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Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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munmap_chunk(): invalid pointer #247

Open yuntaoyang opened 1 year ago

yuntaoyang commented 1 year ago

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 commented 1 year ago

Hello --

How much memory does the server have?

Thank you

yuntaoyang commented 1 year ago

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