# Gromacs Production Runs taking very long somtimes stopped running

**URL:** <https://gromacs.bioexcel.eu/t/gromacs-production-runs-taking-very-long-somtimes-stopped-running/8539>\
**Category:** User discussions\
**Created:** [March 7, 2024, 2:25am UTC](https://gromacs.bioexcel.eu/t/gromacs-production-runs-taking-very-long-somtimes-stopped-running/8539 "2024-03-07T02:25:23Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Aman](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aman/32/2886_2.png) [@Aman](https://gromacs.bioexcel.eu/u/Aman)\
**Post date:** [March 7, 2024, 2:25am UTC](https://gromacs.bioexcel.eu/t/gromacs-production-runs-taking-very-long-somtimes-stopped-running/8539/1 "2024-03-07T02:25:23Z")

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GROMACS version: 2024  
GROMACS modification: Yes

**System Description:**

- Protein simulation in water.
- Systems range from 76,000 to 800,000 atoms.
- Two single node servers, one with a GPU.
- Pre-production run from pdb2gmx to npt executed seamlessly.

**Problem Description:**

- Production run starts smoothly and runs fast.
- However, it freezes at some point (around 600,000 to 1,000,000 steps).
- The process appears to be stuck, not progressing further, without crashing.

System Settings:

- Data prefix: `/usr/local/gromacs`
- Working directory: `/data/emanuel/HECW1/WT`
- Process ID: 169340
- Command line:

gmx mdrun -deffnm md\_0\_1 -ntomp 32 -nb gpu -pin on

**GROMACS Version:**

- Version: 2024.1
- Precision: Mixed
- Memory model: 64-bit
- MPI library: thread\_mpi
- OpenMP support: Enabled (GMX\_OPENMP\_MAX\_THREADS = 128)
- GPU support: CUDA
- NBNxM GPU setup: Super-cluster 2x2x2 / Cluster 8
- SIMD instructions: AVX2\_128
- CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2\_128
- GPU FFT library: cuFFT
- Multi-GPU FFT: None
- RDTSCP usage: Enabled
- TNG support: Enabled
- Hwloc support: Disabled
- Tracing support: Disabled
- C compiler: `/usr/bin/cc GNU 9.4.0`
- C compiler flags: `-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG`

Notes:

- The issue occurs during the production run phase.
- The simulation appears to halt at some point without progressing.
- No error messages or crashes are reported.
- Further investigation is needed to identify the root cause of the freezing. Potential areas for investigation include system resources, potential memory leaks, or algorithmic issues

Input Parameters:  
integrator = md  
tinit = 0  
dt = 0.002  
nsteps = 5000000  
init-step = 0  
simulation-part = 1  
mts = false  
mass-repartition-factor = 1  
comm-mode = Linear  
nstcomm = 100  
bd-fric = 0  
ld-seed = -5517954  
emtol = 10  
emstep = 0.01  
niter = 20  
fcstep = 0  
nstcgsteep = 1000  
nbfgscorr = 10  
rtpi = 0.05  
nstxout = 0  
nstvout = 0  
nstfout = 0  
nstlog = 5000  
nstcalcenergy = 100  
nstenergy = 5000  
nstxout-compressed = 5000  
compressed-x-precision = 1000  
cutoff-scheme = Verlet  
nstlist = 10  
pbc = xyz  
periodic-molecules = false  
verlet-buffer-tolerance = 0.005  
verlet-buffer-pressure-tolerance = 0.5  
rlist = 1

Your help will be highly appreciated.  
Thanks

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**Author:** ![leiming](https://avatars.discourse-cdn.com/v4/letter/l/b77776/32.png) [@leiming](https://gromacs.bioexcel.eu/u/leiming)\
**Post date:** [May 29, 2024, 9:56pm UTC](https://gromacs.bioexcel.eu/t/gromacs-production-runs-taking-very-long-somtimes-stopped-running/8539/2 "2024-05-29T21:56:52Z")

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Hi, Aman. I have the same question. My process has frozen at the same step twice.  
step 66485500, will finish Thu May 30 21:59:14 2024^Zb F 14% pme/F 0.98 F 0.92  
I’m not sure whether the issue is due to software settings or hardware problems.