EP 9 | Compiling Installing GROMACS for Linux system with NVIDIA GPUs (RTX, GTX, etc.)
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- Опубликовано: 28 окт 2022
- Hi,
I am Dr. Dweipayan Goswami,
Welcome to my RUclips channel "Learn at ease"
In this video I have explained how to install Gromacs by deep compilation for systems running on Linux having NVIDIA GPUs
Before you begin this tutorial I recommend you to run following commands in terminal of Linux (Ubuntu) to update, upgrade and install libraries for this compilation
sudo apt update
sudo apt upgrade
sudo apt install gcc
sudo apt install cmake
sudo apt install build-essential
sudo apt install libfftw3-dev OR
sudo apt-get install -y libfftw3-dev
ONCE THE ABOVE COMMANDS ARE INTERED AND LINUX SYSTEM IS UPDATED, PROCEED TO INSTALL GROMACS BY FOLLOWING TUTORIAL
Codes used in this video will be found at Github :
github.com/DweipayanG/GROMACS...
Timestamps
2:50 Installing NVIDIA CUDA TOOLKIT 11.8 installation
9:40 Downloading Gromacs compressed compiler from official website
9:11 Gromacs deep compilation process
15:30 Using CMAKE command
23:20 Executing gmx commands from any working directory by making use of source command
25:55 Checking GPU and CUDA support enabled or not !
28:10 Method to uninstall compiled GROMACS when if needed.
Thank you for the tutorial! Very well explained and worked properly.
Thank you Sir, this tutorial helped so much!!!
Thanks Dweipayan for this elaborate explanation. Going to be a great help for the community. Keep up the good work!
Thanks for appreciating
Have you worked with with plumed? It will be great help if you can create a tutorial on installation of plumed patched gromacs.
Dear my teacher, it was a very nice, explanatory narrative. Thanks to you, I had a smooth and clean installation. I'm following you ;)
Thank you 😊
thank you for your wonderful video sir. during nvt equilibration step using (gmx mdrun -deffnm nvt) this command line I'm stuck with segment fault core dump. how can i proceed with next Equilibration, Phase 2 step
Dr Dweipayan,
Thank you for your excellent tutorial!
Question for the source command, is there a reason you don't permanently assign it through bashrc?
BTW I am very new to Ubuntu. Thank you in advance for all your guidance.
Yes definately you can
hello sir, your tutorial is very helpful and informative. but i am facing an issue while compiling the cuda toolkit for gromacs .
i am getting this issue can you help me out
CMake Error at api/nblib/CMakeLists.txt:60 (add_library):
Target "nblib" links to target "CUDA::cudart" but the target was not found.
Perhaps a find_package() call is missing for an IMPORTED target, or an
ALIAS target is missing?
Sir, is it possible to install in windows subsystem for Linux? I want to use GPU power for running gromacs simulation in WSL
Thanks! Can you please specify best hardware specifications for running gromacs for a linux system. Also how much time it will take for 200 ns simulation for lysozyme? Thank you in advance.
For the GPU i use it takes 2 days for 200 ns ... Any recently launched gpu within gtx or rtx series will work good... It all depends on your budget what you choose... The only catch is that gpu should be not soo old .. minimum 4 gb one i would prefer..
@@DweipayanG great! Okk so gpu is the key here! Thank you so much 🙏🏼what about Ram and SSD. If you can guide on that, will be highly helpful 🙏🏼
@@BasicScienceSeries SSD is preferable over HDD, try to have 512GB one and for RAM 16GB is preferable but try to have at least 8GB of DDR4.
Hello Sir!
Thank you so much for making this series of tutorials. They are extremely helpful for someone like me who is just getting started in the field of bio-informatics.
Can you please tell me your system specs? I'm installing it on my laptop which has an Intel i7-10870H CPU and an RTX 3060 GPU (6 GB). How fast do you think an average protein-ligand MD simulation will run on these hardware specs?
Bro how long does it took for you to simulate a protein-ligand complex???
@@asif4557 I have done a few MD simulations so far. What I have learnt is that the answer to your question depends on 2 factors, one, total number of atoms in your system (protein + ligand + solvent) and, two, how long do you want to simulate the system for. A 5000 atom system simulated for 50 ns took about 8 hours in my laptop.
@@sarthakmohanty997 that's really great🤩, previously I did it in a conventional way utilizing my CPU, and the time is taken for the NVT equilibration alone 17 hours and my protein-ligand system size is around 40K atoms so why I concerned a lot about my MD simulation yet my system configuration was AMD ryzen 9 coupled with RTX 3060 so after this GPU acceleration i hope, I can rest peace for sometimes, lol😂
Thanks Dr. Dweipayan this VDO useful for me. Can you tell me which GPU name used in this VDO?
RTX 2060
Hello sir , thank you for your wonderful videos , they are really helpful , i have one query i have a WSL2 in my system and inbuilt GTX 1650 graphics card is there , but i am not able to do the GPU based GROMACS installation , that CUDA driver is it works with WSL2 please let me know thank you
I have tried it with WSL2.
Hello, Thanks for this tutorial. I followed the steps until I try to compile gromacs-2024.2. The program reported error during cmake. It reads like this: 'CMake Error at /usr/share/cmake-3.28/Modules/CMakeDetermineCUDACompiler .cmake:270 (message): Failed to detect a default CUDA architecture.' could you please tell me how to fix it?
Sir, Is this tutorial valid for Ubuntu OS, which is a Virtual Box?
Thanks for your very informative video but I am getting Cmake error configuration file unable to detect cuda compiler
Although I have installed cuda toolkit
Sir I tried to install gromacs using this method but in using make check command following two test failed. 64 - MDrun Tests Two Ranks
65- MDrun Mpi Tests
How to solve this issue?
Thanks and regards
Hi Dr
Thanks for your tutorial.
Please I am installing Gromacs and this problem occured.
Please sir how can I solve this problem: CMake Error at api/nblib/CMakeLists.txt:60 (add_library):
Target "nblib" links to target "CUDA::cudart" but the target was not found.
Perhaps a find_package() call is missing for an IMPORTED target, or an
ALIAS target is missing?
thanks in advance
I have little idea , ask chat gpt same question it will probably give solutions to resolve issue .
@@DweipayanG Thanks
I used your code to install gpu in ubuntu 20.04 but at the time of md run its says GPU not detected..but after command gmx --version its shows gpu=cuda please help me with these sir
I have HP victus i5(12th gen 8 gbil/512gb ssd) nvdia geforce gtx 1650 windows 11 .. can I install gromacs? And bn can it work
Absolutely yes ... But you have to install linux (probably ubuntu or linux mint) and then you can install gromads. It is advisable to install linux on external ssd or on 128bg 3.0 pen drive which can work as external ssd ..
Unable to install gromacs on nvida a16 gpu. Installed cuda 12, camake latest..
You need to check that gromacs is compatible with your gpu or not
Hello Sir, please help me in installation as I am unable to install
I can't untill i kno exact problem !!
i am getting error when using this command: sudo apt-get -y install cuda
Now it says, "E: Unable to correct problems, you have held broken packages"
what do i do :(
I am using Pop_OS 22.04
Try redownloading the Cuda installer files
@@DweipayanG Man, It worked, thank you so much for this tutorial and the guidance. I can now perform simulations much faster then i was doing it earlier.
Welcome.. Thats great
Sir im finding thir error
CMake Error at cmake/gmxManageCuda.cmake:116 (enable_language):
No CMAKE_CUDA_COMPILER could be found.
Tell CMake where to find the compiler by setting either the environment
variable "CUDACXX" or the CMake cache entry CMAKE_CUDA_COMPILER to the full
path to the compiler, or to the compiler name if it is in the PATH.
Call Stack (most recent call first):
CMakeLists.txt:699 (include)
I followed all the steps but still its saying "Fatal error: Cannot run short-ranged nonbonded interactions on a GPU because no GPU is
detected."
May b your graphic card will not be complicated
@@DweipayanG its nvidia 650
If cuda is not supported then it will now work
Dr, when I install the CUDA toolkit 11.8 I had an error :
dpkg: error: unknown option -�
Type dpkg --help for help about installing and deinstalling packages [*];
Use 'apt' or 'aptitude' for user-friendly package management;
Type dpkg -Dhelp for a list of dpkg debug flag values;
Type dpkg --force-help for a list of forcing options;
Type dpkg-deb --help for help about manipulating *.deb files;
Options marked [*] produce a lot of output - pipe it through 'less' or 'more' !
There is error in dpkg package in your linux system
Try upgrading and updating linux
@@DweipayanG thank you so much
@@DweipayanG
Dr, it remains the same error. please can you help me.
Then pl check the installer file of CUDA tool kit is properly downloaded or not or check its not an incomplete download or something ...
askubuntu.com/questions/1248699/cant-install-or-remove-anything-on-18-04-cause-of-dpkg-error/1248773#1248773
Check this
It seems dpkg package error
Sir im finding this error
CMake Error at cmake/gmxManageCuda.cmake:116 (enable_language):
No CMAKE_CUDA_COMPILER could be found.
Tell CMake where to find the compiler by setting either the environment
variable "CUDACXX" or the CMake cache entry CMAKE_CUDA_COMPILER to the full
path to the compiler, or to the compiler name if it is in the PATH.
Call Stack (most recent call first):
CMakeLists.txt:699 (include)
Did you fix your error?