CH-FROMHOST(1)

NAME
ch-fromhost - Inject files from the host into an image directory, with various magic

SYNOPSIS

            $ ch-fromhost [OPTION ...] [FILE_OPTION ...] IMGDIR

DESCRIPTION

Note:
        This command is experimental. Features may be incomplete and/or buggy. Please report any issues you find, so we can fix them!

Inject files from the host into the Charliecloud image directory IMGDIR.

The purpose of this command is to inject arbitrary host files into a container necessary to access host specific resources; usually GPU or proprietary interconnects. It is not a general copy-to-image tool; see further discussion on use cases below.

It should be run after:code:ch-convert and before ch-run. After invocation, the image is no longer portable to other hosts.

Injection is not atomic; if an error occurs partway through injection, the image is left in an undefined state and should be re-unpacked from storage. Injection is currently implemented using a simple file copy, but that may change in the future.

Arbitrary file and libfabric injection are handled differently.

  Arbitrary files

Arbitrary file paths that contain the strings /bin or /sbin are assumed to be executables and placed in /usr/bin within the container. Paths that are not loadable libfabric providers and contain the strings /lib or .so are assumed to be shared libraries and are placed in the first-priority directory reported by ldconfig (see --lib-path below). Other files are placed in the directory specified by --dest.

If any shared libraries are injected, run ldconfig inside the container (using ch-run -w) after injection.

  Libfabric

MPI implementations have numerous ways of communicating messages over interconnects. We use libfabric (OFI), an OpenFabric framework that exports fabric communication services to applications, to manage these communications with built-in, or loadable, fabric providers.

            •   <https://ofiwg.github.io/libfabric>

            •   <https://ofiwg.github.io/libfabric/v1.14.0/man/fi_provider.3.html>

Using OFI, we can (a) uniformly manage fabric communication services for both OpenMPI and MPICH, and (b) use simplified methods of accessing proprietary host hardware, e.g., Cray’s Gemini/Aries and Slingshot (CXI).

OFI providers implement the application facing software interfaces needed to access network specific protocols, drivers, and hardware. Loadable providers, i.e., compiled OFI libraries that end in -fi.so, for example, Cray’s libgnix-fi.so, can be copied into, and used, by an image with a MPI configured against OFI. Alternatively, the image’s libfabric.so can be overwritten with the host’s. See details and quirks below.

OPTIONS

  To specify which files to inject

            -c, --cmd CMD
                Inject files listed in the standard output of command CMD.

            -f, --file FILE
                Inject files listed in the file FILE.

            -p, --path PATH
                Inject the file at PATH.

            --cray-cxi
                Inject cray-libfabric for slingshot. This is equivalent to --path $CH_FROMHOST_OFI_CXI, where $CH_FROMHOST_OFI_CXI is the path to the Cray host libfabric libfabric.so.

            --cray-gni
                Inject cray gemini/aries GNI libfabric provider libgnix-fi.so. This is equivalent to --fi-provider $CH_FROMHOST_OFI_GNI, where CH_FROMHOST_OFI_GNI is the path to the Cray host ugni provider libgnix-fi.so.

            --nvidia
                Use nvidia-container-cli list (from libnvidia-container) to find executables and libraries to inject.

These can be repeated, and at least one must be specified.

  To specify the destination within the image

            -d, --dest DST
                Place files specified later in directory IMGDIR/DST, overriding the inferred destination, if any. If a file’s destination cannot be inferred and --dest has not been specified, exit with an error. This can be repeated to place files in varying destinations.

  Additional arguments

            --print-cray-fi
                Print inferred destination for libfabric replacement.

            --print-fi
                Print the guest destination path for libfabric provider(s).

            --print-lib
                Print the guest destination path for shared libraries inferred as described above.

            --no-ldconfig
                Don’t run ldconfig even if we appear to have injected shared libraries.

            -h, --help
                Print help and exit.

            -v, --verbose
                Be more verbose about what is going on. Can be repeated.

            --version
                Print version and exit.

Warning:
        ldconfig often prints scary-looking warnings on stderr even everything is going well. By default, we suppress these, but you can see them with sufficient verbosity. For example:

                    $ ch-fromhost --print-lib /var/tmp/bullseye
                    /usr/local/lib
                    $ ch-fromhost -v --print-lib /var/tmp/bullseye
                    asking ldconfig for inferred shared library destination
                    inferred shared library destination: /var/tmp/bullseye//usr/local/lib
                    /usr/local/lib
                    $ ch-fromhost -v -v --print-lib /var/tmp/bullseye
                    asking ldconfig for inferred shared library destination
                    /sbin/ldconfig: Can't stat /usr/local/lib/x86_64-linux-gnu: No such file or directory
                    /sbin/ldconfig: Path `/lib/x86_64-linux-gnu' given more than once
                    /sbin/ldconfig: Path `/usr/lib/x86_64-linux-gnu' given more than once
                    /sbin/ldconfig: /lib/x86_64-linux-gnu/ld-2.31.so is the dynamic linker, ignoring
                    inferred shared library destination: /var/tmp/bullseye//usr/local/lib
                    /usr/local/lib

        See issue #732 <https://github.com/hpc/charliecloud/issues/732> for an example of how this was confusing for users.

WHEN TO USE CH-FROMHOST

This command does a lot of heuristic magic; while it can copy arbitrary files into an image, this usage is discouraged and prone to error. Here are some use cases and the recommended approach:

    1.  I have some files on my build host that I want to include in the image. Use the COPY instruction within your Dockerfile. Note that it’s OK to build an image that meets your specific needs but isn’t generally portable, e.g., only runs on specific micro-architectures you’re using.

    2.  I have an already built image and want to install a program I compiled separately into the image. Consider whether a building a new derived image with a Dockerfile is appropriate. Another good option is to bind-mount the directory containing your program at run time. A less good option is to cp(1) the program into your image, because this permanently alters the image in a non-reproducible way.

    3.  I have some shared libraries that I need in the image for functionality or performance, and they aren’t available in a place where I can use COPY. This is the intended use case of ch-fromhost. You can use --cmd, --file, --ofi, and/or --path to put together a custom solution. But, please consider filing an issue so we can package your functionality with a tidy option like --nvidia.

LIBFABRIC USAGE AND QUIRKS

The implementation of libfabric provider injection and replacement is experimental and has a couple quirks.

    1.  Containers must have the following software installed:

        a.  libfabric (<https://ofiwg.github.io/libfabric/>). See charliecloud/examples/Dockerfile.libfabric.

        b.  Corresponding open source MPI implementation configured and built against the container libfabric, e.g., - MPICH <https://www.mpich.org/>, or - OpenMPI <https://www.open-mpi.org/>. See charliecloud/examples/Dockerfile.mpich and charliecloud/examples/Dockerfile.openmpi.

    2.  At run time, a libfabric provider can be specified with the variable FI_PROVIDER. The path to search for shared providers can be specified with FI_PROVIDER_PATH. These variables can be inherited from the host or explicitly set with the container’s environment file /ch/environment via --set-env.

        To avoid issues and reduce complexity, the inferred injection destination for libfabric providers and replacement will always at the path in the image where libfabric.so is found.

    3.  The Cray GNI loadable provider, libgnix-fi.so, will link to compiler(s) in the programming environment by default. For example, if it is built under the PrgEnv-intel programming environment, it will have links to files at paths /opt/gcc and /opt/intel that ch-run will not bind automatically.

        Managing all possible bind mount paths is untenable. Thus, this experimental implementation injects libraries linked to a libgnix-fi.so built with the minimal modules necessary to compile, i.e.:

        •   modules

        •   craype-network-aries

        •   eproxy

        •   slurm

        •   cray-mpich

        •   craype-haswell

        •   craype-hugepages2M

    A Cray GNI provider linked against more complicated PE’s will still work, assuming 1) the user explicitly bind-mounts missing libraries listed from its ldd output, and 2) all such libraries do not conflict with container functionality, e.g., glibc.so, etc.

    4.  At the time of this writing, a Cray Slingshot optimized provider is not available; however, recent libfabric source activity indicates there may be at some point, see: <https://github.com/ofiwg/libfabric/pull/7839We>.

        For now, on Cray systems with Slingshot, CXI, we need overwrite the container’s libfabric.so with the hosts using --path. See examples for details.

    5.  Tested only for C programs compiled with GCC. Additional bind mount or kludging may be needed for untested use cases. If you’d like to use another compiler or programming environment, please get in touch so we can implement the necessary support.

Please file a bug if we missed anything above or if you know how to make the code better.

NOTES

Symbolic links are dereferenced, i.e., the files pointed to are injected, not the links themselves.

As a corollary, do not include symlinks to shared libraries. These will be re-created by ldconfig.

There are two alternate approaches for nVidia GPU libraries:

            1.  Link libnvidia-containers into ch-run and call the library functions directly. However, this would mean that Charliecloud would either (a) need to be compiled differently on machines with and without nVidia GPUs or (b) have libnvidia-containers available even on machines without nVidia GPUs. Neither of these is consistent with Charliecloud’s philosophies of simplicity and minimal dependencies.

            2.  Use nvidia-container-cli configure to do the injecting. This would require that containers have a half-started state, where the namespaces are active and everything is mounted but pivot_root(2) has not been performed. This is not feasible because Charliecloud has no notion of a half-started container.

Further, while these alternate approaches would simplify or eliminate this script for nVidia GPUs, they would not solve the problem for other situations.

BUGS

File paths may not contain colons or newlines.

ldconfig tends to print stat errors; these are typically non-fatal and occur when trying to probe common library paths. See issue #732 <https://github.com/hpc/charliecloud/issues/732>.

EXAMPLES

  libfabric

Cray Slingshot CXI injection.

Replace image libabfric, i.e., libfabric.so, with Cray host’s libfabric at host path /opt/cray-libfabric/lib64/libfabric.so.

            $ ch-fromhost -v --path /opt/cray-libfabric/lib64/libfabric.so /tmp/ompi
            [ debug ] queueing files
            [ debug ]    cray libfabric: /opt/cray-libfabric/lib64/libfabric.so
            [ debug ] searching image for inferred libfabric destination
            [ debug ]    found /tmp/ompi/usr/local/lib/libfabric.so
            [ debug ] adding cray libfabric libraries
            [ debug ]    skipping /lib64/libcom_err.so.2
            [...]
            [ debug ] queueing files
            [ debug ]    shared library: /usr/lib64/libcxi.so.1
            [ debug ] queueing files
            [ debug ]    shared library: /usr/lib64/libcxi.so.1.2.1
            [ debug ] queueing files
            [ debug ]    shared library: /usr/lib64/libjson-c.so.3
            [ debug ] queueing files
            [ debug ]    shared library: /usr/lib64/libjson-c.so.3.0.1
            [...]
            [ debug ] queueing files
            [ debug ]    shared library: /usr/lib64/libssh.so.4
            [ debug ] queueing files
            [ debug ]    shared library: /usr/lib64/libssh.so.4.7.4
            [...]
            [ debug ] inferred shared library destination: /tmp/ompi//usr/local/lib
            [ debug ] injecting into image: /tmp/ompi/
            [ debug ]    mkdir -p /tmp/ompi//var/lib/hugetlbfs
            [ debug ]    mkdir -p /tmp/ompi//var/spool/slurmd
            [ debug ]    echo '/usr/lib64' >> /tmp/ompi//etc/ld.so.conf.d/ch-ofi.conf
            [ debug ]    /opt/cray-libfabric/lib64/libfabric.so -> /usr/local/lib (inferred)
            [ debug ]    /usr/lib64/libcxi.so.1 -> /usr/local/lib (inferred)
            [ debug ]    /usr/lib64/libcxi.so.1.2.1 -> /usr/local/lib (inferred)
            [ debug ]    /usr/lib64/libjson-c.so.3 -> /usr/local/lib (inferred)
            [ debug ]    /usr/lib64/libjson-c.so.3.0.1 -> /usr/local/lib (inferred)
            [ debug ]    /usr/lib64/libssh.so.4 -> /usr/local/lib (inferred)
            [ debug ]    /usr/lib64/libssh.so.4.7.4 -> /usr/local/lib (inferred)
            [ debug ] running ldconfig
            [ debug ]    ch-run -w /tmp/ompi/ -- /sbin/ldconfig
            [ debug ] validating ldconfig cache
            done

Same as above, except also inject Cray’s fi_info to verify Slingshot provider access.

            $ ch-fromhost -v --path /opt/cray/libfabric/1.15.0.0/lib64/libfabric.so \
                          -d /usr/local/bin \
                          --path /opt/cray/libfabric/1.15.0.0/lib64/libfabric.so \
                          /tmp/ompi
            [...]
            $ ch-run /tmp/ompi/ -- fi_info -p cxi
            provider: cxi
              fabric: cxi
              [...]
              type: FI_EP_RDM
              protocol: FI_PROTO_CXI

Cray GNI shared provider injection.

Add Cray host built GNI provider libgnix-fi.so to the image and verify with fi_info.

            $ ch-fromhost -v --path /home/ofi/libgnix-fi.so /tmp/ompi
            [ debug ] queueing files
            [ debug ]    libfabric shared provider: /home/ofi/libgnix-fi.so
            [ debug ] searching /tmp/ompi for libfabric shared provider destination
            [ debug ]    found: /tmp/ompi/usr/local/lib/libfabric.so
            [ debug ] inferred provider destination: //usr/local/lib/libfabric
            [ debug ] injecting into image: /tmp/ompi
            [ debug ]    mkdir -p /tmp/ompi//usr/local/lib/libfabric
            [ debug ]    mkdir -p /tmp/ompi/var/lib/hugetlbfs
            [ debug ]    mkdir -p /tmp/ompi/var/opt/cray/alps/spool
            [ debug ]    mkdir -p /tmp/ompi/opt/cray/wlm_detect
            [ debug ]    mkdir -p /tmp/ompi/etc/opt/cray/wlm_detect
            [ debug ]    mkdir -p /tmp/ompi/opt/cray/udreg
            [ debug ]    mkdir -p /tmp/ompi/opt/cray/xpmem
            [ debug ]    mkdir -p /tmp/ompi/opt/cray/ugni
            [ debug ]    mkdir -p /tmp/ompi/opt/cray/alps
            [ debug ]    echo '/lib64' >> /tmp/ompi/etc/ld.so.conf.d/ch-ofi.conf
            [ debug ]    echo '/opt/cray/alps/lib64' >> /tmp/ompi/etc/ld.so.conf.d/ch-ofi.conf
            [ debug ]    echo '/opt/cray/udreg/lib64' >> /tmp/ompi/etc/ld.so.conf.d/ch-ofi.conf
            [ debug ]    echo '/opt/cray/ugni/lib64' >> /tmp/ompi/etc/ld.so.conf.d/ch-ofi.conf
            [ debug ]    echo '/opt/cray/wlm_detect/lib64' >> /tmp/ompi/etc/ld.so.conf.d/ch-ofi.conf
            [ debug ]    echo '/opt/cray/xpmem/lib64' >> /tmp/ompi/etc/ld.so.conf.d/ch-ofi.conf
            [ debug ]    echo '/usr/lib64' >> /tmp/ompi/etc/ld.so.conf.d/ch-ofi.conf
            [ debug ]    /home/ofi/libgnix-fi.so -> //usr/local/lib/libfabric (inferred)
            [ debug ] running ldconfig
            [ debug ]    ch-run -w /tmp/ompi -- /sbin/ldconfig
            [ debug ] validating ldconfig cache
            done

            $ ch-run /tmp/ompi -- fi_info -p gni
            provider: gni
              fabric: gni
              [...]
              type: FI_EP_RDM
              protocol: FI_PROTO_GNI

  Arbitrary

Place shared library /usr/lib64/libfoo.so at path /usr/lib/libfoo.so (assuming /usr/lib is the first directory searched by the dynamic loader in the image), within the image /var/tmp/baz and executable /bin/bar at path /usr/bin/bar. Then, create appropriate symlinks to libfoo and update the ld.so cache.

            $ cat qux.txt
            /bin/bar
            /usr/lib64/libfoo.so
            $ ch-fromhost --file qux.txt /var/tmp/baz

Same as above:

            $ ch-fromhost --cmd 'cat qux.txt' /var/tmp/baz

Same as above:

            $ ch-fromhost --path /bin/bar --path /usr/lib64/libfoo.so /var/tmp/baz

Same as above, but place the files into /corge instead (and the shared library will not be found by ldconfig):

            $ ch-fromhost --dest /corge --file qux.txt /var/tmp/baz

Same as above, and also place file /etc/quux at /etc/quux within the container:

            $ ch-fromhost --file qux.txt --dest /etc --path /etc/quux /var/tmp/baz

Inject the executables and libraries recommended by nVidia into the image, and then run ldconfig:

            $ ch-fromhost --nvidia /var/tmp/baz
            asking ldconfig for shared library destination
            /sbin/ldconfig: Can’t stat /libx32: No such file or directory
            /sbin/ldconfig: Can’t stat /usr/libx32: No such file or directory
            shared library destination: /usr/lib64//bind9-export
            injecting into image: /var/tmp/baz
              /usr/bin/nvidia-smi -> /usr/bin (inferred)
              /usr/bin/nvidia-debugdump -> /usr/bin (inferred)
              /usr/bin/nvidia-persistenced -> /usr/bin (inferred)
              /usr/bin/nvidia-cuda-mps-control -> /usr/bin (inferred)
              /usr/bin/nvidia-cuda-mps-server -> /usr/bin (inferred)
              /usr/lib64/libnvidia-ml.so.460.32.03 -> /usr/lib64//bind9-export (inferred)
              /usr/lib64/libnvidia-cfg.so.460.32.03 -> /usr/lib64//bind9-export (inferred)
            [...]
              /usr/lib64/libGLESv2_nvidia.so.460.32.03 -> /usr/lib64//bind9-export (inferred)
              /usr/lib64/libGLESv1_CM_nvidia.so.460.32.03 -> /usr/lib64//bind9-export (inferred)
            running ldconfig

ACKNOWLEDGEMENTS

This command was inspired by the similar Shifter <http://www.nersc.gov/research-and-development/user-defined-images/> feature that allows Shifter containers to use the Cray Aries network. We particularly appreciate the help provided by Shane Canon and Doug Jacobsen during our implementation of --cray-mpi.

We appreciate the advice of Ryan Olson at nVidia on implementing --nvidia.

REPORTING BUGS

If Charliecloud was obtained from your Linux distribution, use your distribution’s bug reporting procedures.

Otherwise, report bugs to: <https://github.com/hpc/charliecloud/issues>

SEE ALSO

charliecloud(7)

Full documentation at: <<https://hpc.github.io/charliecloud>>

Copyright
contributors to the Charliecloud project, which has been established as “Charliecloud a Series of LF Projects, LLC”. For web site terms of use, trademark policy, and related information, please see: https://lfprojects.org.