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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
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>
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Received on Tue Dec 14 2010 - 05:00:03 PST
