[gmx-users] WG: Issue with CUDA and gromacs

[Benson Muite]

The redmine ticket you mention gives output obtained from an execution with verbose output:

gmx mdrun -deffnm md200ns -v

and

gmx mdrun -deffnm md200ns -v -nb gpu -pme cpu

First option fails, but gives a source code line number where to check things. Second one runs. Build uses
-DCMAKE_BUILD_TYPE=RelWithDebug. Is it possible to get more information using these run options?

On 1/30/19 7:29 PM, Tafelmeier, Stefanie wrote:

To your question:
For the trials with newer Gromacs >2016 versions we simply use (as I understood it is not necessary to target the 6.1 with this versions)
cmake .. -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on

for the trials with older gromacs < 2018 Versions we used:
cmake .. -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on GMX_CUDA_TARGET_SM=6.1 GMX_CUDA_TARGET_COMPUTE=6.1

Could it be, that the combination of CUDA 9.2 (or 10), gromacs 2019 and gcc 7.3.0 is making some trouble?
Does anyone have experience with this?

Many thanks in advance for the answer,
Steffi



-----Ursprüngliche Nachricht-----
Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Im Auftrag von Benson Muite
Gesendet: Mittwoch, 30. Januar 2019 18:13
An: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Betreff: Re: [gmx-users] WG: Issue with CUDA and gromacs

What is your cmake build command?

Have you tried to specify compute capabilities?

http://manual.gromacs.org/documentation/2019/install-guide/index.html#cuda-gpu-acceleration

GMX_CUDA_TARGET_SM=6.1

GMX_CUDA_TARGET_COMPUTE=6.1

References:

https://developer.nvidia.com/cuda-gpus

https://www.myzhar.com/blog/tutorials/tutorial-nvidia-gpu-cuda-compute-capability/

On 1/30/19 6:20 PM, Tafelmeier, Stefanie wrote:

Please excuse, the tables didn't work, I hope this is better:



Dear all,



We are facing an issue with the CUDA toolkit.

We tried several combinations of gromacs versions and CUDA Toolkits. No Toolkit older than 9.2 was possible to try as there are no driver for nvidia available for a Quadro P6000.





Gromacs  +  CUDA  =>  Error message



2019  +  10.0  =>  gmx mdrun:

Assertion failed:

Condition: stat == cudaSuccess

Asynchronous H2D copy failed



2019  +  9.2  =>  gmx mdrun:

Assertion failed:

Condition: stat == cudaSuccess

Asynchronous H2D copy failed



2018.5  +  9.2  +  gmx mdrun: Fatal error:

HtoD cudaMemcpyAsync failed: invalid argument



5.1.5  +  9.2  =>Installation make: nvcc fatal   : Unsupported gpu architecture 'compute_20'*



2016.2  +  9.2  =>  Installation make: nvcc fatal   : Unsupported gpu architecture 'compute_20'*





*We also tried to set the target CUDA architectures as described in the installation guide (manual.gromacs.org/documentation/2019/install-guide/index.html). Unfortunately it didn't work.

Performing simulations on CPU only always works, yet of cause are more slowly than they could be with additionally using the GPU.

The issue #2761 (https://redmine.gromacs.org/issues/2762) seems similar to our problem.

Even though this issue is still open, we wanted to ask if you can give us any information about how to solve this problem?



Many thanks in advance.

Best regards,

Stefanie Tafelmeier





Further details if necessary:

The workstation:

2 x Xeon Gold 6152 @ 3,7Ghz (22 K, 44Th, AVX512) Nvidia Quadro P6000 with 3840 Cuda-Cores



The simulations system:

Long chain alkanes (previously used with gromacs 5.1.5 and CUDA 7.5 - worked perfectly)








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