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Re: [lammps-users] Using LAMMPS on Cloud Supercomputers
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Re: [lammps-users] Using LAMMPS on Cloud Supercomputers


From: Titusi Forum <titusiforum@...24...>
Date: Thu, 12 Oct 2017 00:21:01 -0700

Sorry, somehow I missed your message before.
Yes, LAMMPS on Kogence now runs only with MPI threads when on single node.
Please test it and let me know if it is working fine for you.

PS: I would like to know if it does improve performance. Also like to know if KOKKOS is desired.


On Thu, Aug 3, 2017 at 11:07 PM, Xavier Bidault <xavier.bidault@...6504...> wrote:
Hello,

Can we now use Lammps on Kogence with only MPI threads ? 

Xavier B.


-------- Message d'origine --------
De : Titusi Forum <titusiforum@...36.....24...>
Date : 26/07/2017 22:54 (GMT+01:00)
À : xavier.bidault@...36.....6504...
Objet : Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

Thanks. Good to know. I will take a look.

On Jul 26, 2017 1:52 PM, <xavier.bidault@...6504...> wrote:
Lammps is built to run with MPI, not OpenMP (to use OpenMP+MPI with Lammps, it will be with the package KOKKOS installed).
So yes, without KOKKOS, Lammps works better with MPI even on a single node.


De: "Titusi Forum" <titusiforum@...24...>
À: "xavier bidault" <xavier.bidault@...6504...>
Envoyé: Mercredi 26 Juillet 2017 22:45:04
Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

So if you are running simulations on a single node but single node is multi core cpu, then you are saying it's preferable to use MPI for multithreading instead of openMP?
Our experience Is that in a multimode environment MPI is better but in single node openMP multithreading is better. 

On Jul 26, 2017 1:29 PM, <xavier.bidault@...6504...> wrote:
Thank you too! This problem is now solved and i can see the created folder and what Lammps wrote inside of it.

However, i haven't noticed another bug until now. When i choose "n" CPU, the log file of Lammps indicates "n OpenMP per MPI + n MPI". The performances are then not good. This should be only "1 OpenMP per MPI + n MPI".
This bug appears also on the public "Lammps trial" project of Kogence.



De: "Titusi Forum" <titusiforum@...24...>
À: "xavier bidault" <xavier.bidault@...6504...>
Envoyé: Mercredi 26 Juillet 2017 21:10:12

Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

Thanks for your patience Xavier.
This was a bug on our side. When you created folder inside script, somehow nobody had read/write permissions on that folder. 
So our backend could not sync it. Strangely, we have never seen this problem with folders created inside scripts of other simulators.
We have fixed this problem now.
Try running your model now and let me know if it works OK now?

On Wed, Jul 26, 2017 at 10:52 AM, Titusi Forum <titusiforum@...33....24...> wrote:
I am having our backend technical person look at it.
I will get back to you before end of today.

On Wed, Jul 26, 2017 at 10:46 AM, <xavier.bidault@...6504...> wrote:
About 5 min.


De: "Titusi Forum" <titusiforum@...24...>
À: "xavier bidault" <xavier.bidault@...6504...>
Envoyé: Mercredi 26 Juillet 2017 19:18:10

Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

Do you know how long this simulation runs?

On Wed, Jul 26, 2017 at 10:11 AM, <xavier.bidault@...6504...> wrote:
Done. You have admin rights now.


De: "Titusi Forum" <titusiforum@...24...>
À: "xavier bidault" <xavier.bidault@...6504...>
Envoyé: Mercredi 26 Juillet 2017 19:08:53

Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

Xavier: Can you make me an "admin". "Admin" rights are needed to change software commands settings. 

On Wed, Jul 26, 2017 at 6:53 AM, <xavier.bidault@...6504...> wrote:
I don't know if i add you as admin or user. By default i added you as user. You should see the test project called H2O_ReaxFF.



De: "Titusi Forum" <titusiforum@...24...>
À: "xavier bidault" <xavier.bidault@...6504...>
Envoyé: Mercredi 26 Juillet 2017 14:58:32

Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

Xavier, #1 should not happen. Can you privately share your model using "Collaborate" tab with mukul@...7010...
As for #2, we fire a new machine for every run. /tmp is cleaned after every run. But we don't let machine shut until folder has been synced to webserver.

On Jul 25, 2017 11:10 PM, <xavier.bidault@...6504...> wrote:
Hello,

No it does not. In fact, when i do the lammps run followed by xterm in the same job, a "ls" in xterm allows me to see that the directory created by Lammps is there (if not, Lammps would have crashed), and contains the files created by the simulation. Indeed, it is in /tmp/userID/jobID. After the job (lammps + xterm) has stopped, i cannot see this created folder in the Dashboard.

I tried to run that job with only xterm. I am in the right /temp/user/jobID, but now, a "ls" does not show the formerly created directory. It was deleted. Probably when the visualization closed at the end of the previous complete job.

Xavier



De: "Titusi Forum" <titusiforum@...24...>
À: "xavier bidault" <xavier.bidault@...6504...>, "LAMMPS Users Mailing List" <lammps-users@...42...e.net>
Envoyé: Mardi 25 Juillet 2017 23:07:26
Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

Xavier:

You should make sure that all folder you create are under /tmp/userID/jobID folder.
We only sync this top level folder back to webserver.
Also, sync is not real time. Folders sync back after you stop the job.
Let me know if this solves your problem?



On Tue, Jul 25, 2017 at 10:35 AM, <xavier.bidault@...6504...> wrote:
Hello,

OK, i checked by myself. USER-REAXC is there.

But, in some of my script.in, i use shell commands of Lammps (shell mkdir and shell cd). It seems that the directory is created, the simulation runs, so Lammps find the created directory, but this created directory is not accessible from the Kogence Dashboard. Can this problem be fixed?

Regards,
Xavier Bidault


De: "xavier bidault" <xavier.bidault@...6504...>
À: "Titusi Forum" <titusiforum@...24...>
Envoyé: Samedi 22 Juillet 2017 19:26:00

Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

Thank you for your answers.

2) It is only minor changes to fit specific needs to create initial molecular configurations. Datafiles can be created offline and imported in the cloud afterwards.
5) What LAMMPS packages are installed? For example, these days, i'm using QEQ, RIGID, SHOCK and USER-REAXC.



De: "Titusi Forum" <titusiforum@...24...>
À: "xavier bidault" <xavier.bidault@...6504...>, "LAMMPS Users Mailing List" <lammps-users@...42...e.net>
Envoyé: Samedi 22 Juillet 2017 17:52:54
Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers

Xavier,

1. free platform has 8hrs wall time limit. If you are looking to run 2weeks with 64 cores, please send an email to admin@...7010....
2. you can always call LAMMPS as library from your code. Alternatively, do you want your code to be available to everyone. If yes, then we can install it. Otherwise we can do a private setup for you. 
3. yes, not on free platform. Pls contact us if you need it.
4. Yes, we run simulations AWS, Google, Azure as well as some smaller university based clusters. Tens of thousands of cores are generally available at any point of time. All of them have state of the art hardware, reliability and availability. 

On Sat, Jul 22, 2017 at 7:52 AM, <xavier.bidault@...6504...> wrote:
Hello,

I gave it a little try. It is a very interesting tool! Here are some questions :

1) What is the limit of time for one single simulation with LAMMPS? For instance, can it run for 2 weeks with 64 cores ?

2) Is there a way to compile and use my own modified version of LAMMPS?

3) Is there a way to use more than 128 cores?

4) What are the charateristic of this HPC clusters? Does it have a name? In the top 500? What is the total number of cores ?

Best regards,
Xavier Bidault


De: "Titusi Forum" <titusiforum@...24...>
À: "Rajeev Dhongar" <rajeev.dhongar@...24...>, "LAMMPS Users Mailing List" <lammps-users@...42...e.net>
Envoyé: Vendredi 21 Juillet 2017 20:36:32
Objet: Re: [lammps-users] Using LAMMPS on Cloud Supercomputers


Dear Rajeev:
If model is running well on 128 core node then it should run fine on all other nodes.
Can you use the "Collaborate" tab on kogence and share your model privately with mukul@...7010....
I would fix the issues and revert it back private to you.

First time you fire a node, it takes about 1.5minutes for interactive display to get active. Next time you fire a simulation on same node, it will come instantaneously. Also, note that your simulations do not stop/break if you close your browser or shut your machine. You can always reconnect to visualization as long as your job has not finished.

On Fri, Jul 21, 2017 at 9:45 AM, Rajeev Dhongar <rajeev.dhongar@...24...> wrote:
Hi, This is a very useful project. 
Thx for introducing us to Kogence.
I tried running some kappa models on your site.
Stranegely, code runs well on 128core node but crashes on 16core node.
Any idea what is wrong?
I tried using Octave to do some 3D graphics.
But I am not being able to connect to interactive graphics. Can you help.


Rajeev

On Thu, Jul 20, 2017 at 6:22 PM, Titusi Forum <titusiforum@...24...> wrote:
Dear LAMMPS Community,

This may be useful to some of you. Kogence is offering free cloud supercomputing for LAMMPS simulations of materials. You can fire simulations on machines as good as 128cores on single node or cluster many such nodes together. This is a nonprofit effort to match excellent opensource such as LAMMPS with cloud supercompute power.

There are some 30+ public LAMMPS projects that you can fork, modify and execute. Alternatively, you can also create your own project from scratch. You can keep project private or share it with collaborators. Details are provided here :-


If you run into any issues, please feel free to contact me at mukul AT alumni DOT stanford DOT edu. I would also appreciate any feedback you might have for me.


Regards,
Mukul


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