A basic user tool to execute simple Docker containers in user space without requiring root privileges. udocker enables basic download and execution of Docker containers by non-privileged users in Linux systems where Docker is not available. It can be used to access and execute the content of docker containers in Linux batch systems and interactive clusters that are managed by other entities such as grid infrastructures, HPC clusters or other externally managed batch or interactive systems.
udocker does not require any type of privileges nor the deployment of services by system administrators. It can be downloaded and executed entirely by the end user.
udocker is a wrapper around several tools and technologies to mimic a subset of the Docker capabilities including pulling images and running then with minimal functionality. It is mainly meant to execute user applications packaged in Docker containers.
We recommend the use of Docker whenever possible, but when it is unavailable udocker can be the right tool to run your applications.
udocker is a simple tool written in Python, it has a minimal set of dependencies so that can be executed in a wide range of Linux systems. udocker does not make use of Docker nor requires its installation.
udocker "executes" the containers by simply providing a chroot like environment to the extracted container. udocker is meant to integrate several technologies and approaches hence providing an integrated environment that offers several execution options. This version provides execution engines based on PRoot, Fakechroot, runC and Singularity to facilitate the execution of Docker containers without privileges.
The basic usage flow starts by downloading the image from an image repository in the usual way; create the container out of that image (flatenning the image on the filesystem), and finally run the container with the name we gave it in the creation process:
udocker pull busybox
udocker create --name=verybusy busybox
udocker run verybusy
This sequence allows the created container to be executed many times. If simultaneous executions are envisage just make sure that input/output files are not overwritten by giving them different names during execution as the container will be shared among executions.
Containers can also be pulled, created and executed in a single step. However in this case a new container is created for every run invocation thus occupying more storage space. To pull, create and execute in a single step invoke run with an image name instead of container name:
udocker run busybox
Since root privileges are not involved, any operation that really requires privileges is not possible. The following are examples of operations that are not possible:
accessing host protected devices and files;
listening on TCP/IP privileged ports (range below 1024);
the su command will not work;
change the system time;
changing routing tables, firewall rules, or network interfaces.
the current implementation is limited to the pulling of Docker images and its execution;
the actual containers should be built using Docker and dockerfiles;
udocker does not provide all the Docker features, and is not intended as a Docker replacement;
debugging and tracing in the PRoot engine will not work;
the Fakechroot engine does not support execution of statically linked executables;
udocker is mainly oriented at providing a run-time environment for containers execution in user space.
Because of the limitations described in section 1.2 udocker does not offer isolation features such as the ones offered by Docker. If the containers content is not trusted then they should not be executed within udocker as they will run inside the user environment.
Due to the lack of isolation features udocker must not be run by privileged users.
The containers data will be unpacked and stored in the user home directory or other location of choice. Therefore the containers data will be subjected to the same filesystem protections as other files owned by the user. If the containers have sensitive information the files and directories should be adequately protected by the user.
udocker does not require privileges and runs under the identity of the user invoking it.
Users can download the udocker tarball, install in the home directory and execute it from their own accounts without requiring system administration intervention.
udocker provides a chroot like environment for container execution. This is currently implemented by:
PRoot engine via the kernel ptrace system call;
Fakechroot engine via shared library preload;
runC engine using rootless namespaces;
Singularity if available in the host system.
udocker via PRoot offers the emulation of the root user. This emulation mimics a real root user (e.g getuid will return 0). This is just an emulation no root privileges are involved. This feature enables tools that do not require privileges but that check the user id to work properly. This enables for instance software installation with rpm and yum inside the container.
Similarly to Docker, the login credentials for private repositories are stored in a file and can be easily accessed. Logout can be used to delete the credentials. If the host system is not trustable the login feature should not be used as it may expose the login credentials.
The basic flow with udocker is:
The user downloads udocker to its home directory and executes it
Upon the first execution udocker will download additional tools
Container images can be fetched from Docker Hub with
Containers can be created from the images with
Containers can then be executed with
Containers saved with
docker save can be loaded with
udocker load -i
Tarballs created with
docker export can be imported with
udocker can be placed in the user home directory and thus does not require system installation. For further information see the installation manual.
The udocker syntax is very similar to Docker. Since version 1.0.1 the udocker preferred command name changed from udocker.py to udocker. A symbolic link between udocker and udocker.py is provided when installing with the distribution tarball.
udocker [GLOBAL-PARAMETERS] COMMAND [COMMAND-OPTIONS] [COMMAND-ARGUMENTS]
udocker --helpudocker run --helpudocker pull busyboxudocker --insecure pull busyboxudocker create --name=verybusy busyboxudocker run -v /tmp/mydir verybusyudocker run verybusy /bin/ls -l /etcudocker pull --registry=https://registry.access.redhat.com rhel7udocker create --name=rh7 rhel7udocker run rh7
General help about available commands can be obtained with:
Command specific help can be obtained with:
udocker COMMAND --help
udocker install [OPTIONS]
Install of udocker tools. Pulls the tools and installs them in the user home directory under
$HOME/.udocker or in a location defined by the environment variable
UDOCKER_DIR. The pulling may attempt several mirrors.
--force force installation, useful to reinstall.
--purge remove files from older installations.
udocker installudocker install --force --purge
udocker search [-a] STRINGudocker search --list-tags REPO/IMAGE
Search Docker Hub for container images. The command displays containers one page at a time and pauses for user input. Not all registries have search capabilities.
-a display pages continuously without pause.
--list-tags list the tags for a given repository
udocker search busyboxudocker search -a busyboxudocker search iscampos/openqcdudocker search --list-tags centos
udocker pull [OPTIONS] REPO/IMAGE:TAG
Pull a container image from a docker repository by default uses dockerhub. The associated layers and metadata are downloaded from dockerhub. Requires python pycurl or the presence of the curl command.
--index=url specify an index other than index.docker.io
--registry=url specify a registry other than registry-1.docker.io
--httpproxy=proxy specify a socks proxy for downloading
udocker pull busyboxudocker pull fedora:latestudocker pull indigodatacloudapps/disvisudocker pull quay.io/something/somewhereudocker pull --httpproxy=socks4://host:port busyboxudocker pull --httpproxy=socks5://host:port busyboxudocker pull --httpproxy=socks4://user:[email protected]:port busyboxudocker pull --httpproxy=socks5://user:[email protected]:port busybox
udocker images [OPTIONS]
List images available in the local repository, these are images pulled form Docker Hub, and/or load or imported from files.
-l long format, display more information about the images and related layers
udocker imagesudocker images -l
udocker create [OPTIONS] REPO/IMAGE:TAG
Extract a container from an image available in the local repository. Requires that the image has been previously pulled from Docker Hub, and/or load or imported into the local repository from a file. use
udocker images to see the images available to create. If successful the command prints the id of the extracted container. An easier to remember name can also be given with
--name=NAME give a name to the extracted container
udocker create --name=mycontainer indigodatacloud/disvis:latest
udocker ps [options]
List extracted containers. These are not processes but containers extracted and available to the executed with
udocker run. The command displays:
protection mode (e.g. whether can be removed with
whether the container tree is writable (is in a R/W location)
the easier to remember name(s)
the name of the container image from which it was extracted
with option -m adds the execution mode
with option -s adds the container current size in MB
-m show the current execution mode of each container
-s show current disk usage (container size in MB), can be very slow
udocker rmi [OPTIONS] REPO/IMAGE:TAG
Delete a local container image previously pulled/loaded/imported. Existing images in the local repository can be listed with
udocker images. If short of disk space deleting the image after creating the container can be an option.
-f force removal independently from errors
udocker rmi -f indigodatacloud/ambertools\_app:latest
udocker rm [options] CONTAINER-ID
Delete a previously created container. Removes the entire directory tree extracted from the container image and associated metadata. The data in the container tree WILL BE LOST. The container id or name can be used.
-f force removal by changing file permissions
udocker rm 7b2d4456-9ee7-3138-ad01-63d1342d8545udocker rm mycontainer
udocker inspect REPO/IMAGE:TAGudocker inspect [OPTIONS] CONTAINER-ID
Prints container metadata. Applies both to container images or to previously extracted containers, accepts both an image or container id as input.
-p with a container-id prints the pathname to the root of the container directory tree
udocker inspect ubuntu:latestudocker inspect d2578feb-acfc-37e0-8561-47335f85e46dudocker inspect -p d2578feb-acfc-37e0-8561-47335f85e46d
udocker name CONTAINER-ID NAME
Give an easier to remember name to an extracted container. This is an alternative to the use of
udocker name d2578feb-acfc-37e0-8561-47335f85e46d BLUE
udocker rmname NAME
Remove a name previously given to an extracted container with
udocker --name= or with
udocker name. Does not remove the container.
udocker rmname BLUE
udocker rename NAME NEWNAME
Change a container name previously given to an extracted container with
udocker --name= or with
udocker name. Does not change the container id.
udocker rename BLUE GREEN
udocker verify REPO/IMAGE:TAG
Performs sanity checks to verify a image available in the local repository.
udocker verify indigodatacloud/powerfit:latest
udocker import [OPTIONS] TARBALL|- REPO/IMAGE:TAG
Import a tarball from file or stdin. The tarball can be imported into a new image or container. Without options can be used to import a container exported by Docker (with
docker export) creating a new image in the local repository. When using
--tocontainer allows importing directly into containers without creating images in the local repository. Use
--tocontainer alone to import a container exported by docker (with
docker export) into a new container without creating an image. Use
--clone to import a udocker container (e.g. exported with
udocker export --clone) into a new container also without creating an image and allowing to preserve the container metadata and udocker execution modes. The option
--name= adds a name alias to the created container, is used in conjunction with
--mv move the container tarball instead of copy to save space.
--tocontainer import directly into a container.
--clone import udocker container format with both metadata and container
--clone to give an alias to the container
udocker import docker_container.tar myrepo:latestudocker import - myrepo:latest < docker_container.tarudocker import --mv docker_container.tar myrepo:latestudocker import --tocontainer --name=BLUE docker_container.tarudocker import --clone --name=RED udocker_container.tar
udocker load -i IMAGE-FILEudocker load -i IMAGE-FILE NAMEudocker load -
Loads into the local repository a tarball containing a Docker image with its layers and metadata. This is equivalent to pulling an image from Docker Hub but instead loading from a locally available file. It can be used to load a Docker image saved with
docker save. A typical saved image is a tarball containing additional tar files corresponding to the layers and metadata. From version 1.1.4 onwards, udocker can also load images in OCI format. The optional NAME argument can be used to change the name of the loaded image. This argument is particularly relevant to provide adequate names to OCI loaded images as these frequently only provide tag names. If an OCI image does not provide a name and the argument NAME is also not provided in the command line, then udocker will generate a random name.
udocker load -i docker-image.tarudocker load - < docker-image.tarudocker load -i oci-image.tar test-image
udocker protect REPO/IMAGE:TAGudocker protect CONTAINER-ID
Marks an image or container against deletion by udocker. Prevents
udocker rmi and
udocker rm from removing images or containers.
udocker protect indigodatacloud/ambertools\_app:latestudocker protect 3d528987-a51e-331a-94a0-d278bacf79d9
udocker unprotect REPO/IMAGE:TAGudocker unprotect CONTAINER-ID
Removes a mark against deletion placed by
udocker unprotect indigodatacloud/ambertools\_app:latestudocker unprotect 3d528987-a51e-331a-94a0-d278bacf79d9
udocker mkrepo DIRECTORY
Creates a udocker local repository in specify directory other than the default one ($HOME/.udocker). Can be used to place the containers in another filesystem. The created repository can then be accessed with
udocker --repo=DIRECTORY COMMAND.
udocker mkrepo /tmp/myrepoudocker --repo=/tmp/myrepo pull docker.io/fedora/memcachedudocker --repo=/tmp/myrepo images
udocker run [OPTIONS] CONTAINER-ID|CONTAINER-NAMEudocker run [OPTIONS] REPO/IMAGE:TAG
Executes a container. The execution several execution engines are provided. The container can be specified using the container id or its associated name. Additionally it is possible to invoke run with an image name, in this case the image is extracted and run is invoked over the newly extracted container. Using this later approach will create multiple container directory trees possibly occupying considerable disk space, therefore the recommended approach is to first extract a container using "udocker create" and only then execute with "udocker run". The same extracted container can then be executed as many times as required without duplication.
udocker provides several execution modes to support the actual execution within a container. Execution modes can be changed using the command
udocker setup --execmode=<mode> <container-id> for more information on available modes and their characteristics see section 3.25.
--rm delete the container after execution
--workdir=PATH specifies a working directory within the container
--user=NAME username or uid:gid inside the container
--volume=DIR:DIR map an host file or directory to appear inside the container
--novol=DIR excludes a host file or directory from being mapped
--env="VAR=VAL" set environment variables
--env-file=FILE load environment variables from file
--hostauth obtain user account from the host and add it to the container passwd and group
--containerauth use the container passwd and group directly without binding files
--nosysdirs prevent udocker from mapping /proc /sys /run and /dev inside the container
--nometa ignore the container metadata settings
--hostenv pass the user host environment to the container
--cpuset-cpus=<1,2-3> CPUs in which to allow execution
--name=NAME set or change the name of the container useful if running from an image
--bindhome attempt to make the user home directory appear inside the container
--kernel=KERNELID use a specific kernel id to emulate useful when the host kernel is too old
--location=DIR execute a container in a given directory
Options valid only in Pn execution modes:
--publish=HOST_PORT:CONT_PORT map a container port to another host port
--publish-all map all container ports to random different ones
Options valid only in Rn execution modes:
--device=/dev/xxx pass device to container
# Pull fedora from Docker Hubudocker pull fedora:29# create the container named myfed from the image named fedoraudocker create --name=myfed fedora:29# execute a cat inside of the containerudocker run myfed cat /etc/redhat-release# The above three operations could have done with a single command# However each time udocker is invoked this way a new container# directory tree is created consuming additional space and timeudocker run fedora:29 cat /etc/redhat-release# In this example the host /tmp is mapped to the container /tmpudocker run --volume=/tmp myfed /bin/bash# Same as above but running something in /tmpudocker run -v=/tmp myfed /bin/bash -c "cd /tmp; ./myscript.sh"# Run binding a host directory inside the container to make it available# The host $HOME is mapped to /home/user inside the container# The shortest -v form is used instead of --volume=# The option -w same as --workdir is used to change dir to /home/userudocker run -v=$HOME:/home/user -w=/home/user myfed /bin/bash# Install software inside the containerudocker run --user=root myfed yum install -y firefox pulseaudio gnash-plugin# Run as certain uid:gid inside the containerudocker run --user=1000:1001 myfed /bin/id# Run firefoxudocker run --bindhome --hostauth --hostenv \-v /sys -v /proc -v /var/run -v /dev --user=green --dri myfed firefox# Run in a scriptudocker run ubuntu /bin/bash <<EOFcd /etccat motdcat lsb-releaseEOF# Search and pull from another repository than dockerhub# First search for the expression `myrepo` in quay.io# Second list the tags for a given image in quay.io# Third finally pull a given image:tag from quay.ioudocker search quay.io/myrepoudocker search --list-tags quay.io/myrepository/myimageudocker pull quay.io/myrepository/myimage:v2.3.1# Run container in a given directory tree using the DEFAULT EXECUTION MODE# Below ROOT is the complete directory structure of the container operating system# This enables udocker to execute directory trees created by other tools# Much of the udocker functionality is not usable when using --location./udocker run --location=/tmp/u/containers/07b3226e-6513-3f85-884f-e3cfdd2fbc0e/ROOT
Further debugging information can be obtaining by running with
udocker -D pull busybox:latestudocker -D run busybox:latest
The options '-q' or '--quiet' can be specified before each command to reduce verbosity. The verbosity level can also be specified by assigning a value between 0 and 5 to the environment variable UDOCKER_LOGLEVEL.
udocker -q run busybox:latest /bin/lsUDOCKER_LOGLEVEL=2 udocker run busybox:latest /bin/ls
udocker login [--username=USERNAME] [--password=PASSWORD] [--registry=REGISTRY]
Login into a Docker registry using v2 API. Only basic authentication using username and password is supported. The username and password can be prompted or specified in the command line. The username is the username in the repository, not the associated email address.
--username=USERNAME provide the username in the command line
--password=PASSWORD provide the password in the command line
--registry=REGISTRY credentials are for this registry
udocker login --username=xxxx --password=yyyyudocker login --registry="https://hostname:5000"username: xxxxpassword: ****
udocker logout [-a]
Delete the login credentials (username and password) stored by previous logins. Without arguments deletes the credentials for the current registry. To delete all registry credentials use -a.
-a delete all credentials from previous logins
--registry=REGISTRY delete credentials for this registry
udocker logoutudocker logout --registry="https://hostname:5000"udocker logout -a
udocker clone [--name=NAME] CONTAINER-ID|CONTAINER-NAME
Duplicate an existing container creating a complete replica. The replica receives a different CONTAINER-ID. An alias can be assigned to the newly created container by using
--name=NAME assign a name alias to the newly created container
udocker clone f24771be-f0bb-3046-80f0-db301e099517udocker clone --name=RED f24771be-f0bb-3046-80f0-db301e099517udocker clone --name=RED BLUE
udocker save -o IMAGE-FILE REPO/IMAGE:TAGudocker save -o - REPO/IMAGE:TAG
Saves an image including all its layers and metadata to a tarball. The input is an image not a container, to produce a tarball of a container use export. The saved images can be read by udocker or Docker using the command load.
udocker save -o docker-image.tar centos:centos7udocker save -o - > docker-image.tar ubuntu:16.04 ubuntu:18.04 ubuntu:19.04
udocker setup [--execmode=XY] [--force] [--nvidia] [--purge] CONTAINER-ID|CONTAINER-NAME
--execmode chooses an execution mode to define how a given container will be executed, namelly enables selection of an execution engine and its related execution modes. Without options, setup will print the current execution mode for the given container. The option
--nvidia enables access to GPGPUs by adding the necessary host libraries to the container. The option
--force can be used both with
--execmode and with
--nvidia to force the setup of the container to the specified mode. The option
--purge removes mountpoints, auxiliary files and directories created by udockr inside the container directory tree to support its execution. It should only be invoked when there is no execution taking place as it may affect processes running in the container tree.
--execmode=XY choose an execution mode
--nvidia enable access to GPGPUs
--force force the selection of the execution mode, can be used to
force the change of an execution mode when it fails namely if it is
transferred to a remote host while in one of the Fn modes. Can be
used with --nvidia.
--purge remove mountpoints, auxiliary files and directories created
by udocker to support the container execution.
accelerated mode using seccomp
seccomp accelerated mode disabled
exec with direct loader invocation
F1 plus modified loader
F1 + ld.so
fix ELF headers in binaries
F2 + ELF headers
F3 plus enables new executables and libs
same as F3
rootless user mode namespaces
R1 plus P1 for software installation
resolv, passwd, proot
R1 plus P2 for software installation
resolv, passwd, proot
uses singularity if available in the host
The default execution mode is P1 using PRoot and starting in root emulation mode.
The mode P2 also uses PRoot and although has lower performance than P1 can be more reliable. The mode P1 uses PRoot with SECCOMP syscall filtering which provides higher performance in most operating systems. PRoot provides the most universal execution mode in udocker but may also exhibit lower performance on older kernels such as in CentOS 6 systems. The Pn modes also offer root emulation to facilitate software installation and to execute applications that expect to run under root.
The Fakechroot (Fn), runC (Rn) and Singularity (Sn) engines are EXPERIMENTAL. They provide higher performance in most cases, but are less universal thus supporting less Linux distributions.
The udocker Fakechroot engine has four modes that offer increasing compatibility levels. F1 is the least intrusive mode and only changes absolute symbolic links so that they point to locations inside the container. F2 adds changes to the loader to prevent loading of host shareable libraries. F3 adds changes to all binaries (ELF headers of executables and libraries) to remove absolute references pointing to the host shareable libraries. These changes are performed once during the setup, executables added after setup will not have their ELF headers fixed and will fail to run. Notice that setup can be rerun with the --force option to fix these binaries. F4 performs the ELF header changes dynamically (on-the-fly) thus enabling compilation and linking within the container and new executables to be transferred to the container and executed. Executables and libraries in host volumes are not changed and hence cannot be executed from a container in F2, F3 and F4 execution modes. runC with rootless user namespaces requires a recent Linux kernel and is known to work on Ubuntu and Fedora hosts.
Mode Rn requires kernels with support for rootless containers, thus it will not work on some distributions (e.g. CentOS 6 and CentOS 7). The rootless execution modes have inherent limitations related to the manipulation of uids and gids that may cause certain operations to fail such as software installations. To overcome this limitation of the R1 execution mode, udocker provides the R2 and R3 execution modes that combine runc with the proot uid/gid emulation. In these modes the execution chain is
runc -> proot -> executable
When using the Rn modes, udocker will search for a runc executable in the host system, only if it does not find one it will default to use the runc provided with the udockertools. This behavior can be change through environment variables and configuration settings. Fakechroot requires libraries compiled for each guest operating system, udocker provides these libraries for several distributions including Ubuntu 14, Ubuntu 16, Ubuntu 18, CentOS 6 and CentOS 7 and some others. Other guests may or may not work with these same libraries.
Notice that changes performed in Fn and Rn modes will prevent the containers from running in hosts where the directory path to the container is different. In this case convert back to P1 or P2, transfer to the target host, and then convert again from Pn to the desired Fn mode.
Singularity must be available in the host system for execution mode S1. Newer versions of Singularity may run without requiring privileges but need a recent kernel in the host system with support for rootless user mode namespaces similar to runC in mode R1. Singularity cannot be compiled statically due to dependencies on dynamic libraries and therefore is not provided with udocker. In CentOS 6 and CentOS 7 Singularity must be installed with privileges by a system administrator as it requires suid or capabilities. The S1 mode also offers root emulation to facilitate software installation and to execute applications that expected to run under root.
udocker create --name=mycontainer fedora:25udocker setup --execmode=F3 mycontainerudocker setup mycontainer # prints the execution modeudocker run mycontainer /bin/lsudocker setup --execmode=F4 mycontainerudocker run mycontainer /bin/lsudocker setup --execmode=P1 mycontainerudocker run mycontainer /bin/lsudocker setup --execmode=R1 mycontainerudocker run mycontainer /bin/lsudocker setup --execmode=S1 mycontainerudocker run mycontainer /bin/ls
The default execution mode of udocker can also be changed. This has however several limitations, therefore the recommended method to change the execution mode is via the
udocker setup command. The default execution mode can be changed through the configuration files by changing the attribute default_execution_mode or through the environment variable UDOCKER_DEFAULT_EXECUTION_MODE. Only the following modes can be used as default modes: P1, P2, F1, S1, and R1. Changing the default execution mode can be useful in case the default does not work as expected.
UDOCKER_DEFAULT_EXECUTION_MODE=P2 ./udocker run mycontainer /bin/ls
In this section we will use the Lattice QCD simulation software openQCD to demonstrate how to run Open MPI applications with udocker (http://luscher.web.cern.ch/luscher/openQCD). Lattice QCD simulations are performed on high-performance parallel computers with hundreds and thousands of processing units. All the software environment that is needed for openQCD is a compliant C compiler and a local MPI installation such as Open MPI.
In what follows we describe the steps to execute openQCD using udocker in a HPC system with a batch system (e.g. SLURM). An analogous procedure can be followed for other MPI applications.
A container image of openQCD can be downloaded from the Docker Hub repository. From this image a container can be extracted to the filesystem (using udocker create) as described below.
./udocker pull iscampos/openqcd./udocker create --name=openqcd iscampos/openqcdfbeb130b-9f14-3a9d-9962-089b4acf3ea8
Next the created container is executed (notice that the variable LD_LIBRARY_PATH is explicitly set):
./udocker run -e LD_LIBRARY_PATH=/usr/lib openqcd /bin/bash
In this approach the host mpiexec will submit the N MPI process instances, as containers, in such a way that the containers are able to communicate via the low latency interconnect (Infiniband in the case at hand).
For this approach to work, the code in the container needs to be compiled with the same version of MPI that is available in the HPC system. This is necessary because the Open MPI versions of mpiexec and orted available in the host system need to match with the compiled program. In this example the Open MPI version is v2.0.1. Therefore we need to download this version and compile it inside the container.
Note: first the example Open MPI installation that comes along with the openqcd container are removed with:
yum remove openmpi
We download Open MPI v.2.0.1 from https://www.open-mpi.org/software/ompi/v2.0 and compile it.
Openib and libibverbs need to be install to compile Open MPI over Infiniband. For that, install the epel repository on the container. This step is not required if running using TCP/IP is enough.
To install the Infiniband drivers one needs to install the epel repository.
yum install -y epel-release
The list of packages to be installed is:
openiblibibverbs, libibverbs-utils, libibverbs-devellibrdmacm, librdmacm-utils, ibacmlibneslibibumadlibfabric, libfabric-developensm-libsswigibutils-libs, ibutilsopensmlibibmadinfiniband-diags
The driver needs to be installed as well, in our examples the Mellanox driver.
yum install mlx4*x86_64
The installation of both, i686 and x86_64 versions might be conflictive, and lead to an error ("libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs0) if for example the i686 is used. The best approach is to install only the version for the architecture of the machine in this case x86_64.
The Open MPI source is compiled and installed in the container under /usr for convenience:
cd /usrtar xvf openmpi-2.0.1.tgzcd /usr/openmpi-2.0.1./configure --with-verbs --prefix=/usrmakemake install
OpenQCD can then be compiled inside the udocker container in the usual way. The MPI job submission to the HPC cluster succeeds by including this line in the batch script:
/opt/cesga/openmpi/2.0.1/gcc/6.3.0/bin/mpiexec -np 128 \$LUSTRE/udocker-master/udocker run -e LD_LIBRARY_PATH=/usr/lib \--hostenv --hostauth --user=cscdiica -v /tmp \--workdir=/op/projects/openQCD-1.6/main openqcd \/opt/projects/openQCD-1.6/main/ym1 -i ym1.in -noloc
(where $LUSTRE points to the appropriate user filesystem directory in the HPC system)
Notice that depending on the application and host operating system a variable performance degradation may occur when using the default execution mode (Pn). In this situation other execution modes (such as Fn) may provide significantly higher performance. The command
udocker setup --execmode=<mode> <container-id> can be used to change between execution modes (see section 3.25).
The host (either the physical machine or VM) where the container will run has to have the NVIDIA driver installed. Moreover, the NVIDIA driver version has to be known apriori, since the docker image has to have the exact same version as the host
udocker setup --nvidia <container-id> can be used to prepare the container with the drivers necessary to run with nvidia GPGPUs. This will copy the required files from the host into the container.
Another different approach is to have docker images already prepared with the driver files but they must match what is being used in the target host. For instance base docker images with several version of the NVIDIA driver can be found in dockerhub:
In the tags tab one can check which versions are available. Dockerfiles and Ansible roles used to build these images are in the github repository: https://github.com/LIP-Computing/ansible-role-nvidia
Examples of using those NVIDIA base images with a given application are the "disvis" and "powerfit" images whose Dockerfiles and Ansible roles can be found in:
In order to build your docker image with a given CUDA or OpenCL application, the aforementioned images can be used. When the docker image with your application has been built you can run udocker with that image as described in the previous sections.
In udocker, images and containers are stored in the filesystem usually in the user home directory under $HOME/.udocker. If this location is in a shared filesystem such as in a computing farm or cluster then the content will be seen by all the hosts mounting the filesystem and can be used transparently by udocker across these hosts. If the home directory is not shared but some other location is, then you may point the UDOCKER_DIR environment variable to such a location and use it to store the udocker installation, including udockertools, images and containers.
The directory structure of .udocker (or UDOCKER_DIR) is a as follows:
bin/ udocker executables
lib/ udocker libraries
repos/ images pulled or imported by udocker
layers image layers so that they can be shared by several images saving space
containers/ containers extracted from images or imported
For a given container its directory pathname in the filesystem can be obtained as follows:
$ udocker inspect -p ubuntu17/home/user01/.udocker/containers/feb0041d-e1b6-3eee-89d8-2d0617feb13a/ROOT
The pathname in the example is the root of the container filesystem tree. Below ROOT you will find all the files that comprise the container. Upon execution udocker performs a chroot like operation into this directory. You can modify, add, remove files below this location and upon execution these changes will be seen inside the container. This can be used to place or retrieve files to/from the container. By accessing this directory from the host you may also perform copies of the container directory tree e.g. for backup or other purposes.
All containers are stored under the directory "containers". Each container is under a separate directory whose name corresponds to its alphanumeric id. This directory contains control files and the "ROOT" directory for the container filesystem.
Across isolated hosts the correct way to transfer containers is to pull them from a repository such as Docker Hub. However this may implies slow downloads from remote locations and also the need to create the container again from the pulled image.
udocker provides limited support for loading images and importing containers. Containers exported to a file by Docker with
docker export can be imported by udocker using:
udocker import CONTAINER-FILE NEWIMAGE:NEWTAG import the
container file into a new image (not into a new container).
udocker import --tocontainer CONTAINER-FILE import the
container file directly into a new container (without creating an image).
This is udocker specific.
udocker import --tocontainer --clone CONTAINER-FILE import the
container file directly into a new container (without creating an image).
This assumes the container was initially exported by udocker with
udocker export --clone and thus contains not only the ROOT tree of
the container but also all metadata, and control files of udocker.
This is udocker specific.
Images saved by Docker using
docker save can be imported by udocker using
udocker load. Images in OCI format can also be loaded by udocker using
udocker load, the format will be automatically detected.
udocker can also save images in a Docker compliant format using
The example below shows a container named MyContainer being manually transferred to another host and executed. Make sure the udocker executable is in your PATH on both the local and remote hosts.
$ MYC_ROOT=$(udocker inspect -p MyContainer)$ MYC_PATH=$(dirname $MYC_ROOT)$ MYC_ID=$(basename $MYC_PATH)$ MYC_DIR=$(dirname $MYC_PATH)$ cd $MYC_DIR; tar cvf - $MYC_ID | ssh [email protected] "udocker install ; cd ~/.udocker/containers; tar xf -"$ ssh [email protected] "udocker name $MYC_ID MyContainer; udocker run MyContainer"
The behavior and capabilities of running as root inside the containers depends on the execution mode. In the Pn and Rn modes udocker will run as root. In other modes execution as root is achieved by invoking run with the
udocker run --user=root <container-id>`
In the default modes Pn, running as root is emulated, meaning that no root privileges or root capabilities are involved. The root execution is emulated by intercepting system calls and returning id 0 thus emulating a root environment.
In the Fn modes running as root is not supported.
In the Rn (runc) modes execution defaults to run as root, this is however achieved in a very different manner through user namespaces, as implemented in runc. These modes only work in recent Linux distributions that support user namespaces. In these execution modes the user is truly root inside the container, but with several limitations, namely on what regards access to other UIDs and GUIs. Although the user can be root inside the container, it will be a normal user outside, thus protecting the host system if a container process breaks out. The use of user namespaces may require the setup of the system configuration files /etc/subuid and /etc/subgid which require system administrator intervention to be configured. They assign a range of UIDs and GIDs for each user to be used within the user namespaces. To overcome some of the root limitations when running inside user namespaces, udocker offers an overlay execution of proot inside runc through the execution modes R2 and R3. In these modes proot is used to overcome some of the UID and GID issues while still enabling the benefits of isolation and root execution inside de user namespaces.
In the Sn (singularity) execution modes default to the normal unprivileged user. Running as root can be achieved with
udocker run --user=root <container-id>. Execution within singularity requires namespaces and can operate in two different manners. In older distributions and kernels singularity must be installed by the system administrator with privileges. In more recent distributions and kernels singularity can operate similarly to runc and take advantage of the user namespaces. In this later case UID/GID entries might also be required in /etc/subuid and /etc/subgid. Singularity is to package in the udokertools but, udocker can exploit existing singularity installations to execute the udocker containers.
The following table provides a summary of running as root within udocker:
Running as root
Defaults to run as root. Run as root via emulation.
Same as P1
Running as root not supported.
Running as root not supported.
Running as root not supported.
Running as root not supported.
Defaults to run as root. Run as root via user namespaces
Same as R1 plus overlay execution with proot in mode P1.
Same as R1 plus overlay execution with proot in mode P2.
Use --user=root. Run as root via user namespaces
Most applications and services can be run without running as root. However running as root within udocker can be useful to install software packages. Depending on the execution mode, running as root may imply additional overheads and/or security considerations.
If the software installation will need to create/change users and groups then udocker needs to run with direct access to the container passwd and group files as follows:
udocker run --user=root --containerauth <CONTAINER-ID>
For software installation the recommended execution modes are P2, S1 and R3. The emulation is not perfect and issues can still arise. Namelly when using APT it can be required to install using:
apt-get -o APT::Sandbox::User=root updateapt-get -o APT::Sandbox::User=root install <package>
Upon APT errors such as
cannot get security labeling handle: No such file or directory try to run ias above in P2 mode but start udocker as:
udocker.py run --user=root --nosysdirs -v /etc/resolv.conf -v /dev --containerauth <CONTAINER-ID>
udocker as not been designed for nested executions, meaning execution of containers within containers. However there are sucessful examples of using udocker in such scenarios such as SCAR.
For running inside docker and similiar: udocker offers the Fn mode which enables execution within docker or other Linux namespaces based applications.
For running within udocker itself the following guidelines apply:
Fn within Pn: Possible
Pn within Rn: Possible only in R1
Pn within Sn: Possible
Fn within Rn: Possible
Fn within Sn: Possible
Pn within Pn: Not possible or possible with huge overheads
Fn within Fn: Not possible
Pn within Fn: Not possible
The experienced performance in the different execution modes will depend greatly on the application being executed. In general the following considerations may hold:
P1 is faster than P2, unless in older kernels without *SECCOMP
filtering* where both modes will have the same performance.
In heavily multithreaded or I/O intensive applications the P2
mode may exhibit a large performance penalty. This can also
apply to P1 in older kernels without SECCOMP filtering
Fn modes are generally faster than Pn modes and do not have
multithreading or I/O limitations.
Singularity and runC should provide similar performances.
To avoid corruption backups for safeguard or transfer should only be performed when the container is not being executed (not locally nor in any other host if the filesystem is shared).
Containers should only be copied when they are in the execution modes Pn or Rn. The modes Fn perform changes to the containers that will make them fail if they are execute in a different host if the absolute pathname to the container location is different. In this later case convert back to P1 (using: udocker setup --execmode=P1) before performing the backup.
When experiencing issues in the default execution mode (P1) you may try to setup the container to execute using mode P2 or one of the Fn or Rn modes. See section 3.23 for information on changing execution modes.
Some execution modes require the creation of auxiliary files, directories and mountpoints. These can be purged from a given container using "setup --purge", however this operation must be performed when the container is not being executed.
INDIGO DataCloud https://www.indigo-datacloud.eu
Open MPI https://www.open-mpi.org