Gmx mdrun with and without GPU support

User discussions
1

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.

2

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.

3

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

4

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

My guess is that your computer is overheating.