please advice on this error message. I did a default conda installation on Linux Mint 22.1 (essentially Ubuntu 24.04 LTS) with CUDA 12.4.
unigbsa-pipeline -i UNG2_3FCI_protein.pdb -l UNG2_3FCI_ligand.sdf -o gbsa_test.out
08/13/2025 20:34:02 PM - INFO - Build protein topology.
08/13/2025 20:34:07 PM - INFO - Build ligand topology: UNG2_3FCI_ligand
08/13/2025 20:34:14 PM - INFO - Running energy minimization: UNG2_3FCI_ligand
gmx mdrun -v -deffnm minim -nt 1 -ntmpi 1
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing.
There were 3 NOTEs
There was 1 WARNING
GROMACS reminds you: "Nobody ever complained a seminar was too easy to understand." (Ken Dill)
Analysing residue names:
There are: 1 Other residues
There are: 223 Protein residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing Protein...
The largest distance between excluded atoms is 0.419 nm between atom 48 and 56
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x56, spacing 0.114 0.114 0.116
Estimate for the relative computational load of the PME mesh part: 0.67
This run will generate roughly 0 Mb of data
:-) GROMACS - gmx mdrun, 2025.2-conda_forge (-:
Executable: /home/evehom/Programs/miniconda3/envs/gbsa/bin.AVX2_256/gmx
Data prefix: /home/evehom/Programs/miniconda3/envs/gbsa
Working dir: /home/evehom/Data/Sandbox/GBSA/UNG2_3FCI_ligand/complex.GMX
Command line:
gmx mdrun -v -deffnm minim -nt 1 -ntmpi 1
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
Reading file minim.tpr, VERSION 2025.2-conda_forge (single precision)
-------------------------------------------------------
Program: gmx mdrun, version 2025.2-conda_forge
Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 797)
Fatal error:
The total number of threads requested (1) does not match the thread-MPI ranks
(1) times the OpenMP threads (4) requested
For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
-------------------------------------------------------
Traceback (most recent call last):
File "/home/evehom/Programs/miniconda3/envs/gbsa/lib/python3.9/site-packages/unigbsa/pipeline.py", line 155, in single
minimgro, outtop = engine.run_to_minim(grofile, topfile,
File "/home/evehom/Programs/miniconda3/envs/gbsa/lib/python3.9/site-packages/unigbsa/simulation/mdrun.py", line 385, in run_to_minim
minipdb = self.gmx_minim(ionspdb, topfile, mdpfile=os.path.join(MDPFILESDIR, 'minim.mdp'), nt=nt)
File "/home/evehom/Programs/miniconda3/envs/gbsa/lib/python3.9/site-packages/unigbsa/simulation/mdrun.py", line 200, in gmx_minim
outfile = self._mdrun(outtpr, nt)
File "/home/evehom/Programs/miniconda3/envs/gbsa/lib/python3.9/site-packages/unigbsa/simulation/mdrun.py", line 80, in _mdrun
raise Exception('ERROR run mdrun %s. See the logfile for details %s'%(tprfile, os.path.abspath(self.gmxlog)))
Exception: ERROR run mdrun minim.tpr. See the logfile for details /home/evehom/Data/Sandbox/GBSA/UNG2_3FCI_ligand/complex.GMX/gromacs.log
08/13/2025 20:34:14 PM - WARNING - Failed to run simulation for ligand: UNG2_3FCI_ligand
Hi,
please advice on this error message. I did a default conda installation on Linux Mint 22.1 (essentially Ubuntu 24.04 LTS) with CUDA 12.4.
Thank you/Evert