Dear amber users,
I'm experiencing a strange issue when running pmemd.cuda.
The error is:
Error: an illegal memory access was encountered launching kernel kNLSkinTest
I thought this was related to some problem in the simulation, i.e., something exploded or there was a very bad contact. However, when I ran the same simulation on another machine, it worked without a problem. Also, I repeated a simulation that worked fine before, and now it's also failing. So I'm starting to think it's related to the GPU or nvidia driver. I tried recompiling amber but the error still happen.
I'm using Amber24, with a 3060 nvidia gpu, with cuda 12.4 and driver 580. This happened in Ubuntu 22.04, then I updated to 24.04 and recompiled amber again, and nothing changed. I tried to use an old nvidia-driver (550, 560) with no success, so I couldn't test if this is something related to nvidia driver.
The protocol that I'm using is:
1.
Two step minimization --> ok
2.
Raising temperature --> ok
3.
Five restrained NPT steps to relax the system (gradually releasing the restraint in each step). It fails at the third step, i.e, first two are running fine.
4.
One unrestrained NPT. --> also failing (using the restart file obtained from the other machine)
Any clue? Thanks in advance
Tomás Cáceres
Bioquímico UC
Asistente de Investigación | Laboratorio de Simulación Computacional y Diseño de Fármacos
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Received on Sun Oct 19 2025 - 10:30:02 PDT
