[gmx-users] generic hardware assembling for gromacs simulation

pbuscemi at q.com pbuscemi at q.com
Mon Nov 19 15:31:34 CET 2018


Yes, you can do a build with the components you have. The I5 ( 4760 ?)  with
4 cores and no other threads  is not particularly fast but should work
The 1050 has some 640 or 768 cores depending on the version and will produce
approximately a factor of 5x over the CPU alone.
You will need at least 8gig Ram

After you install linux, run the following to get the latest  packages to
save some later headaches:
		'sudo ap-get  update'  then
		'sudo apt-get upgrade ' - this will take some time - go get
some coffee

Install Cuda following
https://linoxide.com/linux-how-to/install-cuda-ubuntu/   this will probably
install CUDA 9.1 which is sufficient.  You do not need to use the Nvidia web
site as the installation guide - unless you want to be tortured. CUDA is now
part of the ppa repository. This is a major blessing.  Check the CUDA
install with nvcc --version

Install the latest version of the repository

Rerun update  BUT NOT UPGRADE

Then install the appropriate driver  for the 1050 with   'sudo apt install
  I do not know if the latest nvidia 400 series  drivers will work with the
1050 but v390 probably will.  You may have to use 3v84.  You do not need to
uninstall the prior driver, the newer installations will take care of that

Then  READ and follow the basic instructions from Gromacs for installation. 
The essential items beyond the basic installation are:
	Add the instruction to use GPU
	check that the version of g++ and gcc match that installed with
CUDA.  You can have all the versions g++-5 to g++-7 in the same lib
location.  CUDA and Gromacs will find them if you state the location during
the build.

There are many web sites with detailed instructions but if you are diligent
( and a bit lucky ) you can go from installing linux to running Gromacs in
about 2 hours

Good luck

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Seketoulie
Sent: Monday, November 19, 2018 7:25 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] generic hardware assembling for gromacs simulation

Dear Users.

I apologise this this not exactly an GROMACs simulation question.

I am a student and currently I trying to build a linux system for gromacs
simulation. I have seen some materials about utilizing GPUs and
multiprocessor but I can't fully understand some problems. I have a system
available with the configuration below:

GPU:  Zotac 1050ti 4gb GPU

Processor: i5 quad core 3.10ghz
RAM: 8GB DDR 4 Corsair ram
Storage: 250 GB had
[also Gigabyte motherboard , 650w power supply, 500 GB external ]

Would it be possible to utilize this GPUs to enhance the MD simulation
performance? If possible would you suggest/hint how to go about this?
Would it be possible to maximise the use of the resources if the OS is
installed with proper configurations?

Thanking you.

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