Segmentation fault for the tutorial

From: Mahmood Naderan (mahmood.nt_at_gmail.com)
Date: Tue Mar 06 2018 - 13:06:11 CST

Hi
I followed the tutorial up to [1]. I also downloaded the files and
build the necessary file with vmd according to that toturial. namd2 is
also installed with cuda and tcl-threaded and it is ok. However the
following command fails.

May I know how to debug more?

mahmood_at_orca:1-1-build$ namd2 ubq_ws_eq.conf
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID:
v6.7.1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Nov-07-136676
Warning> Randomization of stack pointer is turned on in kernel, thread
migration may not work! Run 'echo 0 >
/proc/sys/kernel/randomize_va_space' as root to disable it, or try run
with '+isomalloc_sync'.
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 0.000 seconds.
Info: Built with CUDA version 9000
Did not find +devices i,j,k,... argument, using all
Pe 0 physical rank 0 binding to CUDA device 0 on orca: 'Quadro M2000'
Mem: 4035MB Rev: 5.2
Info: NAMD 2.12 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 60701 for multicore-linux64
Info: Built Tue Mar 6 22:26:21 +0330 2018 by mahmood on orca
Info: 1 NAMD 2.12 Linux-x86_64-multicore-CUDA 1 orca mahmood
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.400351 s
CkLoopLib is used in SMP with a simple dynamic scheduling
(converse-level notification) but not using node-level queue
Info: 356.035 MB of memory in use based on /proc/self/stat
Info: Configuration file is ubq_ws_eq.conf
Info: Working in the current directory /home/mahmood/namd-2.12/bench/1-1-build
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
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: INITIAL TEMPERATURE 310
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 ubq_ws_eq.dcd
Info: DCD FREQUENCY 250
Info: DCD FIRST STEP 250
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME ubq_ws_eq
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME ubq_ws_eq.restart
Info: RESTART FREQUENCY 500
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 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16.5
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE
Info: RADIUS #1 26
Info: FORCE CONSTANT #1 10
Info: EXPONENT #1 2
Info: SPHERE BOUNDARY CENTER(30.3082, 28.805, 15.354)
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: MULTILEVEL SUMMATION METHOD (MSM) FOR ELECTROSTATICS ACTIVE
Info: MSM WITH C1 CUBIC INTERPOLATION AND C2 TAYLOR SPLITTING
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: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1520362840
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ./ubq_ws.pdb
Info: STRUCTURE FILE ./ubq_ws.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ./par_all27_prot_lipid.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 180 BONDS
Info: 447 ANGLES
Info: 566 DIHEDRAL
Info: 46 IMPROPER
Info: 6 CROSSTERM
Info: 119 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.0326149
Info: Reading pdb file ./ubq_ws.pdb
Info: TIME FOR READING PDB FILE: 0.00761604
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 6682 ATOMS
Info: 4871 BONDS
Info: 4074 ANGLES
Info: 3293 DIHEDRALS
Info: 204 IMPROPERS
Info: 74 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 6080 RIGID BONDS
Info: 13966 DEGREES OF FREEDOM
Info: 2419 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 2419 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 41298.8 amu
Info: TOTAL CHARGE = 1.00955e-06 e
Info: *****************************
Info:
Info: Entering startup at 0.450153 s, 360.785 MB of memory in use
Info: Startup phase 0 took 3.60012e-05 s, 360.785 MB of memory in use
Info: ADDED 12209 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.00181603 s, 362.074 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 3.42196e-09 AT 0.0732877
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.000404119 s, 363.164 MB of memory in use
Info: Startup phase 3 took 1.69277e-05 s, 363.164 MB of memory in use
Info: Startup phase 4 took 1.78814e-05 s, 363.164 MB of memory in use
Info: Startup phase 5 took 1.3113e-05 s, 363.164 MB of memory in use
Info: PATCH GRID IS 4 BY 4 BY 4
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.0833122 0.116815 -0.0236598
Info: LARGEST PATCH (26) HAS 434 ATOMS
Info: TORUS A SIZE 1 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.00118899 s, 364.195 MB of memory in use
Info: Startup phase 7 took 2.19345e-05 s, 364.195 MB of memory in use
Segmentation fault (core dumped)
mahmood_at_orca:1-1-build$ ls
1UBQ.pdb download ubqp.pdb ubq_ws_eq.conf
coor par_all27_prot_lipid.inp ubq.psf ubq_ws.pdb
del_water.log top_all27_prot_lipid.inp ubq_wb.log ubq_ws.psf
del_water.pdb ubq.pdb ubq_wb.pdb wat_sphere.tcl
del_water.psf ubq.pgn ubq_wb.psf

[1] http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node8.html

Regards,
Mahmood

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