AMBER Archive (2005)

Subject: Re: AMBER: doesn't work in pmemd, and no output in parallel simulations

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Apr 26 2005 - 16:24:04 CDT

Hwankyu -
Okay, I have no idea what the parallel run issues are; there is insufficient
information here to figure that out. You need to run the amber test suite
in parallel, and get that working, and then you know that sander and pmemd
parallel versions are properly installed. Regarding the pmemd single
processor run, I cannot see any cause for failure; looks to me like the run
may have blown up without flushing buffers. The most common cause for
pmemd not running when sander does run on linux systems is stacksize issues.
Is this a linux system? If so, be sure there is a "limit stacksize
unlimited" in your .cshrc (just having it in .login is often not enough for
parallel runs; if you invoke things with bourne shell, you must use ulimit
instead). Also, set ntpr to something like 1 to debug a run; lots of things
can happen in 500 steps, and you are only dumping output every 500 steps.
Other than that, I don't see anything. You of course do need the parallel
builds of both sander and pmemd (you do have two executables, built
differently, for each?). Also note that while the parallel build of sander
can be run on one processor, parallel pmemd requires a minimum of two
processors (but it should die with a very clear message). Anyway, check
stacksize, set ntpr really low, and see what you get.
Regards - Bob Duke

----- Original Message -----
From: "Hwankyu Lee" <leehk_at_umich.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, April 26, 2005 4:35 PM
Subject: AMBER: doesn't work in pmemd, and no output in parallel simulations

> Dear Amber-users,
>
> I've done energy minimization of my system (~70,000 atoms, including
> water), and
> then run MD with restraints on the solute by using sander. And then, I was
> trying to simulate this system, testing with pmemd and sander with
> parallel and
> no parallel. Sander and pmemd passed example test, so there may be no
> problem
> with installation. When I ran the simulation with sander at single CPU, it
> nicely worked. But, in ohter cases, I got two problems.
>
> 1) When I ran sander in one CPU, it nicely worked. However, when I ran
> sander in
> multiple CPUs, I saw CPUs run but coulnd't see any output files (.out and
> .mdcrd). I'm sure that I made right directory for output files. Could you
> tell
> me why I can't see the output files in the directory
> (/home/leehk/run/g5ace90-par4)? This is script file.
> ---------------------------
> #PBS -S /bin/bash
> #PBS -l nodes=2,walltime=500:00:00
> #PBS -q protein
> #PBS -N sand-cpu4
> #PBS -j oe
> #PBS -M leehk_at_umich.edu
> #PBS -m abe
> #
> echo "I ran on `hostname`"
> cat $PBS_NODEFILE
> #
> export GMPICONF=/home/leehk/.gmpi/$PBS_JOBID
> export PATH=/usr/cac/mpich.eth/bin:$PATH
> #
> cd /home/leehk/run/g5ace90-par4
> mpirun -np 4 -machinefile $PBS_NODEFILE /home/leehk/exe.eth/sander -O -i
> md2.in
> -o md2.out -p g5ace90.prmtop -c md1.rst -r g5ace90-md0.rst -x
> g5ace90-md0.mdcrd
> #
> ---------------------------
>
> 2) When I ran pmemd at one CPU or multiple CPUs, I saw CPUs run, but when
> I
> checked .out file, I saw that .out file stopped like below. Since this
> system
> work with sander, I cannot understand why it didn't work with pmemd.
> I also attach my script file.
> -----------------------------
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 8.0
>
> | Run on 04/26/2005 at 15:28:30
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: md2.in
> | MDOUT: md2.out
> | INPCRD: md1.rst
> | PARM: g5ace90.prmtop
> | RESTRT: g5ace90-md0.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: g5ace90-md0.mdcrd
> | MDINFO: mdinfo
>
>
> Here is the input file:
>
> dendrimer : 2ns of MD
> &cntrl
> imin = 0, irest = 0, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 5.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 298.0, temp0 = 298.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 1000000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 20000
> /
>
>
>
>
> | Largest sphere to fit in unit cell has radius = 40.001
>
> | Duplicated 0 dihedrals
>
> | Duplicated 0 dihedrals
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> getting new box info from bottom of inpcrd
>
> NATOM = 63187 NTYPES = 11 NBONH = 60807 MBONA = 2367
> NTHETH = 6554 MTHETA = 2860 NPHIH = 10308 MPHIA = 3601
> NHPARM = 0 NPARM = 0 NNB = 105162 NRES = 19366
> NBONA = 2367 NTHETA = 2860 NPHIA = 3601 NUMBND = 15
> NUMANG = 26 NPTRA = 7 NATYP = 14 NPHB = 1
> IFBOX = 2 NMXRS = 635 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> | Coordinate Index Table dimensions: 17 17 17
> | Direct force subcell size = 5.7636 5.7636 5.7636
>
> BOX TYPE: TRUNCATED OCTAHEDRON
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
> --------------------------------------------------------------------------------
>
> DEU
>
> General flags:
> imin = 0, nmropt = 0
>
> Nature and format of input:
> ntx = 7, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 500, ntrx = 1, ntwr =
> 20000
> iwrap = 0, 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
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
> ------------------------------------
> Script file is below.
> -------------------------------------
> #PBS -S /bin/bash
> #PBS -l nodes=1,walltime=500:00:00
> #PBS -q protein
> #PBS -N sanpme1cpu
> #PBS -j oe
> #PBS -M leehk_at_umich.edu
> #PBS -m ae
>
> echo "I ran on `hostname`"
>
> cd /home/leehk/run/g5ace90-pme
> /home/leehk/exe.ser/pmemd -O -i md2.in -o md2.out -p g5ace90.prmtop -c
> md1.rst
> -r g5ace90-md0.rst -x g5ace90-md0.mdcrd &
> wait
> -------------------------------------
>
> best,
> Hwankyu.
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