No GPU is detected on yggdrasil


My GROMACS jobs on yggdrasil all failed last night. I resubmitted jobs this afternoon. One runs normally with gpu007, but another one only ran for a few sec on gpu008 and failed.

Some lines of .out file:

Program:     gmx mdrun, version 2023.1
Source file: src/gromacs/taskassignment/findallgputasks.cpp (line 85)
MPI rank:    0 (out of 8)

Fatal error:
Cannot run short-ranged nonbonded interactions on a GPU because no GPU is

[1707228579.325814] [gpu008:1539109:0]           ib_md.c:1234 UCX  WARN  IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued.
[1707228579.325821] [gpu008:1539109:0]           ib_md.c:1235 UCX  WARN  IB: data corruption might occur when using registered memory.

My batchfile:

#SBATCH --job-name="*"
#SBATCH --mail-type=ALL
#SBATCH --mail-user=*
#SBATCH --time=12:00:00
#SBATCH --ntasks-per-core=1
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1
#SBATCH --partition=shared-gpu
#SBATCH --gpus=1
module load GCC/11.3.0
module load OpenMPI/4.1.4
module load GROMACS/2023.1-CUDA-11.7.0

srun gmx_mpi mdrun -ntomp 8 -s *.tpr -deffnm * -nsteps -1 -v -pin on -nb gpu -noappend -cpi *.cpt


Dear @Jingze.Duan

I think I got it! Your job was running fine on gpu007.yggdrasil and no GPUs are seen when same job is running on gpu008.yggdrasil.

Gpu007 is equipped with 8 x Titan RTX cards and gpu008 is equipped with 8x V100 cards (see hpc:hpc_clusters [eResearch Doc]). The V100 has a compute capability of 7.0. Until 06th of December 2023, all the software using GPUs we compiled were compiled for compute capability : 6.0,6.1,7.5,8.0,8.6. We added the 7.0 since then, but not all the software were recompiled.

We saw later the following statement from Nvidia:

Each CUBIN file targets a specific compute capability version and is forward- compatible only with CUDA architectures of the same major version number; e.g., CUBIN files that target compute capability 1.0 are supported on all compute- capability 1.x (Tesla) devices but are not supported on compute-capability 2.0 (Fermi) devices.

It means we no GPU kernel were compatible for this card.

We are recompiling GROMACS right now.

Thank you for your help! My jobs are all fine now.

Dear @Jingze.Duan

Gromac has been recompiled.