Hi,
The way mmpbsa.py is parallelized, it divides the input trajectory
among all threads. This effectively means that the amount of memory
required for an mmpbsa.py.MPI run is N*M, where N is the number of
threads and M is the amount of memory required by a single thread job.
So adding more threads will actually increase your memory
requirements. Try either using fewer threads or if you have access to
multiple nodes use fewer threads per node.
-Dan
On Thu, Feb 9, 2017 at 6:48 PM, wei <lwstudy.sina.com> wrote:
> Hi, I tried MMPBSA.py.MPI and 16 cores were used. Please see my task submitting comman line below: mpiexec.hydra -n 16 -env I_MPI_FABRICS shm:ofa ~/software/amber14/bin/MMPBSA.py.MPI -O -i mm_pbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp complex.prmtop -cp com_nobox.prmtop -rp pro.prmtop -lp lig.prmtop -y ./*.crd > progress.log I thought It works well at first, because no memory-lacking error occurs. But the calculation failed again later and the error reported in the _MMPBSA_complex_nm.out.15 (or other _MMPBSA_complex_nm.out. files) is: ----Convergence Satisfied---- iter Total bad vdW elect nonpolar genBorn frms
> allocation failure in vector: nh = 3127717476
> I found a similar mail posted before (http://archive.ambermd.org/201012/0313.html). It seems that it is still a memory issue. I have no idea if the problem could be solved by using more CPU cores. Any suggestions about it?
> Thanks in advance! Wei--------------------------------
>
>
> ----- 原始邮件 -----
> 发件人："Elvis Martis" <elvis.martis.bcp.edu.in>
> 收件人："lwstudy.sina.com" <lwstudy.sina.com>, AMBER Mailing List <amber.ambermd.org>
> 主题：RE: [AMBER] Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out
> 日期：2017年02月09日 20点08分
>
>
> HI,
> Entropy calculations are very memory hungry jobs. What amount of memory you have on your machine on which you are attempting the calculation? And how many cpu cores are you using?
> Best Regards
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
> -----Original Message-----
> From: wei [mailto:lwstudy.sina.com]
> Sent: Thursday, February 09, 2017 10:07 AM
> To: amber <amber.ambermd.org>
> Subject: [AMBER] Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out
> Dear all, I want to calculate entropy contribution of a relatively huge protein (18574 atoms) binding with it's ligand. I used AMBER14 to perform this computation (AMBER16 was tested as well). The task stopped while calculating the normal mode of the first frame. The error information is: ~/software/amber14/bin/nmode -O -i nmode_com.in -o nmode_com.1.out -c sanmin_com.1.restrt -p ./com_nobox.prmtop not running properly
> For details see: http://ambermd.org/Questions/mm_pbsa.html#calc_NM_entropy_not_running_properly
> Then I open nmode_com.1.out and see: *******************************************************
> Initiate the NMODE module of AMBER 8
> *******************************************************
> File generated by mm_pbsa.pl
> ntrun maxcyc ibelly drms
> 1 100 0 0.50E+01
> rcut scnb scee dielc idiel
> 99.00000 2.00000 1.20000 4.00000 0
> nsave dfpred bdwnhl smx emx alpha ndiag
> 20 0.01000 0.10000 0.08000 0.30000 0.80000 10
> ipol = 0
> i3bod = 0
> idecomp = 0
> nvect = 0
> Binary format used for input coords.
> | New format PARM file being parsed.
> | Version = 1.000 Date = 01/16/17 Time = 12:55:04 PARM file has the title:
> default_nameTotal memory required : -1749912621 real wordsTotal memory required : 175055910 integer wordsTotal memory required : 57116 4-character wordsMaximum nonbond pairs 173752760 Normal mode calculation stopped at this point and no further updates were found. Is this problem caused by the requirement of a huge memory? Have anyone meet this problem before? Looking forward your help. Thanks in advance. Regards,Wei--------------------------------
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 09 2017 - 17:30:02 PST
