Hi,
Typically, the allocation failure message means the program does not have access to enough resources to compete the calculation. Normal mode analysis requires a significant amount of memory/RAM for its calculations (especially for large systems), so my guess is the program doesn’t not have access to enough memory for the requested nmode calculation.
-Bill
> On Apr 7, 2024, at 4:27 AM, SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <amber.ambermd.org> wrote:
>
> Hello,
>
> I am calculating entropy using nmode and I am getting the following error
> with com.prmtop. I have used the same file for MMPBSA analysis and it
> worked fine. But, It is showing errors with entropy calculation.
>
> File "/home/apps/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
>
> app.run_mmpbsa()
>
> File
> "/home/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>
> self.calc_list.run(rank, self.stdout)
>
> File
> "/home/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
>
> calc.run(rank, stdout=stdout, stderr=stderr)
>
> File
> "/home/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 323, in run
>
> Calculation.run(self, rank, stdout=self.output % rank)
>
> File
> "/home/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
>
> self.prmtop))
>
> CalcError: /home/apps/amber18/bin/mmpbsa_py_nabnmode failed with prmtop
> com.prmtop!
>
> Error occured on rank 0.
>
> Exiting. All files have been retained.
>
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
> FATAL: allocation failure in vector()
>
> FATAL: allocation failure in vector()
>
> FATAL: allocation failure in vector()
>
> FATAL: allocation failure in vector()
>
>
> Here is the input file-
>
>
> Input file for running entropy calculations using NMode
>
> &general
>
> endframe=20000, keep_files=0,
>
> verbose=1, use_sander=1
>
> /
>
> &nmode
>
> nmstartframe=10200, nmendframe=20000,
>
> nminterval=200,
>
> maxcyc=50000, drms=0.0001,
>
> /
>
>
> Kindly help me in resolving the issue.
>
>
> Thank you
>
> --
> *Yours Sincerely*
> *Subhasmita Mahapatra*
> *Ph.D. Scholar (PMRF)*
> *Computational Biophysics Group*
> *Department of Biosciences and Biomedical Engineering*
> *Indian Institute of Technology, Indore*
> *Madhya Pradesh, India (453552)*
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Received on Sun Apr 07 2024 - 06:00:02 PDT
