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munmap_chunk(): invalid pointer #247

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yuntaoyang opened this issue Oct 4, 2022 · 2 comments
Open

munmap_chunk(): invalid pointer #247

yuntaoyang opened this issue Oct 4, 2022 · 2 comments

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@yuntaoyang
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Hi APBS developers,

Describe the bug
I ran APBS using a PDB file for a protein complex. But APBS was aborted and got the following error message. How to fix this issue?

log file
This executable compiled on May 30 2019 at 19:36:46
Parsing input file Myo1_Myo1.in...
rank 0 size 1...
read
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from Myo1_Myo1.pqr.
63126 atoms
Centered at (5.216e+01, 5.426e+01, -7.410e+00)
Net charge -4.00e+01 e
Preparing to run 2 PBE calculations.
CALCULATION #1: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 93259.980 MB total, 93259.980 MB high water
Using cubic spline charge discretization.
Grid dimensions: 545 x 801 x 929
Grid spacings: 0.777 x 0.807 x 0.811
Grid lengths: 422.617 x 645.682 x 752.906
Grid center: (52.160, 54.262, -7.410)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Vbuildband: dpbfa problem: 1
Vbuildband: leading principle minor not PD...
Vbuildops: Changing your mgsolv to iterative
Total electrostatic energy = -NAN kJ/mol
Calculating forces...
CALCULATION #2: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
munmap_chunk(): invalid pointer
Aborted (core dumped)

To Reproduce
Steps to reproduce the behavior:

  1. pdb2pqr30 --apbs-input Myo1_Myo1.in --whitespace Myo1_Myo1.pdb Myo1_Myo1.pqr
  2. apbs Myo1_Myo1.in

Server: CentOS

Thank you so much for your help!

Best,
Yuntao Yang

@sobolevnrm
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Hello --

How much memory does the server have?

Thank you

@yuntaoyang
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Hello --

How much memory does the server have?

Thank you

Hi Nathan,

The total memory is about 6000 GB. The available memory was about 3000 GB when I ran the program.

Best,
Yuntao

@yuntaoyang yuntaoyang reopened this Oct 5, 2022
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