Hello,
I am new to MD simulations, Ubuntu and also for GPU powered computing. I had run some basic simulations using gromacs earlier but with a non GPU system. Now I have upgraded my work station with a nvidia rtx2070 gpu and want to run some intense simulations. I have installed the appropriate graphic drivers and also CUDA and ubuntu is displaying the installed graphics card and display details (with command sudo nvidia-smi for which the screenshot is attached). I have installed gromacs 2018 with cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON.
When i invoke mdrun the program is getting killed with the message mentioned below (also attached the screenshot for more details)
Reading file em.tpr, VERSION 2018 (single precision)
No option -multi
Using 1 MPI thread
Using 12 OpenMP threads
1 GPU auto-selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
Killed
Can anyone suggest me where i am doing wrong and please suggest me the right commands to utilize the GPU for my simulations.
Yes plz goto setting and disable hyper threading , Intel has a lot problem so a am using only AMD radon processor. Ubuntu also not fully functional OS check error log there should me vector memory dump error in paging or pipeline still error sustain plz send me error log.
Dear Sandipta Kumar Sahu,
Thanks for your suggestion. I searched for hyper threading in my system but i was unable to find it. my system is with processor: AMD Ryzen 5 2600 Six-Core Processor, 16GiB System Memory, Nvidia Rtx 2070 GPU and ASUSTeK PRIME B450M-A motherboard running with ubuntu 16.04 lts.
I tried different ways by following some tutorials but nothing worked. I need your help in running a successful simulation. I am attaching my .mdp files (i decreased the values to get faster results ) and target protein along with error log generated during energy minimization. I am also including the gromacs commands i used to test my simulation in gromacs 2018 which worked for gromacs 5.12 version which i got installed using sudo apt-get install gromacs command.
Please help solve my problem....
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