From: Q=C1=D2=D8=D1_=FB=C1=CC=C1=C5=D7=C1?= (skorovesna_at_inbox.ru)
Date: Mon Mar 01 2010 - 09:38:43 CST
Hello NAMD users,
I'm trying to run protein MD in Amber FF using NAMD 2.7b2 on 4 local CPUs. The problem is that I have to launch NAMD several time to start a successful run.
That means, starting NAMD in absolutely the same conditions - same folder, same input files and same files currently in the folder (FFTW_NAMD_2.7b2_Linux-x86_64-MPI.txt is being manually removed after each unsuccessful run) has a different result.
Do you have any suggestions of how this could happen? Could AMBER in NAMD be dependent on some pseudo-random number generated from time-seed?
Thanks,
Daria
PS
Unsuccessful start looks like this:
da_shal_at_linux-s6ps:~/SUBVERSION/AMBER_PREPARE/1l8t> mpirun -n 4 namd2 1l8t.em1.conf
WARNING: Unable to read mpd.hosts or list of hosts isn't provided. MPI job will be run on the current machine only.
Charm++> Running on MPI version: 2.0 multi-thread support: MPI_THREAD_SINGLE (max supported: MPI_THREAD_SINGLE)
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'.
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-MPI
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 60200 for mpi-linux-amd64
Info: Built Sun Jan 24 00:59:32 MSK 2010 by sda on linux-s6ps
Info: 1 NAMD 2.7b2 Linux-x86_64-MPI 4 linux-s6ps da_shal
Info: Running on 4 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0023849 s
Info: 36.3047 MB of memory in use based on /proc/self/stat
Info: Configuration file is 1l8t.em1.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 74.125 0 0
Info: PERIODIC CELL BASIS 2 0 74.393 0
Info: PERIODIC CELL BASIS 3 0 0 75.109
Info: PERIODIC CELL CENTER 0.0719321 -0.145147 -0.0488507
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
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: PME 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 0
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME 1l8t.em1.dcd
Info: DCD FREQUENCY 100
Info: DCD FIRST STEP 100
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME 1l8t.em1.xst
Info: XST FREQUENCY 100
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME 1l8t.em1
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME 1l8t.em1.restart
Info: RESTART FREQUENCY 100
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 2.5
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 19
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 0
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 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 80 80 80
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from FFTW_NAMD_2.7b2_Linux-x86_64-MPI.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.7b2_Linux-x86_64-MPI.txt
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 1267454429
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE ./1l8t.prmtop
Info: AMBER COORDINATE FILE ./1l8t.inpcrd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (./1l8t.prmtop) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: Found 11041 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 43 BONDS
Info: 89 ANGLES
Info: 42 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 171 VDW_PAIRS
Info: TIME FOR READING PDB FILE: 9.53674e-07
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 37437 ATOMS
Info: 37440 BONDS
Info: 7814 ANGLES
Info: 16431 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 56553 EXCLUSIONS
Info: 35222 RIGID BONDS
Info: 77089 DEGREES OF FREEDOM
Info: 13256 HYDROGEN GROUPS
Info: TOTAL MASS = 230892 amu
Info: TOTAL CHARGE = -8.17166e-06 e
Info: MASS DENSITY = 0.925718 g/cm^3
Info: ATOM DENSITY = 0.0903883 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 0.190294 s, 48.1016 MB of memory in use
Info: Startup phase 0 took 0.000167847 s, 48.1016 MB of memory in use
------------- Processor 0 Exiting: Caught Signal ------------
Signal: 11
[0] Stack Traceback:
[0:0] /lib64/libc.so.6 [0x7facbf080560]
[0:1] memcpy+0xa0 [0x7facbf0cd990]
[0:2] _ZN8MOStream3PutEPcm+0x73 [0x82ae63]
[0:3] _ZN10Parameters15send_ParametersEP8MOStream+0x17d9 [0x867cd9]
[0:4] _ZN4Node11namdOneSendEv+0x92 [0x858aa2]
[0:5] _ZN4Node7startupEv+0x738 [0x85bd38]
[0:6] CkDeliverMessageFree+0x34 [0x9508c3]
[0:7] _Z15_processHandlerPvP11CkCoreState+0x2c3 [0x95523c]
[0:8] CmiHandleMessage+0x27 [0x9c101c]
[0:9] CsdScheduleForever+0x5e [0x9c31f7]
[0:10] CsdScheduler+0xd [0x9c3284]
[0:11] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x28 [0x8af748]
[0:12] TclInvokeStringCommand+0x84 [0x9e38a9]
[0:13] namd2 [0xa1b001]
[0:14] Tcl_EvalEx+0x173 [0xa1c393]
[0:15] Tcl_EvalFile+0x1b0 [0xa13942]
[0:16] _ZN9ScriptTcl3runEPc+0x14 [0x8af464]
[0:17] _Z18after_backend_initiPPc+0x29c [0x50f4cc]
[0:18] main+0x22 [0x50f562]
[0:19] __libc_start_main+0xfd [0x7facbf06ca7d]
[0:20] namd2 [0x50a079]
[cli_0]: [cli_1]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[cli_2]: [cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
rank 3 in job 1 linux-s6ps_46591 caused collective abort of all ranks
exit status of rank 3: killed by signal 9
rank 2 in job 1 linux-s6ps_46591 caused collective abort of all ranks
exit status of rank 2: killed by signal 9
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