Dear all,
I am using Amber11 to do a similiar simulation of tuturial B1 with TIP3P water. In the first minimization, I fixed the protein and moved the water molecules, it's normal. In the second minimization, equilibrizing the whole system, this step aborted. I didn't have a clue why this happened. The input file is following,
initial minimisation whole system
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 0,
cut = 12.0
/
And the result part of output file is below.
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1722533
| TOTAL SIZE OF NONBOND LIST = 78418862
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.0295E+05 9.1686E+00 7.7145E+02 C6 308
BOND = 60593.7210 ANGLE = 5040.9684 DIHED = 612.7736
VDWAALS = 126083.9779 EEL = -701604.8092 HBOND = 0.0000
1-4 VDW = 3164.4257 1-4 EEL = 3162.9864 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -5.2167E+05 1.2398E+00 2.9306E+02 C5 349
BOND = 45529.9871 ANGLE = 2781.2259 DIHED = 1491.7468
VDWAALS = 126154.9984 EEL = -701705.9715 HBOND = 0.0000
1-4 VDW = 832.7570 1-4 EEL = 3249.6987 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -4.4681E+06 7.1244E+07 2.6789E+10 S1 398
BOND = 46159.5204 ANGLE = 2385.6132 DIHED = 1556.2627
VDWAALS = 126237.1143 EEL = -4648371.6181 HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3847 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -2.4679E+08 2.7734E+11 1.0428E+14 S1 398
BOND = 46159.6403 ANGLE = 2385.6251 DIHED = 1556.2638
VDWAALS = 126237.1776 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -3.1904E+07 4.5039E+09 1.6935E+12 S1 398
BOND = 46159.6269 ANGLE = 2385.6238 DIHED = 1556.2637
VDWAALS = 126237.1706 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
250 -9.2121E+07 3.8369E+10 1.4427E+13 S1 398
BOND = 46159.6370 ANGLE = 2385.6248 DIHED = 1556.2638
VDWAALS = 126237.1759 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -3.3412E+08 5.0890E+11 1.9135E+14 H1 32234
BOND = 46159.6437 ANGLE = 2385.6255 DIHED = 1556.2639
VDWAALS = 126237.1794 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
350 -1.3769E+08 8.6039E+10 3.2352E+13 S1 398
BOND = 46159.6388 ANGLE = 2385.6250 DIHED = 1556.2638
VDWAALS = 126237.1768 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -2.6312E+09 3.1646E+13 1.1899E+16 H1 32234
BOND = 46159.6425 ANGLE = 2385.6253 DIHED = 1556.2638
VDWAALS = 126237.1788 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
450 -4.9544E+07 1.0990E+10 4.1322E+12 H1 32234
BOND = 46159.6521 ANGLE = 2385.6263 DIHED = 1556.2639
VDWAALS = 126237.1838 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -1.9633E+08 1.7533E+11 6.5926E+13 S1 398
BOND = 46159.6398 ANGLE = 2385.6251 DIHED = 1556.2638
VDWAALS = 126237.1774 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -1.9490E+08 1.7278E+11 6.4969E+13 H1 32234
BOND = 46159.6447 ANGLE = 2385.6256 DIHED = 1556.2639
VDWAALS = 126237.1800 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -1.2147E+08 6.6891E+10 2.5152E+13 H1 32234
BOND = 46159.6462 ANGLE = 2385.6257 DIHED = 1556.2639
VDWAALS = 126237.1808 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
650 -3.0910E+07 4.2229E+09 1.5879E+12 S1 398
BOND = 46159.6264 ANGLE = 2385.6237 DIHED = 1556.2637
VDWAALS = 126237.1703 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
700 -1.1550E+08 6.0452E+10 2.2731E+13 H1 32234
BOND = 46159.6465 ANGLE = 2385.6257 DIHED = 1556.2639
VDWAALS = 126237.1809 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
750 -6.6564E+08 2.0229E+12 7.6064E+14 S1 398
BOND = 46159.6415 ANGLE = 2385.6252 DIHED = 1556.2638
VDWAALS = 126237.1783 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
800 -1.6059E+08 1.1716E+11 4.4053E+13 S1 398
BOND = 46159.6393 ANGLE = 2385.6250 DIHED = 1556.2638
VDWAALS = 126237.1771 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
850 -5.5618E+08 1.4119E+12 5.3089E+14 H1 32234
BOND = 46159.6431 ANGLE = 2385.6254 DIHED = 1556.2639
VDWAALS = 126237.1791 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
900 -1.4405E+08 9.4199E+10 3.5420E+13 S1 398
BOND = 46159.6389 ANGLE = 2385.6250 DIHED = 1556.2638
VDWAALS = 126237.1769 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
950 -3.0888E+08 4.3481E+11 1.6350E+14 S1 398
BOND = 46159.6407 ANGLE = 2385.6252 DIHED = 1556.2638
VDWAALS = 126237.1778 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -2.4432E+08 2.7181E+11 1.0220E+14 H1 32234
BOND = 46159.6442 ANGLE = 2385.6255 DIHED = 1556.2639
VDWAALS = 126237.1797 EEL = ************* HBOND = 0.0000
1-4 VDW = 650.9821 1-4 EEL = 3271.3848 RESTRAINT = 0.0000
The file produced by HPC when job finished is following,
Disabling ondemand cpu frequency scaling: FATAL: Module cpufreq_ondemand is in use.
[ OK ]
-bash: module: line 1: syntax error: unexpected end of file
-bash: error importing function definition for `module'
Module intel already loaded
Module gcc already loaded
sander.MPI:2641 terminated with signal 11 at PC=54928e SP=7fff361d8490. Backtrace:
/share/apps/amber11/bin/sander.MPI(ewald_force_+0x413e)[0x54928e]
/share/apps/amber11/bin/sander.MPI(force_+0x2696)[0x770826]
/share/apps/amber11/bin/sander.MPI(sander_+0x5f33)[0x4e2e73]
/share/apps/amber11/bin/sander.MPI(MAIN__+0x11fb)[0x4dceab]
/share/apps/amber11/bin/sander.MPI(main+0x3c)[0x443b1c]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x35d501ecdd]
/share/apps/amber11/bin/sander.MPI[0x443a29]
--------------------------------------------------------------------------
mpirun has exited due to process rank 1 with PID 2641 on
node compute1131 exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
PBS Job Statistics:
PBS Input:
#!/bin/bash
#PBS -l nodes=5:ppn=12
#PBS -q tiny12core
#PBS -l walltime=02:30:00
#PBS -N ion20_min2
#PBS -j oe
#PBS -V
set echo
cd /scratch/xs005/130902pssaion20
NP=$(wc -l < $PBS_NODEFILE)
mpirun -np NP -machinefile $PBS_NODEFILE $AMBER_HOME/bin/sander.MPI -O -i min2.in -o min2.out -p pssaion20_wat.prmtop -c min1.rst -r min2.rst -inf min2info
PBS Job ID: 600061.sched
Resource List: neednodes=5:ppn=12,nodes=5:ppn=12,walltime=02:30:00
Resources Used: cput=01:20:43,mem=9012520kb,vmem=25112264kb,walltime=00:02:04
Queue Name: tiny12core
Program Return Code: 1
Head Node:
compute1131
Slave Nodes:
compute1132
compute1133
compute1134
compute1135
nnodes= 5 ncores= 60 njobs=1
Module gcc already loaded
Module gcc already loaded
Module gcc already loaded
Module gcc already loaded
/etc/init.d/cpuspeed: line 86: echo: write error: Invalid argument
/etc/init.d/cpuspeed: line 86: echo: write error: Invalid argument
Enabling ondemand cpu frequency scaling: [ OK ]
And there is another new file I never see before in a normal job, which is below,
sander.MPI:2641 terminated with signal 11 at PC=54928e SP=7fff361d8490. Backtrace:
/share/apps/amber11/bin/sander.MPI(ewald_force_+0x413e)[0x54928e]
/share/apps/amber11/bin/sander.MPI(force_+0x2696)[0x770826]
/share/apps/amber11/bin/sander.MPI(sander_+0x5f33)[0x4e2e73]
/share/apps/amber11/bin/sander.MPI(MAIN__+0x11fb)[0x4dceab]
/share/apps/amber11/bin/sander.MPI(main+0x3c)[0x443b1c]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x35d501ecdd]
/share/apps/amber11/bin/sander.MPI[0x443a29]
Does anyone give some advice to deal with the problem?
Sincerely,
Xiaoquan Sun.
2013-09-02
X Sun
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Received on Mon Sep 02 2013 - 21:00:02 PDT
