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?
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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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> Bill Miller III
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-6715
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> _______________________________________________
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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 - 08:00:02 PST
