Re: Namd job terminates after ~10000+ itrations

From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Tue Dec 23 2008 - 05:57:16 CST

can you just provide your input file as well? that will be easier to check

 

-- 
Rudra
JRF; SNBNCBS
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----- Original Message ----
From: Sangamesh B <forum.san_at_gmail.com>
To: NAMD ML <namd-l_at_ks.uiuc.edu>
Sent: Tuesday, 23 December, 2008 11:59:25 AM
Subject: namd-l: Namd job terminates after ~10000+ itrations
Hello Namd users,
     I'm benchmarking Namd-2.6 built on Rocks-4.3 Linux cluster( Intel
Xeon, 3.6 GHz)-Intel 10 compilers, with an input file given by one of
our customers.
I've tried to run Namd with both versions of charm++ - i.e. with MPI
and w/o MPI.
But in each case, the job fails, with the following error:
WRITING COORDINATES TO DCD FILE AT STEP 14000
LDB:  LOAD: AVG 2.19086 MAX 2.72057  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
LDB:  LOAD: AVG 2.19086 MAX 2.23459  MSGS: TOTAL 161 MAXC 10 MAXP 7  Refine
ENERGY:   15000       109.2174       351.9875       167.0691
17.0719         -96871.8411      9005.0313         0.0000
0.0000     16199.7877         -71021.6761       300.6049
-70992.4608    -70992.0088       300.8596         -20865.8855
102.9266    265795.4607        -2.6098        -3.2279
WRITING COORDINATES TO DCD FILE AT STEP 15000
Stack Traceback:
  [0] CmiAbort+0x51  [0x7a956c]
  [1] __cmi_assert+0x47  [0x7b51f3]
  [2] /opt/apps/namd26_intel/Linux-x86_64-netIB-gnu/namd2 [0x7ae963]
  [3] infi_CmiAlloc+0x16  [0x7ae823]
  [4] CmiAlloc+0x16  [0x7b4663]
  [5] CqsPrioqGetDeq+0xff  [0x7b6f4b]
  [6] CqsEnqueueGeneral+0xae  [0x7b7525]
  [7] CldHandler+0xa7  [0x4c06d5]
  [8] CmiHandleMessage+0x76  [0x7b2512]
  [9] CsdScheduleForever+0x5f  [0x7b276b]
  [10] CsdScheduler+0x16  [0x7b26e4]
  [11] _ZN7BackEnd4initEiPPc+0x1a0  [0x4c6ea0]
  [12] main+0x19  [0x4c3ce9]
  [13] __libc_start_main+0xdb  [0x3021d1c3fb]
  [14] __gxx_personality_v0+0x12a  [0x4c058a]
The detailed output ia pasted below:
$ cat out.60.Namd-Net-gnu24
Charmrun> IBVERBS version of charmrun
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.6 for Linux-x86_64-netIB-gnu
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 50914 for net-linux-x86_64-ibverbs
Info: Built Mon Dec 22 17:45:48 IST 2008 by root on rapideye.igib.res.in
Info: 1 NAMD  2.6  Linux-x86_64-netIB-gnu  20    compute-0-5.local  locuz
Info: Running on 20 processors.
Info: 49816 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is npt03.inp
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE   npt02.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        3000000
Info: STEPS PER CYCLE        8
Info: PERIODIC CELL BASIS 1  63.1779 0 0
Info: PERIODIC CELL BASIS 2  0 59.2372 0
Info: PERIODIC CELL BASIS 3  0 0 71.0325
Info: PERIODIC CELL CENTER   0 0 0
Info: LOAD BALANCE STRATEGY  Other
Info: LDB PERIOD             1600 steps
Info: FIRST LDB TIMESTEP     40
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS    50
Info: MAX PAIR PARTITIONS    20
Info: SELF PARTITION ATOMS   125
Info: PAIR PARTITION ATOMS   200
Info: PAIR2 PARTITION ATOMS  400
Info: MIN ATOMS PER PATCH    100
Info: VELOCITY FILE          npt02.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           npt03.dcd
Info: DCD FREQUENCY          1000
Info: DCD FIRST STEP         1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           npt03.xst
Info: XST FREQUENCY          10000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        npt03
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       npt03
Info: RESTART FREQUENCY      10000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           12
Info: SWITCHING OFF          13.5
Info: PAIRLIST DISTANCE      15
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                 0.525
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        18.025
Info: ENERGY OUTPUT STEPS    1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    10000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   300
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info:        TARGET PRESSURE IS 1 BAR
Info:     OSCILLATION PERIOD IS 200 FS
Info:             DECAY TIME IS 500 FS
Info:     PISTON TEMPERATURE IS 300 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS -1.51206e-05 -1.51206e-05 -1.51206e-05
Info:       CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE               1e-06
Info: PME EWALD COEFFICIENT       0.227942
Info: PME INTERPOLATION ORDER     4
Info: PME GRID DIMENSIONS         80 80 80
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-x86_64-netIB-gnu.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-x86_64-netIB-gnu.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      4
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: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED     1230007678
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         abp_8776wat.pdb
Info: STRUCTURE FILE         abp_8776wat.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             par_all22_prot.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     npt02.coor
Info: SUMMARY OF PARAMETERS:
Info: 139 BONDS
Info: 345 ANGLES
Info: 452 DIHEDRAL
Info: 43 IMPROPER
Info: 0 CROSSTERM
Info: 95 VDW
Info: 0 VDW_PAIRS
Warning: Ignored 8776 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 26958 ATOMS
Info: 18185 BONDS
Info: 9914 ANGLES
Info: 1647 DIHEDRALS
Info: 116 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 26636 RIGID BONDS
Info: 54238 DEGREES OF FREEDOM
Info: 9098 HYDROGEN GROUPS
Info: TOTAL MASS = 162683 amu
Info: TOTAL CHARGE = 5.02914e-07 e
Info: *****************************
Info: Entering startup phase 0 with 52292 kB of memory in use.
Info: Entering startup phase 1 with 52292 kB of memory in use.
Info: Entering startup phase 2 with 54412 kB of memory in use.
Info: Entering startup phase 3 with 54624 kB of memory in use.
Info: PATCH GRID IS 3 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC)
Info: REMOVING COM VELOCITY -0.02348 -0.0695335 -0.0196877
Info: LARGEST PATCH (6) HAS 1041 ATOMS
Info: CREATING 4376 COMPUTE OBJECTS
Info: Entering startup phase 4 with 56344 kB of memory in use.
Info: PME using 20 and 20 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
Info: Entering startup phase 5 with 56344 kB of memory in use.
Info: Entering startup phase 6 with 56344 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 56344 kB of memory in use.
Info: CREATING 4376 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1..05879e-22 AT 13.4141
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.02133e-16 AT 13.4141
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.05879e-22 AT 13.4141
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 2.27424e-16 AT 13.4141
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 13.6359
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.64771e-15 AT 13.4141
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.2326e-32 AT 13.4141
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 3.49897e-16 AT 13.4141
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 2.06795e-25 AT 13.3393
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 3.90841e-16 AT 13.4141
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 13.4141
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 2.44315e-16 AT 13.4141
Info: Entering startup phase 8 with 56344 kB of memory in use.
Info: Finished startup with 56344 kB of memory in use.
ETITLE:      TS           BOND          ANGLE          DIHED
IMPRP               ELECT            VDW       BOUNDARY           MISC
       KINETIC               TOTAL           TEMP         TOTAL2
  TOTAL3        TEMPAVG            PRESSURE      GPRESSURE
VOLUME       PRESSAVG      GPRESSAVG
ENERGY:       0       121.1806       333.7596       170.1716
22.8872         -96614.8429      8841.2352         0.0000
0.0000     16138.1887         -70987.4200       299.4619
-70956.3288    -70956.3288       299.4619         -21073.5083
-161.4623    265837.8454    -21073.5083      -161.4623
OPENING EXTENDED SYSTEM TRAJECTORY FILE
Info: Initial time: 20 CPUs 0.107109 s/step 1.23969 days/ns 56344 kB memory
LDB:  LOAD: AVG 2.34175 MAX 4.32288  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
Info: Adjusted background load on 11 nodes.
LDB:  LOAD: AVG 2.4291 MAX 2.43265  MSGS: TOTAL 161 MAXC 10 MAXP 7  Alg7
LDB:  LOAD: AVG 2.4291 MAX 2.43265  MSGS: TOTAL 161 MAXC 10 MAXP 7  Alg7
Info: Initial time: 20 CPUs 0.106527 s/step 1.23295 days/ns 57212 kB memory
LDB:  LOAD: AVG 2.3116 MAX 3.00669  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
LDB:  LOAD: AVG 2.3116 MAX 2.35658  MSGS: TOTAL 161 MAXC 10 MAXP 7  Refine
Info: Initial time: 20 CPUs 0.0767132 s/step 0.887884 days/ns 57212 kB memory
LDB:  LOAD: AVG 2.25647 MAX 2.80525  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
LDB:  LOAD: AVG 2.25647 MAX 2.30153  MSGS: TOTAL 161 MAXC 10 MAXP 7  Refine
Info: Benchmark time: 20 CPUs 0.0717251 s/step 0.830152 days/ns 57212 kB memory
Info: Benchmark time: 20 CPUs 0.0703394 s/step 0..814113 days/ns 57212 kB memory
Info: Benchmark time: 20 CPUs 0.0701201 s/step 0.811575 days/ns 57212 kB memory
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE AT STEP 1000
ENERGY:    1000       127.8373       351.8293       177.3696
18.2626         -96272.9784      8691.6459         0.0000
0.0000     16181.0105         -70725.0232       300.2565
-70694.1834    -70697.6964       302.5369         -21064.6199
-222.6916    265616.0510         6.1947         6.3844
[locuz_at_rapideye net-gnu2]$ cat out.60.Namd-Net-gnu24
Charmrun> IBVERBS version of charmrun
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.6 for Linux-x86_64-netIB-gnu
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 50914 for net-linux-x86_64-ibverbs
Info: Built Mon Dec 22 17:45:48 IST 2008 by root on rapideye.igib.res.in
Info: 1 NAMD  2.6  Linux-x86_64-netIB-gnu  20    compute-0-5.local  locuz
Info: Running on 20 processors.
Info: 49816 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is npt03.inp
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE   npt02.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        3000000
Info: STEPS PER CYCLE        8
Info: PERIODIC CELL BASIS 1  63.1779 0 0
Info: PERIODIC CELL BASIS 2  0 59.2372 0
Info: PERIODIC CELL BASIS 3  0 0 71.0325
Info: PERIODIC CELL CENTER   0 0 0
Info: LOAD BALANCE STRATEGY  Other
Info: LDB PERIOD             1600 steps
Info: FIRST LDB TIMESTEP     40
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS    50
Info: MAX PAIR PARTITIONS    20
Info: SELF PARTITION ATOMS   125
Info: PAIR PARTITION ATOMS   200
Info: PAIR2 PARTITION ATOMS  400
Info: MIN ATOMS PER PATCH    100
Info: VELOCITY FILE          npt02..vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           npt03.dcd
Info: DCD FREQUENCY          1000
Info: DCD FIRST STEP         1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           npt03.xst
Info: XST FREQUENCY          10000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        npt03
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       npt03
Info: RESTART FREQUENCY      10000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           12
Info: SWITCHING OFF          13.5
Info: PAIRLIST DISTANCE      15
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                 0.525
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        18.025
Info: ENERGY OUTPUT STEPS    1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    10000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   300
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info:        TARGET PRESSURE IS 1 BAR
Info:     OSCILLATION PERIOD IS 200 FS
Info:             DECAY TIME IS 500 FS
Info:     PISTON TEMPERATURE IS 300 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS -1.51206e-05 -1.51206e-05 -1.51206e-05
Info:       CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE               1e-06
Info: PME EWALD COEFFICIENT       0.227942
Info: PME INTERPOLATION ORDER     4
Info: PME GRID DIMENSIONS         80 80 80
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-x86_64-netIB-gnu.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-x86_64-netIB-gnu.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      4
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: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED     1230007678
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         abp_8776wat.pdb
Info: STRUCTURE FILE         abp_8776wat.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             par_all22_prot.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     npt02.coor
Info: SUMMARY OF PARAMETERS:
Info: 139 BONDS
Info: 345 ANGLES
Info: 452 DIHEDRAL
Info: 43 IMPROPER
Info: 0 CROSSTERM
Info: 95 VDW
Info: 0 VDW_PAIRS
Warning: Ignored 8776 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 26958 ATOMS
Info: 18185 BONDS
Info: 9914 ANGLES
Info: 1647 DIHEDRALS
Info: 116 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 26636 RIGID BONDS
Info: 54238 DEGREES OF FREEDOM
Info: 9098 HYDROGEN GROUPS
Info: TOTAL MASS = 162683 amu
Info: TOTAL CHARGE = 5.02914e-07 e
Info: *****************************
Info: Entering startup phase 0 with 52292 kB of memory in use.
Info: Entering startup phase 1 with 52292 kB of memory in use.
Info: Entering startup phase 2 with 54412 kB of memory in use.
Info: Entering startup phase 3 with 54624 kB of memory in use.
Info: PATCH GRID IS 3 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC)
Info: REMOVING COM VELOCITY -0.02348 -0.0695335 -0.0196877
Info: LARGEST PATCH (6) HAS 1041 ATOMS
Info: CREATING 4376 COMPUTE OBJECTS
Info: Entering startup phase 4 with 56344 kB of memory in use.
Info: PME using 20 and 20 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
Info: Entering startup phase 5 with 56344 kB of memory in use.
Info: Entering startup phase 6 with 56344 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 56344 kB of memory in use.
Info: CREATING 4376 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.05879e-22 AT 13.4141
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.02133e-16 AT 13.4141
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.05879e-22 AT 13.4141
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 2.27424e-16 AT 13.4141
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 13.6359
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.64771e-15 AT 13.4141
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.2326e-32 AT 13.4141
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 3.49897e-16 AT 13.4141
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 2.06795e-25 AT 13.3393
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 3.90841e-16 AT 13.4141
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 13.4141
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 2.44315e-16 AT 13.4141
Info: Entering startup phase 8 with 56344 kB of memory in use.
Info: Finished startup with 56344 kB of memory in use.
ETITLE:      TS           BOND          ANGLE          DIHED
IMPRP               ELECT            VDW       BOUNDARY           MISC
       KINETIC               TOTAL           TEMP         TOTAL2
  TOTAL3        TEMPAVG            PRESSURE      GPRESSURE
VOLUME       PRESSAVG      GPRESSAVG
ENERGY:       0       121.1806       333.7596       170.1716
22.8872         -96614.8429      8841.2352         0.0000
0.0000     16138.1887         -70987.4200       299.4619
-70956.3288    -70956.3288       299.4619         -21073.5083
-161.4623    265837.8454    -21073.5083      -161.4623
OPENING EXTENDED SYSTEM TRAJECTORY FILE
Info: Initial time: 20 CPUs 0.107109 s/step 1.23969 days/ns 56344 kB memory
LDB:  LOAD: AVG 2.34175 MAX 4.32288  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
Info: Adjusted background load on 11 nodes.
LDB:  LOAD: AVG 2.4291 MAX 2.43265  MSGS: TOTAL 161 MAXC 10 MAXP 7  Alg7
LDB:  LOAD: AVG 2.4291 MAX 2.43265  MSGS: TOTAL 161 MAXC 10 MAXP 7  Alg7
Info: Initial time: 20 CPUs 0.106527 s/step 1.23295 days/ns 57212 kB memory
LDB:  LOAD: AVG 2.3116 MAX 3.00669  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
LDB:  LOAD: AVG 2.3116 MAX 2.35658  MSGS: TOTAL 161 MAXC 10 MAXP 7  Refine
Info: Initial time: 20 CPUs 0.0767132 s/step 0.887884 days/ns 57212 kB memory
LDB:  LOAD: AVG 2.25647 MAX 2.80525  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
LDB:  LOAD: AVG 2.25647 MAX 2.30153  MSGS: TOTAL 161 MAXC 10 MAXP 7  Refine
Info: Benchmark time: 20 CPUs 0.0717251 s/step 0.830152 days/ns 57212 kB memory
Info: Benchmark time: 20 CPUs 0.0703394 s/step 0.814113 days/ns 57212 kB memory
Info: Benchmark time: 20 CPUs 0.0701201 s/step 0.811575 days/ns 57212 kB memory
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE AT STEP 1000
ENERGY:    1000       127.8373       351.8293       177.3696
18.2626         -96272.9784      8691.6459         0.0000
0.0000     16181.0105         -70725..0232       300.2565
-70694.1834    -70697.6964       302.5369         -21064.6199
-222.6916    265616.0510         6.1947         6.3844
LDB:  LOAD: AVG 2.21514 MAX 2.69827  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
LDB:  LOAD: AVG 2.21514 MAX 2.25925  MSGS: TOTAL 161 MAXC 10 MAXP 7  Refine
ENERGY:    2000       115.0802       333.6503       174.2795
23.1469         -96405.3595      8737.9491         0.0000
0.0000     16256.0032         -70765.2503       301.6480
-70735.7045    -70735.8084       302.4557         -20885.7694
-23.9166    265749.0243        -3.7921        -2.7705
WRITING COORDINATES TO DCD FILE AT STEP 2000
WRITING COORDINATES TO DCD FILE AT STEP 3000
ENERGY:    3000       123.9842       354.4409       164.2527
19.0929         -96814.6635      8930.0369         0.0000
0.0000     16079.0666         -71143.7892       298.3648
-71113.2322    -71115.0260       301.6379         -20846.0039
153.8439    265187.2389        -2.1004        -2.0211
...
.......
WRITING COORDINATES TO DCD FILE AT STEP 14000
LDB:  LOAD: AVG 2.19086 MAX 2.72057  MSGS: TOTAL 161 MAXC 10 MAXP 7  None
LDB:  LOAD: AVG 2.19086 MAX 2.23459  MSGS: TOTAL 161 MAXC 10 MAXP 7  Refine
ENERGY:   15000       109.2174       351.9875       167.0691
17.0719         -96871.8411      9005.0313         0.0000
0.0000     16199.7877         -71021.6761       300.6049
-70992.4608    -70992.0088       300.8596         -20865.8855
102.9266    265795.4607        -2.6098        -3.2279
WRITING COORDINATES TO DCD FILE AT STEP 15000
Stack Traceback:
  [0] CmiAbort+0x51  [0x7a956c]
  [1] __cmi_assert+0x47  [0x7b51f3]
  [2] /opt/apps/namd26_intel/Linux-x86_64-netIB-gnu/namd2 [0x7ae963]
  [3] infi_CmiAlloc+0x16  [0x7ae823]
  [4] CmiAlloc+0x16  [0x7b4663]
  [5] CqsPrioqGetDeq+0xff  [0x7b6f4b]
  [6] CqsEnqueueGeneral+0xae  [0x7b7525]
  [7] CldHandler+0xa7  [0x4c06d5]
  [8] CmiHandleMessage+0x76  [0x7b2512]
  [9] CsdScheduleForever+0x5f  [0x7b276b]
  [10] CsdScheduler+0x16  [0x7b26e4]
  [11] _ZN7BackEnd4initEiPPc+0x1a0  [0x4c6ea0]
  [12] main+0x19  [0x4c3ce9]
  [13] __libc_start_main+0xdb  [0x3021d1c3fb]
  [14] __gxx_personality_v0+0x12a  [0x4c058a]
Any one has faced such problem? Any optimization flags needs to be set?
The executable is linked with libraries as follows:
MPI version of NAMD with Voltaire MPI:
# ldd /opt/apps/namd26_intel/Linux-x86_64-VltMPI/namd2
        libdl.so.2 => /lib64/libdl.so.2 (0x00000034b1300000)
        libtcl8.4.so => /usr/lib64/libtcl8.4.so (0x00000034b1700000)
        libsrfftw.so.2 =>
/opt/libraries/fftw_intel/2.1.5/lib/libsrfftw.so.2
(0x0000002a9557a000)
        libsfftw.so.2 =>
/opt/libraries/fftw_intel/2.1.5/lib/libsfftw.so.2 (0x0000002a956ab000)
        libm.so.6 => /lib64/tls/libm.so.6 (0x00000034b1100000)
        libpmpich++.so.1.0 =>
/opt/vltmpi/OPENIB/mpi.icc.rsh/lib/shared/libpmpich++.so.1.0
(0x0000002a957e6000)
        libmpich.so.1.0 =>
/opt/vltmpi/OPENIB/mpi.icc.rsh/lib/shared/libmpich.so.1.0
(0x0000002a95909000)
        libmpichfstub.so.1.0 =>
/opt/vltmpi/OPENIB/mpi.icc.rsh/lib/shared/libmpichfstub.so.1.0
(0x0000002a95b07000)
        libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x0000002a95c08000)
        libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x00000034b1500000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000034b4600000)
        libc.so.6 => /lib64/tls/libc.so.6 (0x00000034b0e00000)
        /lib64/ld-linux-x86-64.so.2 (0x00000034b0a00000)
        libimf.so => /opt/intel/cce/10.1.018/lib/libimf.so (0x0000002a95d14000)
        libsvml.so => /opt/intel/cce/10.1.018/lib/libsvml.so
(0x0000002a96079000)
        libintlc.so.5 => /opt/intel/cce/10.1.018/lib/libintlc.so.5
(0x0000002a96204000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000034b3900000)
Charm++ version of NAMD:
# ldd /opt/apps/namd26_intel/Linux-x86_64-netIB/namd2
        libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x0000002a95579000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00000034b1300000)
        libtcl8..4.so => /opt/libraries/tcl84_intel/lib/libtcl8.4.so
(0x0000002a95685000)
        libsrfftw.so.2 =>
/opt/libraries/fftw_intel/2.1.5/lib/libsrfftw.so.2
(0x0000002a958b4000)
        libsfftw.so.2 =>
/opt/libraries/fftw_intel/2.1.5/lib/libsfftw.so.2 (0x0000002a959e6000)
        libm..so.6 => /lib64/tls/libm.so.6 (0x00000034b1100000)
        libstdc++.so..6 => /usr/lib64/libstdc++.so.6 (0x00000034b4600000)
        libc.so.6 => /lib64/tls/libc.so.6 (0x00000034b0e00000)
        libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x00000034b1500000)
        /lib64/ld-linux-x86-64.so.2 (0x00000034b0a00000)
        libmpich.so.1.0 =>
/opt/vltmpi/OPENIB/mpi.icc.rsh/lib/shared/libmpich.so.1.0
(0x0000002a95b22000)
        libmpichfstub.so.1.0 =>
/opt/vltmpi/OPENIB/mpi.icc.rsh/lib/shared/libmpichfstub.so.1.0
(0x0000002a95d1f000)
        libimf.so => /opt/intel/cce/10.1.018/lib/libimf.so (0x0000002a95e20000)
        libsvml.so => /opt/intel/cce/10.1.018/lib/libsvml.so
(0x0000002a96184000)
        libintlc.so.5 => /opt/intel/cce/10.1.018/lib/libintlc.so.5
(0x0000002a96310000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000034b3900000)
Thanks,
Sangamesh
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This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:18 CST