Dear All,
The job didn't even start properly, mdout file is very small (pasted below,
only 7 KB).
The restart and trajectory file are not generated.
Other explicit solvent jobs are running well, have reached expected temp
and am running the equilibration job.
Yes, this error is appearing only with this job, although I haven't tried
other implicit simulations yet (since I'm stuck here).
The PBS error file is attached herein if it helps identify the problem. Is
this issue related to MPI installation/usage or my input files?
If it is MPI issue, I will forward your comments/suggestions to the system
admin (since they will know if other users are facing a similar issue with
parallel jobs).
thanks.
-------------------------------------------------------
Amber 18 SANDER 2018
-------------------------------------------------------
| Run on 06/02/2019 at 14:49:49
| Executable path: sander.MPI
| Working directory:
/mnt/iusers01/ceas01/r11831vd/P450-md/3A4/3A4-implicit-sol
| Hostname: node702.pri.csf3.alces.network
[-O]verwriting output
File Assignments:
| MDIN: heat3.in
| MDOUT: heat3.out
|INPCRD: P450-1W0E-gas-heat2.rst7
| PARM: P450-1W0E-gas.prmtop
|RESTRT: P450-1W0E-gas-heat3.rst7
| REFC: P450-1W0E-gas-heat2.rst7
| MDVEL: mdvel
| MDFRC: mdfrc
| MDEN: mden
| MDCRD: P450-1W0E-gas-heat3.nc
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
| REMLOG: rem.log
| REMTYPE: rem.type
| REMSTRIP:
| SAVEENE: saveene
|CLUSTERINF: cluster.info
| RESERVOIR: reserv/frame
| REMDDIM:
Here is the input file:
Implicit solvent constant pH initial heating mdin
&cntrl
imin=0, irest=0, ntx=1,
ntpr=500, ntwx=500, nstlim=10000000,
dt=0.002, ntt=3, tempi=0,
temp0=300, tautp=2.0, ig=-1,
ntp=0, ntc=2, ntf=2, cut=30,
ntb=0, igb=2, tol=0.000001,
nrespa=1, saltcon=0.1, icnstph=1,
ntcnstph=100000000,
gamma_ln=5.0, ntwr=500, ioutfm=1,
nmropt=1, ntr=1,
/
&wt
TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
VALUE1=0.0, VALUE2=300.0,
/
&wt TYPE='END' /
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 05/31/19 Time = 19:37:03
NATOM = 7760 NTYPES = 16 NBONH = 3916 MBONA = 3945
NTHETH = 8951 MTHETA = 5355 NPHIH = 17577 MPHIA = 14063
NHPARM = 0 NPARM = 0 NNB = 43203 NRES = 473
NBONA = 3945 NTHETA = 5355 NPHIA = 14063 NUMBND = 67
NUMANG = 156 NPTRA = 82 NATYP = 41 NPHB = 0
IFBOX = 0 NMXRS = 73 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
| Memory Use Allocated
| Real 632408
| Hollerith 23755
| Integer 439987
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 6752 kbytes
| 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
Note: ig = -1. Setting random seed to 698715 based on wallclock time in
microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 500, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 0, igb = 2, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000
gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 0.00000
Molecular dynamics:
nstlim = 10000000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 698715
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 5.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
Constant pH options:
icnstph = 1
ntcnstph =********
solvph = 7.00000
| MPI Timing options:
| profile_mpi = 0
|reading charge increments from file: P450-1W0E-gas-min.cpin
| INFO: Old style inpcrd file read
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
On Mon, Jun 3, 2019 at 12:58 PM David A Case <david.case.rutgers.edu> wrote:
> On Sun, Jun 02, 2019, Vaibhav Dixit wrote:
>
> > NSTEP = 1500000 TIME(PS) = 3000.000 TEMP(K) = 270.99 PRESS =
> >0.0
> > NSTEP = 1500000 TIME(PS) = 3000.000 TEMP(K) = 69.08 PRESS =
> >0.0
> >.
> >ERROR message from the PBS
> >----------------
> >[r11831vd.hlogin1 [csf3] 3A4-implicit-sol]$ tail amber-heat1.e441494
> >sander.MPI 000000000048E81E main Unknown
> Unknown
> >libc-2.17.so 00002B8EBCC55C05 __libc_start_main Unknown
> Unknown
> >sander.MPI 000000000048E729 Unknown Unknown
> Unknown
> >--------------------------------------------------------------------------
> >mpirun detected that one or more processes exited with non-zero status,
> >thus causing
>
> Look at the mdout file: it looks like the job essentially finished (you
> reached the maximum number of steps). Did the restart file get written?
> It sometimes happens that problems occur turing writing out of the
> timings, or an mpi_finalize command. Try to see if this is the case.
>
> Does this error happen only for this run? Or do you ever see this
> behavior on other parallel jobs?
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 03 2019 - 05:30:03 PDT
