# Simulations hang on AMD CPU system

**URL:** <https://gromacs.bioexcel.eu/t/simulations-hang-on-amd-cpu-system/5127>\
**Category:** User discussions\
**Tags:** mdrun, installation-error\
**Created:** [October 28, 2022, 4:07pm UTC](https://gromacs.bioexcel.eu/t/simulations-hang-on-amd-cpu-system/5127 "2022-10-28T16:07:48Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Chase](https://avatars.discourse-cdn.com/v4/letter/c/76d3ee/32.png) [@Chase](https://gromacs.bioexcel.eu/u/Chase)\
**Post date:** [October 28, 2022, 4:07pm UTC](https://gromacs.bioexcel.eu/t/simulations-hang-on-amd-cpu-system/5127/1 "2022-10-28T16:07:48Z")

</div>

GROMACS version: 2022.3  
GROMACS modification: No

I am attempting to run ~150 ns simulations that take ~12 hours on a single-node AMD CPU system, but the simulations sometimes hang after ~8 hours of run time (i.e. the system resources remain occupied but the simulation fails to progress). This is the same issue reported [here](https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/c2dRlO5U/gmx-users-simulation-freezes-but-the-job-keeps-on-running), but my understanding is that the work-around solution of using intelmpi is incompatible with my system.

For reference, here is my GROMACS and system info:

```auto
GROMACS version: 2022.3
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: disabled
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/clang Clang 10.0.0
C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler: /usr/bin/clang++ Clang 10.0.0
C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -Weverything -Wno-c++98-compat -Wno-c++98-compat-pedantic -Wno-source-uses-openmp -Wno-c++17-extensions -Wno-documentation-unknown-command -Wno-covered-switch-default -Wno-switch-enum -Wno-extra-semi-stmt -Wno-weak-vtables -Wno-shadow -Wno-padded -Wno-reserved-id-macro -Wno-double-promotion -Wno-exit-time-destructors -Wno-global-constructors -Wno-documentation -Wno-format-nonliteral -Wno-used-but-marked-unused -Wno-float-equal -Wno-conditional-uninitialized -Wno-conversion -Wno-disabled-macro-expansion -Wno-unused-macros -fopenmp=libomp -O3 -DNDEBUG

Running on 1 node with total 32 cores, 64 processing units
Hardware detected:
  CPU info:
    Vendor: AMD
    Brand: AMD Ryzen Threadripper 3970X 32-Core Processor
    Family: 23 Model: 49 Stepping: 0
    Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
  Hardware topology: Basic
    Packages, cores, and logical processors:
    [indices refer to OS logical processors]
      Package 0: [0 40] [1 9] [2 10] [3 11] [4 12] [5 13] [6 14] [7 15] [8 16] [17 25] [18 26] [19 27] [20 28] [21 29] [22 30] [23 31] [24 32] [33 41] [34 42] [35 43] [36 44] [37 45] [38 46] [39 47] [48 56] [49 57] [50 58] [51 59] [52 60] [53 61] [54 62] [55 63]
    CPU limit set by OS: -1 Recommended max number of threads: 64

```

I compiled GROMACS with clang because I experienced the make check issue that was reported [here](https://gromacs.bioexcel.eu/t/gromacs-2022-1-installation-mdrun-mpi-coordination-constraints-test-failed-for-make-check/4311).

Any advice would be much appreciated - thank you for your help!

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<div class="post-metadata">

**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\
**Post date:** [November 1, 2022, 11:44am UTC](https://gromacs.bioexcel.eu/t/simulations-hang-on-amd-cpu-system/5127/2 "2022-11-01T11:44:02Z")

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> [@Chase](#):
>
> This is the same issue reported [here](https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/c2dRlO5U/gmx-users-simulation-freezes-but-the-job-keeps-on-running), but my understanding is that the work-around solution of using intelmpi is incompatible with my system.

While you are seeing the same symptom, the cause is unlikely to be the same.

> [@Chase](#):
>
> I compiled GROMACS with clang because I experienced the make check issue that was reported [here](https://gromacs.bioexcel.eu/t/gromacs-2022-1-installation-mdrun-mpi-coordination-constraints-test-failed-for-make-check/4311).
> 
> Any advice would be much appreciated - thank you for your help!

You could verify that the mdrun hanging does occur with:

- using gcc
- using OpenMP only, i.e. -ntmpi 1 -ntomp 32 ot 64 (assuming you are using the default domain decomposition)
- using lib-MPI (install MPI and configure with `-DGMX_MPI=ON`).

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<div class="post-metadata">

**Author:** ![pimooni](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pimooni/32/2056_2.png) [@pimooni](https://gromacs.bioexcel.eu/u/pimooni)\
**Post date:** [April 11, 2023, 1:01am UTC](https://gromacs.bioexcel.eu/t/simulations-hang-on-amd-cpu-system/5127/3 "2023-04-11T01:01:37Z")

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Hi Chase,

Have you figured out any solution for this freeze?

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<div class="post-metadata">

**Author:** ![Chase](https://avatars.discourse-cdn.com/v4/letter/c/76d3ee/32.png) [@Chase](https://gromacs.bioexcel.eu/u/Chase)\
**Post date:** [April 11, 2023, 1:28am UTC](https://gromacs.bioexcel.eu/t/simulations-hang-on-amd-cpu-system/5127/4 "2023-04-11T01:28:05Z")

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No unfortunately not - I decided to change simulation engines rather than continuing to troubleshoot this.