Re: Segmentation fault for the tutorial

From: Mahmood Naderan (mahmood.nt_at_gmail.com)
Date: Tue Mar 06 2018 - 13:58:56 CST

Update:
In the previous post, I built namd with cuda using the following command

    ./config Linux-x86_64-g++ --charm-arch multicore-linux64
--with-cuda --cuda-prefix /usr/local/cuda-9.0 --with-tcl --tcl-prefix
/home/mahmood/namd-2.12/NAMD_2.12_Source/tcl

That failed as I said. Then I dropped the cuda and ran

    ./config Linux-x86_64-g++ --charm-arch multicore-linux64
--with-tcl --tcl-prefix /home/mahmood/namd-2.12/NAMD_2.12_Source/tcl

Now the following command

    namd2 ubq_ws_eq.conf

works without any error. So, it seems that there is a problem with the
cuda option. Any thought?
Regards,
Mahmood

On Tue, Mar 6, 2018 at 10:36 PM, Mahmood Naderan <mahmood.nt_at_gmail.com> wrote:
> 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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