docker_single_zone

This is the Webnucleo single-zone reaction network docker image repository. You first need to have installed docker and be able to run it. You can verify that docker is properly installed, for example, by running the Hello, World image in an appropriate shell. To do so, type:

docker run hello-world

With docker correctly installed, you can build and run the single-zone network image.

Steps to build and run the default docker image.

First clone the repository. Type:

git clone http://github.com/mbradle/docker_single_zone

Now change into the cloned directory. Type:

cd docker_single_zone

If you have previously cloned the repository, you can update by typing:

git pull

Now build the image. Type:

docker build -t single_zone:default .

The docker image that gets built is single_zone:default. The :default is a tag that allows you to distinguish other single zone images. Of course you can provide your own name for both the image and the tag.

Now create a directory for the input and output. Type:

mkdir work

mkdir work/input

mkdir work/output

cp input/run.rsp work/input/

Now download the necessary data. First, record the current location. Type

pwd

In the instructions below, you should simply be able to use the commands verbatim (most likely, you will simply cut and paste). If that does not work, replace the ${PWD} present with the string that is returned by the pwd command. Now download the data. Type:

docker run -it -v ${PWD}/work/input/data_pub:/data_directory -e VAR=data webnucleo/data_download

Now edit work/input/run.rsp. Run the calculation. For example, type:

docker run -it -v `PWD`/work/input:/input_directory -v `PWD`/work/output:/output_directory -e VAR=@/input_directory/run.rsp single_zone:default

The output will be in the directory work/output. Note that `PWD` is equivalent to ${PWD}.

One can add options into the response file run.rsp or directly into the command line. For example, type:

docker run -it -v `PWD`/work/input:/input_directory -v `PWD`/work/output:/output_directory -e VAR="@/input_directory/run.rsp --t_end 1." single_zone:default

This calculation cuts off the expansion after 1 second instead of the default 1.e6 seconds.

Linux users may find they need to prepend sudo to run docker. For example, they may need to type:

sudo docker run -it -v ${PWD}/work/input/data_pub:/data_directory -e VAR=data webnucleo/data_download

Here are some notes on running without sudo that may be of interest.

Steps to list possible options or an example execution.

To get a help statement for a single-zone network docker image, type:

docker run -e VAR=--help single_zone:default

The output lists a usage statement for the underlying single-zone network code. Any of the suggested commands can be entered as input through the VAR variable. For example, you can type:

docker run -e VAR=--example single_zone:default

to get the example execution (of the underlying single-zone network code). The options in the example execution would be added to the response file or the command line (through VAR). To get the listing of all possible options, type:

docker run -e VAR="--prog all" single_zone:default

The input to VAR is between quotes to ensure that it is recognized as a single input string. To get options for a particular class, select that class as input to the program_options option. For example, type:

docker run -e VAR="--prog network_time" single_zone:default

Steps to build with a different master.h file.

First, it's useful to prune any dangling containers by typing:

docker system prune

The command

docker system prune -a

will clear out everything and start over if you prefer.

Be sure that you have the single_zone:default image available. Type:

docker build -t single_zone:default .

Next, download the default master.h to the $PWD directory. Type:

docker run -it -v ${PWD}:/header_directory -e HEADER_COPY_DIRECTORY=/header_directory single_zone:default

Edit master.h. Now rebuild, but set the WN_USER flag:

docker build -t single_zone:tag --build-arg WN_USER=1 .

where tag is a tag to distinguish the new image from the default. You can now edit work/input/run.rsp appropriately. Then run as before using the new tag.

As an example, edit master.h. In particular, change the lines in the file that read

 #include "hydro/single_zone/standard/detail/default.hpp"
 #include "hydro/single_zone/standard/hydro.hpp"

to instead read

 #include "hydro/single_zone/trajectory/detail/time_t9_rho.hpp"
 #include "hydro/single_zone/trajectory/hydro.hpp"

and then run

docker build -t single_zone:time_t9_rho --build-arg WN_USER=1 .

This new docker image will run a calculation in which the temperature and density are determined by interpolation from a file. Create a file (call it my_file.txt) in the work/input directory that reads, for example

 0  10.  1.e8
 1  5.   1.e7
 2  5.   1.e7
 3  2.   1.e4
 4  2.   1.e4
 5  0.1  1.e2

This file gives the time (in seconds in column 1), the t9 (temperature in billions of K in column 2), and the density (in g/cc in column 3). Now edit the file work/input/run.rsp to read

--interp_file /input_directory/my_file.txt
--network_xml /input_directory/data_pub/my_net.xml
--nuc_xpath "[z <= 30]" --xml_steps 2
--output_xml /output_directory/out.xml
--init_mass_frac "{h1; 0.5}" "{n; 0.5}"

Now run the code by typing:

docker run -it -v `PWD`/work/input:/input_directory -v `PWD`/work/output:/output_directory -e VAR="@/input_directory/run.rsp" single_zone:time_t9_rho

How to force a rebuild of one of your images.

If you suspect that the underlying code has been updated since your latest docker build, you can force a rebuild by using the --no-cache option. For example, you can type:

docker build --no-cache -t single_zone:default .

This will force docker to pull any new changes to the underlying codes down before rebuilding.

Using Docker Hub for your images.

Once you have an image that you would like to share with your collaborators, you can set up a repository on Docker Hub. You can push images to the repository that others can then pull down and use. This site provides more information.