Installing PRISMS-PF using Docker

[Stephen DeWitt]

Hello all,

Recently, we started supporting a new way to install PRISMS-PF using Docker. This a great way to get PRISMS-PF working quickly on your machine without adding too much performance overhead. If you aren't familiar with Docker, you can get a quick overview here. A few people that have tried it have said that it is much easier than installing deal.II from scratch. For optimal performance on a cluster, your best bet still is a traditional installation (at least until we get Singularity working with PRISMS-PF).

Until I get the installation instructions on the new PRISMS-PF website, here's how to do the Docker installation:

The steps:

1. Install Docker.
2. Create a directory on your computer to hold the PRISMS-PF applications folder (e.g. $ mkdir ~/DockerWorkspace) and go to that directory (e.g. $ cd ~/DockerWorkspace)
3. Clone the PRISMS-PF repository ($ git clone https://github.com/prisms-center/phaseField)
4. Get the PRISMS-PF Docker image ($ docker pull stvdwtt/prismspf:prismspf)
5. Now, launch the Docker container, linking the PRISMS-PF applications folder in the container to your local one: (e.g.  $ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications stvdwtt/prismspf:prismspf)

Now you should have a working PRISMS-PF environment. The core library will already be compiled, but you'll need to compile any applications that you want to use. Any changes that you make or output files that you create should be found at ~/DockerWorkspace on your host computer.

To get out of the container, type:

$ exit

If you have any questions or any suggestions on how to improve these instructions, please post a response here.

Best,

Steve

[Kamalnath Kadirvel]

Hi Steve,

Does PRISMS-PF support Singularity now ? Our HPC cluster provides only Singularity for managaing containers

-Kamal

[stv...@gmail.com]

Hi Kamal,

To my knowledge, no one has tried PRISMS-PF with Singularity yet (although I would be happy to be wrong on that). In the Singularity docs there's a section on interoperability between Docker and Singularity:

https://sylabs.io/guides/3.6/user-guide/singularity_and_docker.html#overview

That might be worth a try. One note of caution though -- for a different code I tried following the steps listed there and I ran into a number of issues with the Singularity image, so it might not be as easy as it looks. On the other hand, a colleague of mine recently tried it with his code and it went smoothly. If you give it a try, let us know how it goes.

Thanks,

Steve

[David Montiel Taboada]

Thank you, Steve. I will look into this.

David

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[Kamalnath Kadirvel]

Thank you, Steve.

I created a singularity container from docker image: singularity build prisms-pf-core.img docker://stvdwtt/prismspf:prismspf  

But I don't know how to link my local applications folder to the one given in the containers.

"Now, launch the Docker container, linking the PRISMS-PF applications folder in the container to your local one: (e.g.  $ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications stvdwtt/prismspf:prismspf)"

I am getting this error message for now.

Regards,

Kamal

[David Montiel Taboada]

---------- Forwarded message ---------
From: David Montiel Taboada <dmon...@umich.edu>
Date: Thu, Oct 29, 2020 at 11:56 PM
Subject: Re: [prisms-pf-users] Re: Installing PRISMS-PF using Docker
To: Kamalnath Kadirvel <kkamal...@gmail.com>

Hello Kamalnath,

What is the error message you are referring to?

By the way, we have updated the docker image for PRISMS-PF v.2.1.2 (prismspf/prismspf:2.1.2)

Please refer to this page: https://prisms-center.github.io/phaseField/doxygen_files/install_prismspf.html

to see the updated installation (although this may not be related to the problem you are facing). 

Best,

David

To view this discussion on the web visit https://groups.google.com/d/msgid/prisms-pf-users/463358ca-b3f9-44ec-b12b-99a8b9879323n%40googlegroups.com.

[Kamalnath Kadirvel]

I am sorry that I forgot to paste the image. The above image is the error I am getting.

-Kamal

[Kamalnath Kadirvel]

Hi David and Steve,

Finally, I was able to get PRISMS-PF running with Singularity. The main problem was environment variable DEAL_II_DIR which defaulted to "~/dealii-v8.4.2". I changed it to "/home/dealii/dealii-v8.4.2". Then I was to able to compile and run the example applications. 

-Kamal

[sina shokuhi]

hello all

what is mean of 

1. Get the PRISMS-PF Docker image ($ docker pull stvdwtt/prismspf:prismspf)?

thanks

On Tuesday, May 1, 2018 at 9:38:54 AM UTC-4 stv...@gmail.com wrote:

[David Montiel Taboada]

Hello Sina,

 It is the command to download the PRISMS-PF image from the Docker hub. To do so you need to

1) Open a terminal

2) Create a directory on your computer to hold the PRISMS-PF applications folder

3) Go to that directory on your terminal

4) Type:

docker pull prismspf/prismspf:2.1.2

(The symbol "$" represents the prompt)

Note that the command is different from the one you posted because the docker image was updated a few months ago. 

You can get the complete updated instructions here (see the Docker Installation section): https://prisms-center.github.io/phaseField/doxygen_files/install_prismspf.html

I hope this helps, but let me know if it is still not clear.

Best,

David

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[Richard Zhang]

HI Steve,

I have just installed PRISMS-PF through docker method following the user manual. I have had no issues running the examples in the application folders and each steps seemed to be all right (cmake . ; make debug;  mpirun -n 1 main). However, after the simulations were over, I just could not find the output files in the example folders or anywhere else. Appreciate it if you could help.

Thanks,

Rich

On Tuesday, May 1, 2018 at 9:38:54 AM UTC-4 stv...@gmail.com wrote:

[David Montiel Taboada]

Hello Richard, 

Do you not even see the output files when you are inside the container?

If you do see them, it may be that you have not correctly linked to your local applications folder. 

Have you verified that you included the "-v" option and the correct local path in step 5 of the Docker section in this page of the manual? For example:

$ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications prismspf/prismspf:2.1.2

I hope this helps, 

Best,

David

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[Richard Zhang]

Hi David,

Thanks  for your kind reply. I have re-installed docker and got PRISM-PF docker image again, following extactly what the manual indicates, including the specific command you questioned, i.e., sudo docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications prismspf/prismspf:2.1.2.

Unfortunately, it doesn't help. Again everything works fine but there were no output files at the end of simulations. Any other suggestions?

Thanks,

Rich

[David Montiel Taboada]

OK, I will look into this and get back to you.

 Can I ask, what type of operation system you are using (Mac OS, Linux or Windows)? Ana what version?

Thanks!

[Richard Zhang]

Thanks David. I am using Linux Ubuntu 18.04.4. I have also attached a screenshot of the final screen after running an example in case it might be helpful.

[David Montiel Taboada]

Thank you, Richard, 

I will look into it tomorrow. 

I am just curious, can you also show me a screenshot of the files in that directory? Just type "ls -lhtr" right after the simulation ends.

Thank you, 

David

[Richard Zhang]

David,

Thanks for your help. Please see the screenshot below. I see the output files in the virtual folder. Previously I only looked at the local folder and couldn't find the files (screenshot is also attached). So my question becomes how I can see the files in the local folder?

[Richard Zhang]

Hi David, after last email, I tried again to launch a new container by sudo docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications prismspf/prismspf:2.1.2. This time, after cmake ., make debug and mpi -n 1 main, the simulation won't run (screenshot is as below:


[David Montiel Taboada]

Hello Richard, 

That is odd. Did you do anything different or modified the cahnHilliard application? I noticed that there is a message that there are 0 constants, which is odd because the cahnHilliard application has two constants.

Could you also send me the path where you have PRISMS-PF installed? Not inside the container but on your computer.

At this point it might be easier to have a Zoom meeting. Would you have some time to meet on Monday?

Best,

David

[Richard Zhang]

Hi David,

No, I didn't do anything to the examples. I tried a few other examples and got similar error that said parameter.in could not be open and there are 0 constants. One example is in the screenshot. Also the path where I have PRISMS-PF installed is also shown in the screenshot.

I will be available after 3pm Monday. Please let me know what time works for you.

Thanks,

Rich