From: Odysseas Axillews (blackmask1928_at_yahoo.gr)
Date: Sun Mar 21 2010 - 20:24:30 CDT
hello everyone!
i am a quite old but not very experienced user of namd and a newcomer to mailing list. I am really happy to be in this group, I would also like to contribute.
I have the following problem. I have recently obtained a new system with the following configutration
1. intel core i 5
2. asus motherboard
3.gpu ati 4350
4. 4 gb ram
5 1TB w.digital hard disk
6. scientific linux 5.4 operating system
all my simulations become aborted after 300000-700000 steps (every step 2 fs)
i get the following error in the log file before the abortion
[1] Stack Traceback:
[0] /lib64/libc.so.6 [0x34f3a302d0]
[1] _ZN20ComputeNonbondedUtil9calc_pairEP9nonbonded+0x239b [0x596ee7]
[2] _ZN20ComputeNonbondedPair7doForceEPP8CompAtomPP11CompAtomExtPP7Results+0xa35 [0x59185f]
[3]
_ZN16ComputePatchPair6doWorkEv+0xa7 [0x73ab63]
[4] _ZN11WorkDistrib12enqueueWorkBEP12LocalWorkMsg+0x16 [0x9a43be]
[5] _ZN19CkIndex_WorkDistrib31_call_enqueueWorkB_LocalWorkMsgEPvP11WorkDistrib+0xf [0x9a43a5]
[6] CkDeliverMessageFree+0x21 [0xa343cb]
[7] _Z15_processHandlerPvP11CkCoreState+0x530 [0xa339bc]
[8] CsdScheduleForever+0xa5 [0xabd4b9]
[9] CsdScheduler+0x1c [0xabd0ba]
[10] _Z11master_initiPPc+0x2d6 [0x512386]
[11] _ZN7BackEnd4initEiPPc+0x31 [0x5120a9]
[12] main+0x2f [0x50d99f]
[13] __libc_start_main+0xf4 [0x34f3a1d994]
[14] _ZNSt8ios_base4InitD1Ev+0x52 [0x508d5a]
and this in a second simulation
Stack Traceback:
[0] /lib64/libc.so.6 [0x34f3a302d0]
[1] _ZN20ComputeNonbondedUtil9calc_pairEP9nonbonded+0x21ac [0x536f6c]
[2]
_ZN20ComputeNonbondedPair7doForceEPP8CompAtomPP7Results+0x5da [0x52fc9e]
[3] _ZN16ComputePatchPair6doWorkEv+0x85 [0x615dd1]
[4] _ZN11WorkDistrib12enqueueWorkAEP12LocalWorkMsg+0x16 [0x728cd6]
[5] _ZN19CkIndex_WorkDistrib31_call_enqueueWorkA_LocalWorkMsgEPvP11WorkDistrib+0xf [0x728cbd]
[6] CkDeliverMessageFree+0x21 [0x786a6b]
[7] _Z15_processHandlerPvP11CkCoreState+0x455 [0x786075]
[8] CsdScheduleForever+0xa2 [0x7f18a2]
[9] CsdScheduler+0x1c [0x7f14a0]
[10] _Z10slave_initiPPc+0x10 [0x4baea4]
[11] _ZN7BackEnd4initEiPPc+0x28f [0x4bae89]
[12] main+0x47 [0x4b67ef]
[13] __libc_start_main+0xf4 [0x34f3a1d994]
[14] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b2b5a]
in the start of the log file i get a warning i do not know if this warning is related to the abortion of my
runs.
Charm warning> Randomization of stack pointer is turned on in Kernel, run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it. Thread migration may not work!
i have ran the line that it is refered at the start of the log file (echo...) from the terminal as root, but i continue to get the same stack error and all my jobs continue to become aborted.
I would be grateful if you could provide me some help!!
Stefanos pentas
Charm++> cpu topology info is being gathered.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Info: NAMD 2.7b2 for Linux-x86_64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
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 60103 for net-linux-x86_64-iccstatic
Info: Built Thu Nov 12 22:12:21 CST 2009 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD
2.7b2 Linux-x86_64 4 localhost.localdomain root
Info: Running on 4 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.038754 s
Info: 1.63213 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is a2eq4.txt
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
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: MAX SELF PARTITIONS 20
Info: MAX PAIR PARTITIONS 8
Info: SELF PARTITION ATOMS 154
Info: SELF2 PARTITION ATOMS 154
Info: PAIR PARTITION ATOMS 318
Info: PAIR2 PARTITION ATOMS 637
Info: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 600
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME a2eq4.dcd
Info: DCD FREQUENCY 500
Info: DCD FIRST
STEP 500
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME a2eq4
Info: RESTART FILENAME a2eq4.restart
Info: RESTART FREQUENCY 500
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
Info:
HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE
Info: RADIUS #1 40
Info: FORCE CONSTANT #1 10
Info: EXPONENT #1 2
Info: SPHERE BOUNDARY CENTER(0, 0, 0)
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 600
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
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 1268422196
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB a2eq3.pdb
Info: STRUCTURE FILE a2.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_na_urea.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 250 BONDS
Info: 624 ANGLES
Info: 1050 DIHEDRAL
Info: 74 IMPROPER
Info: 0 CROSSTERM
Info: 130 VDW
Info: 0 VDW_PAIRS
Info: TIME FOR READING PSF FILE:
0.342469
Info: TIME FOR READING PDB FILE: 0.046067
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 25385 ATOMS
Info: 19186 BONDS
Info: 17606 ANGLES
Info: 13731 DIHEDRALS
Info: 2862 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 20807 RIGID BONDS
Info: 55348 DEGREES OF FREEDOM
Info: 9999 HYDROGEN GROUPS
Info: TOTAL MASS = 165378 amu
Info: TOTAL CHARGE = 3.76869e-05 e
Info: *****************************
Info:
Info: Entering startup at 0.470892 s, 8.29982 MB of memory in use
Info: Startup phase 0 took 0.034914 s, 8.29991 MB of memory in use
Info: Startup phase 1 took 0.091989 s, 12.4677 MB of memory in use
Info: Startup phase 2 took 0.036057 s, 12.6648 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 0.00509809 0.0202283 -0.00759836
Info: LARGEST PATCH (39) HAS 563
ATOMS
Info: CREATING 1250 COMPUTE OBJECTS
Info: Startup phase 3 took 0.116038 s, 15.8826 MB of memory in use
Info: Startup phase 4 took 0.0359981 s, 15.8825 MB of memory in use
Info: Startup phase 5 took 0.064003 s, 13.5387 MB of memory in use
LDB: Measuring processor speeds ... Done.
Info: Startup phase 6 took 1.20407 s, 13.5669 MB of memory in use
Info: CREATING 1250 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 1.69407e-21 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.13046e-16 AT 11.9974
Info: Startup phase 7 took 0.048105 s, 15.3198 MB of memory in use
Info: Startup phase 8 took 0.000268936 s, 17.0862 MB of memory in use
Info: Finished startup at 2.10233 s, 17.0862 MB of memory in use
REINITIALIZING VELOCITIES AT STEP 0 TO 600 KELVIN.
TCL:
Running for 100000000 steps
PRESSURE: 0 0 0 0 0 0 0 0 0 0
GPRESSURE: 0 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL
TOTAL3 TEMPAVG
ENERGY: 0 4314.4789 7753.0739 3137.5824 867.4275 -166988.2096 2204.2726 107.7347 0.0000 33420.6082 -115183.0313 607.7190 -148603.6395 -114997.3554 607.7190
LDB: ============= START OF LOAD BALANCING ============== 6.78262
LDB: ============== END OF LOAD BALANCING =============== 6.78282
Info: Initial time: 4 CPUs 0.0902221 s/step 0.522119 days/ns 28.1713 MB memory
LDB: ============= START OF LOAD
BALANCING ============== 11.4016
LDB: TIME 11.4027 LOAD: AVG 3.88616 MAX 4.60915 PROXIES: TOTAL 57 MAXPE 22 MAXPATCH 3 None 0.519055
LDB: TIME 11.4042 LOAD: AVG 3.88616 MAX 4.66338 PROXIES: TOTAL 90 MAXPE 34 MAXPATCH 3 TorusLB 0.519055
LDB: TIME 11.4241 LOAD: AVG 3.88616 MAX 4.07946 PROXIES: TOTAL 90 MAXPE 34 MAXPATCH 3 TorusLB 0.519055
LDB: ============== END OF LOAD BALANCING =============== 11.4329
PRESSURE: 100 0 0 0 0 0 0 0 0 0
GPRESSURE: 100 0 0 0 0 0 0 0 0 0
PRESSAVG: 100 0 0 0 0 0 0 0 0 0
GPRESSAVG: 100 0 0 0 0 0 0 0 0 0
Info: Initial time: 4 CPUs 0.089551 s/step 0.518235 days/ns 29.0045 MB memory
ENERGY: 100 4345.4452 8004.8547 3161.5787 928.3700 -167410.1654
2403.8067 106.7217 0.0000 33393.7236 -115065.6649 607.2301 -148459.3886 -114860.3031 601.4117
LDB: ============= START OF LOAD BALANCING ============== 16.0638
LDB: TIME 16.0649 LOAD: AVG 4.09756 MAX 4.37523 PROXIES: TOTAL 57 MAXPE 22 MAXPATCH 3 None 0.595697
LDB: TIME 16.0663 LOAD: AVG 4.09756 MAX 4.29352 PROXIES: TOTAL 90 MAXPE 34 MAXPATCH 3 RefineTorusLB 0.595697
LDB: ============== END OF LOAD BALANCING =============== 16.0682
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