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