[gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 63
Seketoulie Keretsu
sekekeretsu at gmail.com
Tue Nov 20 07:10:47 CET 2018
Dear Benson,
Thank you for answering .
I am using Centos 6. My current simulation time for protein-ligand
systems is about 1.6 ns/day. I am wondering if installing the GTX 1050
or GTX 970 can boost the output significantly (maybe 2 or 3 times more
?). I am installing just as mentioned below.
tar xfz gromacs-2018.4.tar.gz
cd gromacs-2018.4
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC
Do i need to pass some other options during the configuration for the GPU?
Many thanks.
Seke
On Mon, Nov 19, 2018 at 11:33 PM
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. generic hardware assembling for gromacs simulation
> (Seketoulie Keretsu)
> 2. Re: generic hardware assembling for gromacs simulation
> (Benson Muite)
> 3. VMD visualization of clusters (Rahma Dahmani)
> 4. Re: VMD visualization of clusters (Benson Muite)
> 5. Re: generic hardware assembling for gromacs simulation
> (pbuscemi at q.com)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 19 Nov 2018 22:25:00 +0900
> From: Seketoulie Keretsu <sekekeretsu at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] generic hardware assembling for gromacs
> simulation
> Message-ID:
> <CAKY9VjCc9gu6ZSm5TL=4A7-eAQ=cChvceihiUgZSUJUVgENBdQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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.
>
> Sincerely,
> Seke
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 19 Nov 2018 13:29:12 +0000
> From: Benson Muite <benson.muite at ut.ee>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] generic hardware assembling for gromacs
> simulation
> Message-ID: <357c7c1f-cd34-1423-3099-b1f85e04b5bd at ut.ee>
> Content-Type: text/plain; charset="utf-8"
>
> This should probably work. What operating system are you using? Are you
> using a later build of Gromacs, such as 2018.4 ? IF so have you tried
> the instructions here:
>
> http://manual.gromacs.org/documentation/current/install-guide/index.html
>
> Have you tried building an CUDA example programs?
>
> On 11/19/18 2:25 PM, Seketoulie Keretsu wrote:
> > 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.
> >
> > Sincerely,
> > Seke
>
> ------------------------------
>
> Message: 3
> Date: Mon, 19 Nov 2018 14:57:32 +0100
> From: Rahma Dahmani <rahma.dahmani at fst.utm.tn>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] VMD visualization of clusters
> Message-ID:
> <CADeDvBGj6cXqRBezR1FUN3un9B30ABS+RORy1bm0fOa7MR5hQg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi GMX users,
>
> After visualization of one of my clusters generated by g-cluster command in
> gromacs , i couldn't change the representation type in VMD from lines to
> new cartoon or secondary structure....
> so i am wondering if this is related to the structure of cluster ? ... why
> i can visualize the cluster only in lines ?
>
> Thank you!
>
> --
>
>
>
>
>
>
> *Rahma Dahmani Doctorante en CHIMIE Unit? de Recherche: Physico-Chimie des
> Mat?riaux ? l'?tat condens?, Laboratoire de Chimie Th?orique et
> Spectroscopie Mol?culaireUniversit? de Tunis El Manar, Facult? des Sciences
> de Tunis Campus Universitaire Farhat Hached - BP n ? 94 - Rommana 1068,
> Tunisie T?l: (+216) 28151042*
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 19 Nov 2018 14:15:29 +0000
> From: Benson Muite <benson.muite at ut.ee>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] VMD visualization of clusters
> Message-ID: <b0545d09-88a8-af10-239f-0d5cdbec600a at ut.ee>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Rahma,
>
> Have you tried any other visualization programs? Is there an example
> file one could try for visualization?
>
> Benson
>
> On 11/19/18 2:57 PM, Rahma Dahmani wrote:
> > Hi GMX users,
> >
> > After visualization of one of my clusters generated by g-cluster command in
> > gromacs , i couldn't change the representation type in VMD from lines to
> > new cartoon or secondary structure....
> > so i am wondering if this is related to the structure of cluster ? ... why
> > i can visualize the cluster only in lines ?
> >
> > Thank you!
> >
>
> ------------------------------
>
> Message: 5
> Date: Mon, 19 Nov 2018 08:31:27 -0600
> From: <pbuscemi at q.com>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] generic hardware assembling for gromacs
> simulation
> Message-ID: <000a01d48014$8ec16fd0$ac444f70$@q.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Seke,
>
> 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
> https://itsfoss.com/ubuntu-official-ppa-graphics/
>
> Rerun update BUT NOT UPGRADE
>
> Then install the appropriate driver for the 1050 with 'sudo apt install
> nvidia-390'
> 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
> task.
>
> 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
> Paul
>
>
> -----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
> Keretsu
> 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.
>
> Sincerely,
> Seke
> --
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