Dear amber users,
Iam trying to run production step in GPU (AMBER 12). At the end
of the job i can see some information in output file but there is 0 size
in rst and crd file. i think its not running MD step. Iam using CUDA-5.5
version, Here iam attaching my Pbs script and output file. please kindly
help me, any suggestions can be appreciated.
Thanks in advance,
*The pbs script as follows:*
#!/bin/bash
#PBS -l nodes=2:ppn=16:GPU
#PBS -l walltime=07:00:00:00
#PBS -q GPUq
#PBS -e err_""$PBS_JOBID
#PBS -o out_""$PBS_JOBID
#PBS -r n
#PBS -V
#PBS -M bo14resch11004.iith.ac.in
export I_MPI_JOB_CONTEXT=$PBS_JOBID
export OMP_NUM_THREADS=2
echo PBS JOB id is $PBS_JOBID
echo PBS_NODEFILE is $PBS_NODEFILE
echo PBS_QUEUE is $PBS_QUEUE
NPROCS=`wc -l < $PBS_NODEFILE`
echo NPROCS is $NPROCS
NRINGS=`cat $PBS_NODEFILE |sort|uniq|wc -l`
echo NRINGS is $NRINGS
NGPUS=`expr $NRINGS \* 2`
echo NGPUS is $NGPUS
cd $PBS_O_WORKDIR
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/CUDA-5.5/lib64
itr=1
set AMBERHOME="/home/external/iith/yajjugal/programs/amber_gpu/amber12"
echo $itr
while [ $itr -le 2 ]
do
itr1=`expr ${itr} - 1`
if [ ${itr} == 1 ]
then
mpirun -np $NGPUS -perhost 2
/home/external/iith/yajjugal/programs/amber_gpu/amber12/bin/pmemd.cuda.MPI
-O -i mdp.inp -o pstep_${itr}.out -r pstep_${itr}.rst -x
pstep_${itr}.crd -p ../input/prmtop -c ../equilibration/step10.rst
else
mpirun -np $NGPUS -perhost 2
/home/external/iith/yajjugal/programs/amber_gpu/amber12/bin/pmemd.cuda.MPI
-O -i mdp.inp -o pstep_${itr}.out -r pstep_${itr}.rst -
x pstep_${itr}.crd -p ../input/prmtop -c pstep_${itr1}.rst
fi
chmod 400 pstep_${itr}.*
gzip pstep_${itr}.crd
mv restrt pstep_${itr}.rst
itr=`expr ${itr} + 1`
done
*The output file as follows: *
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 12/24/2015 at 17:02:01
[-O]verwriting output
File Assignments:
| MDIN: mdp.inp
| MDOUT: pstep_1.out
| INPCRD: ../equilibration/step10.rst
| PARM: ../input/prmtop
| RESTRT: pstep_1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: pstep_1.crd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
Production Run
&cntrl
imin = 0, irest = 1, ntx = 7,
ig=-1,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 250, ntwx = 500, ntwr = 10000, iwrap = 1
/
Note: ig = -1. Setting random seed based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.0
|
| 03/19/2012
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
| Duncan Poole (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPDP] - Hybrid Single/Double Precision (Default).
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| Task ID: 0
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 1
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 1
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 2
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 3
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 1
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| CUDA
| Largest sphere to fit in unit cell has radius = 63.727
| New format PARM file being parsed.
| Version = 1.000 Date = 08/11/15 Time = 13:42:38
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 260718 NTYPES = 20 NBONH = 246203 MBONA = 14741
NTHETH = 33303 MTHETA = 19898 NPHIH = 64925 MPHIA = 49941
NHPARM = 0 NPARM = 0 NNB = 469698 NRES = 79044
NBONA = 14741 NTHETA = 19898 NPHIA = 49941 NUMBND = 59
NUMANG = 124 NPTRA = 64 NATYP = 39 NPHB = 1
IFBOX = 1 NMXRS = 39 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 21 21 26
| Direct force subcell size = 6.1285 6.0692 6.2264
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 7, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 250, ntrx = 1, ntwr =
10000
iwrap = 1, ntwx = 500, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 500000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 169460
temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 250
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 128.698 Box Y = 127.454 Box Z = 161.886
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 128 NFFT2 = 128 NFFT3 = 168
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 0
| fft_blk_y_divisor = 2
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 70.000 ps
Regards
yoogi
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Received on Thu Dec 31 2015 - 06:00:03 PST
