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atzberg / mango-selm

Simulation methods for particle systems, materials, and complex fluids with fluctuating hydrodynamics approaches (stochastic immersed boundary methods, stochastic eulerian-lagrangian methods) [interfaces with LAMMPS MD package]
http://atzberger.org/
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"Invalid data file section: Angles" error running FENE dimer example with LAMMPS (7 Feb 2014) and Mango-Selm 1.0.1.alpha-linux #21

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Compile LAMMPS (7 Feb 2014) with Mango-Selm 1.0.1.alpha-linux and LAMMPS 
packages listed below and MPI stubs

What is the expected output? What do you see instead?
Expected: FENE dimer example runs successfully.

Instead: "Invalid data file section: Angles"
LAMMPS (7 Feb 2014)
Reading data file ...
  triclinic box = (-202.5 -202.5 -202.5) to (202.5 202.5 202.5) with tilt (0 0 0)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  scanning bonds ...
  1 = max bonds/atom
ERROR: Invalid data file section: Angles (../read_data.cpp:231)

What version of the product are you using? On what operating system?
Mango-Selm 1.0.1.alpha-linux and LAMMPS 7 feb 2014. RHEL6 Linux.

Please provide any additional information below.

LAMMPS packages used for compilation are listed below.  As noted, the molecule 
package is included, as required by the Mango-Selm installation instructions.

Couldn't run provided binary due to glibc 2.14 dependency.

Installed YES: package ASPHERE
Installed YES: package BODY
Installed YES: package CLASS2
Installed YES: package COLLOID
Installed YES: package DIPOLE
Installed YES: package FLD
Installed  NO: package GPU
Installed YES: package GRANULAR
Installed  NO: package KIM
Installed YES: package KSPACE
Installed YES: package MANYBODY
Installed YES: package MC
Installed  NO: package MEAM
Installed YES: package MISC
Installed YES: package MOLECULE
Installed  NO: package MPIIO
Installed YES: package OPT
Installed YES: package PERI
Installed  NO: package POEMS
Installed  NO: package REAX
Installed YES: package REPLICA
Installed YES: package RIGID
Installed YES: package SHOCK
Installed YES: package SRD
Installed  NO: package VORONOI
Installed YES: package XTC

Original issue reported on code.google.com by dbarajas...@gmail.com on 6 Feb 2014 at 10:31

GoogleCodeExporter commented 9 years ago 
The "Angles" feature is associated with the MOLECULE package.  It appears your 
code is not compiling with the glibc library.  Perhaps this is resulting in an 
error in linking the MOLECULE package.  Try a clean compile of LAMMPS after 
fixing the glibc linking issue...   Another solution may be to use an older 
base version of LAMMPS.  We run with March 2013 for example.

Original comment by atzb...@gmail.com on 16 Feb 2014 at 5:44