[gmx-users] genbox_mpi and "Error: Invalid number of threads defined"

lswierczewski . luk.swierczewski at gmail.com
Fri Jul 25 17:20:29 CEST 2014

Dear GROMACS Users,

I have a problem when running genbox_mpi.

Below is information from the console.

[lswiercz at nostromo ~/gromacs]$ srun --nodes 1 genbox_mpi -cp
1AKI_newbox.gro -cs spc216.gro -p topol.top -o solvated.gro
srun: job 5026 queued and waiting for resources
srun: job 5026 has been allocated resources
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                  :-)  /opt/gromacs/4.6.3/bin/genbox_mpi  (-:

Option     Filename  Type         Description
 -cp 1AKI_newbox.gro  Input, Opt!  Structure file: gro g96 pdb tpr etc.
 -cs     spc216.gro  Input, Opt!, Lib. Structure file: gro g96 pdb tpr etc.
 -ci     insert.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -o   solvated.gro  Output       Structure file: gro g96 pdb etc.
  -p      topol.top  In/Out, Opt! Topology file

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    19      Set the nicelevel
-box         vector 0 0 0   Box size
-nmol        int    0       Number of extra molecules to insert
-try         int    10      Try inserting -nmol times -try times
-seed        int    1997    Random generator seed
-vdwd        real   0.105   Default van der Waals distance
-shell       real   0       Thickness of optional water layer around solute
-maxsol      int    0       Maximum number of solvent molecules to add if
                            they fit in the box. If zero (default) this is
-[no]vel     bool   no      Keep velocities from input solute and solvent

Reading solute configuration
Containing 2194 atoms in 207 residues
Initialising van der waals distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 4x4x4 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 13824 residues
Calculating Overlap...
box_margin = 0.315
Removed 0 atoms that were outside the box
1587-119 Error: Invalid number of threads defined.

Why does the system returns the "Error: Invalid number of threads defined"?

Best Regards

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