Dear Support list:
I am running accelerated MD for the first time using AMBER 12
(pmemd.cuda.MPI). I made calculations from 50ns runs using conventional MD
and below is my input file for aMD.
&cntrl
irest=1,ntx=5,
nstlim=5000000,dt=0.002,
temp0=310.0,ntt=1,tautp=1.0,
ntc=2,ntf=2,
cut=10.0,
ntpr=5000,ntwx=5000,ntwv=0,ntwe=0,
ntb=2,ntp=1,pres0=1.0,taup=1.0,
ipol=0,igb=0,
ntr=0, iwrap=1, ig=-1,
iamd=3,EthreshD=380.4756,
alphaD=20.8,EthreshP=-28056.1468, alphaP=1512.48,
/
I am currently using 2 gpus on 1 node for testing. Here is my error message
[cn7:mpi_rank_0][error_sighandler] Caught error: Segmentation fault (signal
11)
Warning! Rndv Receiver is expecting 69696 Bytes But, is receiving 69672
Bytes
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
I tried increasing the memory but it didn't help. The job crashes (the
output is pasted below). Your guidance is appreciated.
Cheers,
Neha
PMEMD implementation of SANDER, Release 11
| Run on 03/21/2013 at 19:10:05
[-O]verwriting output
File Assignments:
| MDIN:
sander.in5
| MDOUT:
prod6.out2
| INPCRD:
prod5.rst
| PARM:
test.prmtop
| RESTRT:
prod6.rst
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
prod6.mdcrd
| MDINFO:
mdinfo
|LOGFILE:
logfile
Here is the input file:
AVP dt=2.0fs with SHAKE, NPT aMD boost pot and
dih
&cntrl
irest=1,ntx=5,
nstlim=5000000,dt=0.002,
temp0=310.0,ntt=1,tautp=1.0,
ntc=2,ntf=2,
cut=10.0,
ntpr=5000,ntwx=5000,ntwv=0,ntwe=0,
ntb=2,ntp=1,pres0=1.0,taup=1.0,
ipol=0,igb=0,
ntr=0, iwrap=1,
ig=-1,
iamd=3,EthreshD=380.4756,
alphaD=20.8,EthreshP=-28056.1468,
alphaP=1512.48,
/
Note: ig = -1. Setting random seed based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
| Using Accelerated MD (AMD) to enhance sampling iamd = 3
| AMD boost to total energy: EthreshP,alphaP -28056.146799999999
1512.480000000000
| AMD boost to dihedrals: EthreshD,alphaD 380.475600000000
20.800000000000
|--------------------- 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 C1060
| CUDA Device Global Mem Size: 4095 MB
| CUDA Device Num Multiprocessors: 30
| 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 C1060
| CUDA Device Global Mem Size: 4095 MB
| CUDA Device Num Multiprocessors: 30
| 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 = 20.419
| New format PARM file being parsed.
| Version = 1.000 Date = 11/14/12 Time = 18:20:21
| 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 = 9453 NTYPES = 18 NBONH = 9254 MBONA = 199
NTHETH = 494 MTHETA = 273 NPHIH = 882 MPHIA = 706
NHPARM = 0 NPARM = 0 NNB = 14355 NRES = 3043
NBONA = 199 NTHETA = 273 NPHIA = 706 NUMBND = 31
NUMANG = 68 NPTRA = 32 NATYP = 23 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 7 6 8
| Direct force subcell size = 6.8290 6.8063 6.1708
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 5000, ntrx = 1, ntwr =
500
iwrap = 1, ntwx = 5000, 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 = 5000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 310.00000, tempi = 0.00000, tautp = 1.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 5000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 47.803 Box Y = 40.838 Box Z = 49.366
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 48 NFFT2 = 48 NFFT3 = 56
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
--------------------------------------------------------------------------------
begin time read from input coords = 70100.000 ps
Number of triangulated 3-point waters found: 3013
Sum of charges from parm topology file = -0.00000001
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 746615
| Integers 453224
| Nonbonded Pairs Initial Allocation: 1851842
| GPU memory information:
| KB of GPU memory in use: 38678
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Received on Thu Mar 21 2013 - 04:00:02 PDT
