# Gmx mdrun with and without GPU support

**URL:** <https://gromacs.bioexcel.eu/t/gmx-mdrun-with-and-without-gpu-support/310>\
**Category:** User discussions\
**Created:** [June 14, 2020, 6:13pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-with-and-without-gpu-support/310 "2020-06-14T18:13:13Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mw00847](https://avatars.discourse-cdn.com/v4/letter/m/ecd19e/32.png) [@mw00847](https://gromacs.bioexcel.eu/u/mw00847)\
**Post date:** [June 14, 2020, 6:13pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-with-and-without-gpu-support/310/1 "2020-06-14T18:13:13Z")

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GROMACS version:gmx, version 2020

GROMACS modification: Yes/No  
Here post your question

two questions,

- do I need to uninstall gmx to reinstall with GPU support? or can I just update CMake? if so what is the cleanest way to remove gmx from ubuntu?

- would running mdrun from the basic installation without GPU support possibly cause crashes on longer runs?

additional

have been running gromacs using ’ Quick and dirty installation’ (without CPU support).

when running some of the extended tutorials, computer began crashing.

updated graphics card (XFX Radeon), worked well for first few runs no problem, but has now begun crashing.

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**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\
**Post date:** [June 14, 2020, 10:54pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-with-and-without-gpu-support/310/2 "2020-06-14T22:54:50Z")

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You should post exactly what commands you have used and what the exact output is (copy and paste, do not type it out). “Crashing” doesn’t provide any useful information.

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**Author:** ![mw00847](https://avatars.discourse-cdn.com/v4/letter/m/ecd19e/32.png) [@mw00847](https://gromacs.bioexcel.eu/u/mw00847)\
**Post date:** [June 15, 2020, 5:33am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-with-and-without-gpu-support/310/3 "2020-06-15T05:33:25Z")

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OK, when I say crashed - the PC turns off and restarts. Would gromacs provide a log file if this is the case?

Below looks like the job that has failed,

GROMACS: gmx mdrun, version 2020  
Executable: /usr/local/gromacs/bin/gmx  
Data prefix: /usr/local/gromacs  
Working dir: /home/mat/gromacs/OPA\_NPG  
Process ID: 5277  
Command line:  
gmx mdrun -deffnm npt -v

GROMACS version: 2020  
Verified release checksum is c8f31ed8bc66001c3c8d6e5ddb61aab8bb1d400b5f5dba93c53473fa79c1a50a  
Precision: single  
Memory model: 64 bit  
MPI library: thread\_mpi  
OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64)  
GPU support: disabled  
SIMD instructions: AVX\_256  
FFT library: fftw-3.3.8-sse2-avx-avx2-avx2\_128  
RDTSCP usage: enabled  
TNG support: enabled  
Hwloc support: disabled  
Tracing support: disabled  
C compiler: /usr/bin/cc GNU 9.3.0  
C compiler flags: -mavx -fexcess-precision=fast -funroll-all-loops  
C++ compiler: /usr/bin/c++ GNU 9.3.0  
C++ compiler flags: -mavx -fexcess-precision=fast -funroll-all-loops -fopenmp

Running on 1 node with total 4 cores, 8 logical cores  
Hardware detected:  
CPU info:  
Vendor: Intel  
Brand: Intel® Xeon® CPU E5-1620 v2 @ 3.70GHz  
Family: 6 Model: 62 Stepping: 4  
Features: aes apic avx clfsh cmov cx8 cx16 f16c htt intel lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic  
Hardware topology: Basic  
Sockets, cores, and logical processors:  
Socket 0: [0 4] [1 5] [2 6] [3 7]  
…

Energies (kJ/mol)  
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14  
7.23909e+03 8.17915e+03 4.21270e+03 1.97360e+03 6.04172e+03  
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.  
5.90837e+04 4.53050e+03 -6.37956e-04 -6.30953e+04 1.70867e+03  
LJ recip. Potential Kinetic En. Total Energy Conserved En.  
-2.99717e+04 -9.78776e+01 1.92780e+04 1.91801e+04 7.66620e+04  
Temperature Pres. DC (bar) Pressure (bar)  
2.95836e+02 -1.05489e-04 -3.05719e+02

Writing checkpoint, step 896200 at Sun Jun 14 10:09:49 2020

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<div class="post-metadata">

**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\
**Post date:** [June 15, 2020, 6:15am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-with-and-without-gpu-support/310/4 "2020-06-15T06:15:06Z")

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That is a hardware issue, not a GROMACS, software one.

My guess is that your computer is overheating.