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
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 ?
==============================================
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
>> > _______________________________________________
>> > AMBER mailing list
>> > 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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Received on Wed Dec 15 2010 - 03:30:04 PST
