On Wed, Dec 15, 2010 at 4:40 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Dec 15, 2010 at 6:11 AM, mish <smncbr.gmail.com> wrote:
>
> > Hi Bill,
> > I finished a new simulation where I used 12CPU's, with 48GB of RAM for
> > the calculation and the problems still persist. I can see the same error
> > "allocation failure in vector: nh = 276948109" in _complex_nm.out file. I
> >
>
> This indicates a malloc failure (allocation). It's trying to allocate
> 276948109 "double" numbers. On a typical machine I think that's 8 bytes
> (64-bit real), so it's trying to allocate a total of 2.063 GB of memory, I
> think, and for some reason it's failing.
>
>
> > have ran another calculation in 4CPU's with 48 GB of RAM and calculation
> > are
> > running. However, in that running_MMPBSA_complex.mdcrd.1 calculation I
> cant
> > see values of entropy in
> > the _MMPBSA_complex_nm.out.1, _MMPBSA_complex_nm.out.2,
> > _MMPBSA_complex_nm.out.3
> > files. After each minimization is message "allocation failure in vector:
> > nh " in the place of values of entropies. What could be other source of
> > error ?? is there something wrong with my input file ?
> >
>
> Did you clean all temporary files before re-running? It could be you're
> seeing the remnants of previous attempts?. Perhaps there's a memory leak
> as
> well... can you determine how much memory is being used during the
> simulation?
>
Yes I clean all the temporary file before rerunning the calculations. When I
look for the memory use during the simulation its about 8GB where as I had
assigned 48GB in for the calculations. What could be other possible source
of such error ?
Sincerely
Sushil
> All the best,
> Jason
>
>
> > ==============================================
> >
> > Input file for running entropy calculations using NMode
> > &general
> > endframe=200, keep_files=2,
> > /
> > &nmode
> > nmstartframe=1, nmendframe=200,
> > nminterval=25, nmode_igb=1, nmode_istrng=0.1,
> > /
> > ===============================================
> >
> >
> > Sincerely
> > Mish
> >
> > On Tue, Dec 14, 2010 at 1:35 PM, mish <smncbr.gmail.com> wrote:
> >
> > > Thanks for the reply. I performed only this calculation in 8 CPUs (-np
> 8)
> > > with 8GB of RAM, Then I reduced the number of processors (-np) to 4
> with
> > 8GB
> > > of RAM but problem still persists. I can try 2 threads (i.e. mpirun
> -np
> > -2
> > > MMPBSA.py.MPI) and let you in the case problem still persist.
> > >
> > > ..S
> > >
> > >
> > > On Tue, Dec 14, 2010 at 1:22 PM, Bill Miller III <
> brmilleriii.gmail.com
> > >wrote:
> > >
> > >> This is almost certainly a memory issue. Each normal mode calculation
> > can
> > >> take a couple of gigabytes of RAM. How many calculations are you
> > >> attempting
> > >> to perform at the same time with the 8 GB of RAM allotted? The memory
> > >> required is obviously dependent on the size of the system. This is the
> > >> reason you do not see the "allocation failure" error in
> > >> _MMPBSA_ligand_nm.out. The ligand is small enough that it does not
> > require
> > >> much memory to perform the normal mode calculation. I would suggest
> > using
> > >> less threads for the parallel calculation, or use more processors with
> > >> more
> > >> available RAM. With 8 GB of RAM available, I would not do more than
> > >> probably
> > >> 2 threads (i.e. mpirun -np -2 MMPBSA.py.MPI) at one time for an
> > >> average-sized protein system.
> > >>
> > >> I hope that helps.
> > >>
> > >> -Bill
> > >>
> > >> On Tue, Dec 14, 2010 at 7:11 AM, mish <smncbr.gmail.com> wrote:
> > >>
> > >> > Hi all,
> > >> > I tried normal mode calculations in a protein (268 aa long). I used
> > >> > parallel
> > >> > version of MMPBSA.py.MPI (python script) for calculating the
> entropy.
> > >> The
> > >> > no
> > >> > results written out in FINAL_RESULTS_MMPBSA.dat . following is the
> > >> output,
> > >> > can you please point the possible places where I am doing wrong. The
> > >> > _MMPBSA
> > >> > _complex_nm.out and _MMPBSA_receptor_nm.out files contain an error
> > >> > "allocation failure in vector: nh = 284339701 ", where as
> > >> > _MMPBSA_ligand_nm.out
> > >> > doesnot have this error. This looks like an memory allocation
> problem
> > >> but I
> > >> > had also tried the calculations by assigning 8GB of memory and the
> > >> problem
> > >> > still persist. Can any of you point out teh origin of errors in the
> > >> > calculations.
> > >> >
> > >> >
> > >> > -----------------FINAL_RESULTS_MMPBSA.dat----------------
> > >> >
> > >> > | Run on Tue Dec 14 02:33:44 CET 2010
> > >> >
> > >> > |Input file:
> > >> > |--------------------------------------------------------------
> > >> > |Input file for running entropy calculations using NMode
> > >> > |&general
> > >> > | endframe=50, keep_files=2,
> > >> > |/
> > >> > |&nmode
> > >> > |nmstartframe=5, nmendframe=45,
> > >> > |nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> > >> > |/
> > >> > |
> > >> > |
> > >> > |--------------------------------------------------------------
> > >> > |Complex topology file: com.prmtop
> > >> > |Receptor topology file: rec.prmtop
> > >> > |Ligand topology file: lig.prmtop
> > >> > |Initial mdcrd(s): prod.mdcrd
> > >> > |
> > >> > |Best guess for receptor mask: ":1-266"
> > >> > |Best guess for ligand mask: ":267-268"
> > >> >
> > >> > |Calculations performed using 50 frames.
> > >> > |NMODE calculations performed using 9 frames.
> > >> > |
> > >> > |All units are reported in kcal/mole.
> > >> > |All entropy results have units kcal/mole (Temperature is 298.15 K).
> > >> >
> > >> >
> > >>
> >
> -------------------------------------------------------------------------------
> > >> >
> > >> >
> > >>
> >
> -------------------------------------------------------------------------------
> > >> > NO NMODE ENTROPY CALCULATED. SNAPSHOTS NOT MINIMIZED!
> > >> >
> > >> >
> > >> >
> > >>
> >
> -------------------------------------------------------------------------------
> > >> >
> > >> >
> > >>
> >
> -------------------------------------------------------------------------------
> > >> >
> > >> >
> > >> > ================== _MMPBSA_complex_nm.out
> > >> > ====================================
> > >> > ----Convergence Satisfied----
> > >> >
> > >> > iter Total bad vdW elect nonpolar genBorn
> > >> > frms
> > >> > ff: 1 -1716.85 2410.88 -1792.90 -1732.53 0.00
> -602.30
> > >> > 9.68e-04
> > >> >
> > >> > Energy = -1.7168452022e+03
> > >> > RMS gradient = 9.6806388713e-04
> > >> > allocation failure in vector: nh = 280631737
> > >> > Reading parm file (com.prmtop)
> > >> >
> > >> >
> > >>
> >
> ============================================================================
> > >> >
> > >> >
> > >> > Thanking you in advance
> > >> >
> > >> > .S
> > >> > _______________________________________________
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> > >> >
> > >>
> > >>
> > >>
> > >> --
> > >> Bill Miller III
> > >> Quantum Theory Project,
> > >> University of Florida
> > >> Ph.D. Graduate Student
> > >> 352-392-6715
> > >> _______________________________________________
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> > >> AMBER.ambermd.org
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> > >>
> > >
> > >
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Wed Dec 15 2010 - 08:00:03 PST
