Yambo via Docker - Revision history

Daniele at 09:36, 23 February 2024

2024-02-23T09:36:21Z

← Older revision		Revision as of 09:36, 23 February 2024
Line 2:		Line 2:
	An alternative to get the Yambo code is to install the Yambo container in your machine and this can be done in few steps:		An alternative to get the Yambo code is to install the Yambo container in your machine and this can be done in few steps:

	* Install the docker platform (Linux or Mac). Follow the instruction in the docker [https://docs.docker.com/engine/install/ website].		* Install the docker platform (Linux or Mac). Follow the instruction in the docker [https://docs.docker.com/engine/install/ website].

	It is possible to run Docker by a normal user without the sudo privileges. In order to do that you have to add your username to the group "docker" (suggested on Linux!).		It is possible to run Docker by a normal user without the sudo privileges. In order to do that, you have to add your username to the group "docker" (suggested on Linux!).

	For Linux users:		For Linux users:
Line 20:		Line 20:
	If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.		If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.

	* Download the script file "[https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun drun]" that will help you ~~hiding~~ the many options needed by the container:		* Download the script file "[https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun drun]" that will help you to hide the many options needed by the container:

	wget https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun		wget https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun
Line 54:		Line 54:
	should provide in output the help for yambo usage.		should provide in output the help for yambo usage.

	* To delete the container images downloaded you can use this command:		* To delete the container images downloaded, you can use this command:

	docker image rm <image_name>		docker image rm <image_name>

	To remove all the stopped containers use this command:		To remove all the stopped containers, use this command:

	docker system prune		docker system prune

Nicolaspallanzani at 10:09, 1 April 2022

2022-04-01T10:09:32Z

← Older revision		Revision as of 10:09, 1 April 2022
Line 45:		Line 45:
	-np N # Number of MPI tasks for a parallel run (default 0, i.e. serial run)		-np N # Number of MPI tasks for a parallel run (default 0, i.e. serial run)
	-t N # Number of threads per process/task (default 1)		-t N # Number of threads per process/task (default 1)
	--env-file FILE # to set the path of an environment file (default ./env.txt)		--env-file FILE # set the path of an environment file (default ./env.txt)
			-c IMAGE:TAG # set the name and tag of the container image (default maxcentre/yambo:5.1.0_gcc9)

	If the yambo container is working correctly this command		If the yambo container is working correctly this command

Nicolaspallanzani at 08:37, 31 March 2022

2022-03-31T08:37:27Z

← Older revision		Revision as of 08:37, 31 March 2022
Line 34:		Line 34:
	./drun -i		./drun -i

	this command will pull the container if not already done and will create a file named env.txt needed by the container to run Yambo.		this command will pull the container (needs ~1.8GB in your filesystem) if not already done and will create a file named env.txt needed by the container to run Yambo.

	* Now you can run yambo like in this example:		* Now you can run yambo like in this example:
Line 40:		Line 40:
	./drun yambo -F yambo.in -J yambo.out		./drun yambo -F yambo.in -J yambo.out

	~~Some useful~~ options of the script drun:		These are the options of the script drun:

	~~-np N # n. of MPI tasks for a parallel run~~
	~~-t N # n. of threads per task~~
	~~--env-file FILE # to use a different environment file~~
	-i # container initialization		-i # container initialization
			-np N # Number of MPI tasks for a parallel run (default 0, i.e. serial run)
			-t N # Number of threads per process/task (default 1)
			--env-file FILE # to set the path of an environment file (default ./env.txt)

	If the yambo container is working correctly this command		If the yambo container is working correctly this command

Nicolaspallanzani at 21:56, 30 March 2022

2022-03-30T21:56:46Z

← Older revision		Revision as of 21:56, 30 March 2022
Line 40:		Line 40:
	./drun yambo -F yambo.in -J yambo.out		./drun yambo -F yambo.in -J yambo.out

	Some useful options of the script drun ~~are~~:		Some useful options of the script drun:

	-np N # n. of MPI tasks for a parallel run		-np N # n. of MPI tasks for a parallel run

Nicolaspallanzani at 20:35, 30 March 2022

2022-03-30T20:35:53Z

← Older revision		Revision as of 20:35, 30 March 2022
Line 20:		Line 20:
	If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.		If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.

	* Download the script file "[https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun drun]" that will help you:		* Download the script file "[https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun drun]" that will help you hiding the many options needed by the container:

	wget https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun		wget https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun

Nicolaspallanzani at 20:33, 30 March 2022

2022-03-30T20:33:08Z

← Older revision		Revision as of 20:33, 30 March 2022
Line 40:		Line 40:
	./drun yambo -F yambo.in -J yambo.out		./drun yambo -F yambo.in -J yambo.out

	If the ~~yambo container is working correctly you should obtain~~:		Some useful options of the script drun are:

	.~~/drun yambo~~		-np N # n. of MPI tasks for a parallel run
			-t N # n. of threads per task
	yambo~~: cannot access CORE database (SAVE/db1 and/or SAVE/wf)~~		--env-file FILE # to use a different environment file
			-i # container initialization

			If the yambo container is working correctly this command

	./drun yambo -h		./drun yambo -h

Nicolaspallanzani at 16:29, 30 March 2022

2022-03-30T16:29:11Z

← Older revision		Revision as of 16:29, 30 March 2022
Line 20:		Line 20:
	If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.		If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.

	* Download the script file drun		* Download the script file "[https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun drun]" that will help you:

			wget https://raw.githubusercontent.com/nicspalla/yambo-containers/main/drun

	then give the file execute privileges:		then give the file execute privileges:

Nicolaspallanzani at 16:13, 30 March 2022

2022-03-30T16:13:00Z

← Older revision		Revision as of 16:13, 30 March 2022
Line 20:		Line 20:
	If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.		If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.

	* ~~Pull~~ the ~~Yambo container:~~		* Download the script file drun

	~~docker pull maxcentre/yambo:5.1.0_gcc9~~

	* You are done. To run Yambo into the container:

	~~docker run -ti --user $(id -u):$(id -g) \~~
	~~--mount type=bind,source="$(pwd)",target=/tmpdir \~~
	~~-e OMP_NUM_THREADS=4 \~~
	~~maxcentre/yambo:5.1.0_gcc9 \~~
	~~yambo -F yambo.in -J yambo.out~~

	~~Otherwise (suggested!), copy and paste the code below in a~~ file~~, i.e called~~ drun~~.sh:~~

	~~#!/bin/bash~~
	~~threads=1~~
	~~environment="--env-file env.txt"~~
	~~container="maxcentre/yambo:5.1.0_gcc9"~~
	~~command_prefix=""~~

	~~### MAIN ###~~
	~~while [[ $1 == -* ]]; do~~
	~~case $1 in~~
	~~-t \| --threads ) threads=$2~~
	~~shift 2~~
	;;
	~~-c \| --container) container=$2~~
	~~shift 2~~
	;;
	~~-np \| --nprocess ) command_prefix="mpirun --use-hwthread-cpus -np $2"~~
	~~shift 2~~
	;;
	~~--env-file ) environment="--env-file $2"~~
	~~shift 2~~
	;;
	~~-i \| --init ) docker pull ${container}~~
	~~docker run -ti --user $(id -u):$(id -g) \~~
	~~--mount type=bind,source="$(pwd)",target=/scratch \~~
	~~${container} cat /opt/spack/env.txt > env.txt~~
	~~exit 0~~
	;;
	* ) echo "Error: \"$1\" unrecognized argument."
	~~exit 1~~
	~~esac~~
	~~done~~

	~~docker run -ti --user $(id -u):$(id -g) \~~
	~~--mount type=bind,source="$(pwd)",target=/scratch \~~
	~~-e OMP_NUM_THREADS=${threads} ${environment} \~~
	~~${container} ${command_prefix} $@~~

	then give the file execute privileges:		then give the file execute privileges:

	chmod +x drun~~.sh~~		chmod +x drun

	Move (or copy) this file in the directory where you want to use Yambo and use it as prefix of your Yambo calculation.		Move (or copy) this file in the directory where you want to use Yambo and use it as prefix of your Yambo calculation.

	First you have to initialize the environment needed by the container:		* First you have to initialize the environment needed by the container:

	./drun~~.sh~~ -i		./drun -i

	this command will pull the container if not already done and will create a file named env.txt needed by the container to run Yambo.		this command will pull the container if not already done and will create a file named env.txt needed by the container to run Yambo.

	Now you can run yambo like in this example:		* Now you can run yambo like in this example:

	./drun~~.sh~~ yambo -F yambo.in -J yambo.out		./drun yambo -F yambo.in -J yambo.out

	If the yambo container is working correctly you should obtain:		If the yambo container is working correctly you should obtain:

	./drun~~.sh~~ yambo		./drun yambo

	yambo: cannot access CORE database (SAVE/db1 and/or SAVE/wf)		yambo: cannot access CORE database (SAVE/db1 and/or SAVE/wf)

	./drun~~.sh~~ yambo -h		./drun yambo -h

	should provide in output the help for yambo usage.		should provide in output the help for yambo usage.

	To delete the container images downloaded you can use this command:		* To delete the container images downloaded you can use this command:

	docker image rm <image_name>		docker image rm <image_name>

Nicolaspallanzani at 16:02, 30 March 2022

2022-03-30T16:02:10Z

← Older revision		Revision as of 16:02, 30 March 2022
Line 96:		Line 96:

	should provide in output the help for yambo usage.		should provide in output the help for yambo usage.

			To delete the container images downloaded you can use this command:

			docker image rm <image_name>

			To remove all the stopped containers use this command:

			docker system prune

Nicolaspallanzani at 15:56, 30 March 2022

2022-03-30T15:56:51Z

← Older revision		Revision as of 15:56, 30 March 2022
Line 41:		Line 41:

	### MAIN ###		### MAIN ###
	while \[\[ $1 == -* \]\]; do		while [[ $1 == -* ]]; do
	case $1 in		case $1 in
	-t \| --threads ) threads=$2		-t \| --threads ) threads=$2