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#!/bin/sh
# The basic algorithm here is that we build up a list of file
# source:destination pairs separated by newlines, then walk through them and
# copy them into the image.
#
# The colon separator is to avoid the difficulty of iterating through a
# sequence of pairs with no arrays or structures in POSIX sh. We could avoid
# it by taking action immediately upon encountering each file in the argument
# list, but that would (a) yield a half-injected image for basic errors like
# misspellings on the command line and (b) would require the image to be first
# on the command line, which seems awkward.
#
# The newline separator is for the same reason and also because it's
# convenient for input from --cmd and --file.
#
# Note on looping through the newlines in a variable: The approach in this
# script is to set IFS to newline, loop, then restore. This is awkward but
# seemed the least bad. Alternatives include:
#
# 1. Piping echo into "while read -r": This executes the while in a
# subshell, so variables don't stick.
#
# 2. Here document used as input, e.g.:
#
# while IFS= read -r FILE; do
# ...
# done <<EOF
# $FILES
# EOF
#
# This works but seems more awkward.
#
# 3. Here string, e.g. 'while IFS= read -r FILE; do ... done <<< "$FILES"'.
# This is a bashism.
ch_lib=$(cd "$(dirname "$0")" && pwd)/../lib
. "${ch_lib}/base.sh"
set -e
usage=$(cat <<EOF
Inject files from the host into an image directory, with various magic.
Usage:
$ ch-fromhost [OPTION ...] [FILE_OPTION ...] IMGDIR
Which files to inject (one or more required; can be repeated):
-c, --cmd CMD listed in the stdout of CMD
-f, --file FILE listed in file FILE
-p, --path PATH inject the file at PATH
--cray-cxi inject cray’s libfabric and cxi libraries from cray host
--cray-gni inject gemini/aries libfabric for MPI on xc40 machines
--nvidia recommended by nVidia (via \"nvidia-container-cli list\")
Destination within image:
-d, --dest DST place following files in IMGDIR/DST, overriding inference
Options:
--print-cray-fi print inferred destination for libfabric replacement
--print-fi print inferred destination for libfabric provider(s)
--print-lib print inferred destination for shared libraries
--no-ldconfig don’t run ldconfig even if we injected shared libraries
-h, --help print this help and exit
-q, --quiet make the program more quiet, can be repeated
-v, --verbose list the injected files
--version print version and exit
NOTE: This command is experimental. Features may be incomplete and/or buggy.
EOF
)
dest=
image=
newline='
'
inject_files= # source:destination files to inject
inject_mkdirs= # directories to create in image (image-rooted)
inject_unlinks= # files to rm -f (not rmdir or rm -Rf) (image-rooted)
cray_fi_dest=
cray_fi_found=
fi_prov_dest=
fi_prov_found=
lib_dest=
lib_found=
print_cray_fi_dest=
print_fi_dest=
print_lib_dest=
no_ldconfig=
ensure_nonempty () {
[ "$2" ] || FATAL -- "$1 must not be empty"
}
is_bin () {
case $1 in
*/bin*|*/sbin*)
return 0
;;
*)
return 1
esac
}
is_so () {
case $1 in
*/lib*)
return 0
;;
*.so)
return 0
;;
*)
return 1
esac
}
enqueue_file () {
old_ifs="$IFS"
IFS="$newline"
d="${dest:-$2}"
VERBOSE "enqueue file(s)"
for f in $1; do
case $f in
*:*)
FATAL "paths can't contain colon: ${f}"
;;
esac
if is_so "$f"; then
case $f in
*libfabric.so)
if ldd "$f" | grep libcxi > /dev/null 2>&1; then
DEBUG "cray libfabric: ${f}"
cray_fi_found=yes
host_libfabric=$f
else
DEBUG "libfabric: ${f}"
lib_found=yes
fi
;;
*-fi.so)
DEBUG "libfabric shared provider: ${f}"
fi_prov_found=yes
# Providers, like Cray's libgnix-fi.so, link against paths that
# need to be bind-mounted at run-time. Some of these paths need
# to be added to ldconf; thus, add the linked paths to a ldconf
# list to be added into the image.
ldds=$(ldd "$f" 2>&1 | grep lib | awk '{print $3}' | sort -u)
for l in $ldds; do
ld=$(dirname "$(readlink -f "$l")")
# Avoid duplicates and host libfabric.so.
if [ "$(echo "$ld_conf" | grep -c "$ld")" -eq 0 ] \
&& [ "$(echo "$ld" | grep -c "libfabric.so")" -eq 0 ]; \
then
enqueue_ldconf "$ld"
fi
done
;;
*)
DEBUG "shared library: ${f}"
lib_found=yes
;;
esac
fi
# This adds a delimiter only for the second and subsequent files.
# https://chris-lamb.co.uk/posts/joining-strings-in-posix-shell
#
# If destination empty, we'll infer it later.
inject_files="${inject_files:+$inject_files$newline}$f:$d"
done
IFS="$old_ifs"
}
enqueue_ldconf () {
[ "$1" ]
ld_conf="${ld_conf:+$ld_conf$newline}$1"
}
queue_mkdir () {
[ "$1" ]
inject_mkdirs="${inject_mkdirs:+$inject_mkdirs$newline}$1"
}
queue_unlink () {
[ "$1" ]
inject_unlinks="${inject_unlinks:+$inject_unlinks$newline}$1"
}
warn () {
printf '< warn >! %s\n' "$1" 1>&2
}
warn_fi_var () {
if [ -n "$FI_PROVIDER" ]; then
warn "FI_PROVIDER=$FI_PROVIDER set; this will be preferred provider at runtime."
fi
if [ -n "$FI_PROVIDER_PATH" ]; then
warn "FI_PROVIDER_PATH=$FI_PROVIDER_PATH set; --dest required"
fi
}
if [ "$#" -eq 0 ]; then
usage 1
fi
while [ $# -gt 0 ]; do
opt=$1; shift
if ! parse_basic_arg "$opt"; then
case $opt in
-c|--cmd)
ensure_nonempty --cmd "$1"
out=$($1) || FATAL "command failed: $1"
enqueue_file "$out"
shift
;;
--cray-cxi)
warn_fi_var
if [ -z "$CH_FROMHOST_OFI_CXI" ]; then
FATAL "CH_FROMHOST_OFI_CXI is not set"
fi
enqueue_file "$CH_FROMHOST_OFI_CXI"
;;
--cray-gni)
warn_fi_var
if [ -z "$CH_FROMHOST_OFI_GNI" ]; then
FATAL "CH_FROMHOST_OFI_GNI is not set"
fi
enqueue_file "$CH_FROMHOST_OFI_GNI"
;;
-d|--dest)
ensure_nonempty --dest "$1"
dest=$1
shift
;;
-f|--file)
ensure_nonempty --file "$1"
out=$(cat "$1") || FATAL "cannot read file: ${1}"
enqueue_file "$out"
shift
;;
# Note: Specifying any of the --print-* options along with one of
# the file specification options will result in all the file
# gathering and checking work being discarded.
--print-cray-fi)
cray_fi_found=yes
print_cray_fi_dest=yes
;;
--print-fi)
fi_prov_found=yes
print_fi_dest=yes
;;
--print-lib)
lib_found=yes
print_lib_dest=yes
;;
--no-ldconfig)
no_ldconfig=yes
;;
--nvidia)
out=$(nvidia-container-cli list --binaries --libraries) \
|| FATAL "nvidia-container-cli failed; does this host have GPUs?"
enqueue_file "$out"
;;
-p|--path)
ensure_nonempty --path "$1"
enqueue_file "$1"
shift
;;
-*)
INFO "invalid option: ${opt}"
usage
;;
*)
ensure_nonempty "image path" "${opt}"
[ -z "$image" ] || FATAL "duplicate image: ${opt}"
[ -d "$opt" ] || FATAL "image not a directory: ${opt}"
image="$opt"
;;
esac
fi
done
if [ -n "$FI_PROVIDER_PATH" ] && [ -n "$fi_prov_found" ] && [ -z "$dest" ]; then
FATAL "FI_PROVIDER_PATH set; missing --dest"
fi
[ "$image" ] || FATAL "no image specified"
if [ -n "$cray_fi_found" ]; then
# There is no Slingshot provider CXI; to leverage slingshot we need to
# replace the image libfabric.so with Cray's.
VERBOSE "searching image for inferred libfabric destination"
img_libfabric=$(find "$image" -name "libfabric.so")
[ -n "$img_libfabric" ] || FATAL "libfabric.so not found in $image"
DEBUG "found $img_libfabric"
if [ "$(echo "$img_libfabric" | wc -l)" -ne 1 ]; then
warn 'found more than one libfabric.so'
fi
img_libfabric_path=$(echo "$img_libfabric" | sed "s@$image@@")
cray_fi_dest=$(dirname "/$img_libfabric_path")
# Since cray's libfabric isn't a standard provider, to use slingshot we
# must also add any missing linked libraries from the host.
VERBOSE "adding cray libfabric libraries"
ldds=$(ldd "$host_libfabric" 2>&1 | grep lib | awk '{print $3}' | sort -u)
for l in $ldds; do
# Do not replace any libraries found in the image, experimentation has
# shown this to be problematic. Perhaps revisit in the future. For now,
# both MPICH and OpenMPI examples work with this conservative approach.
file_found=$(find "${image}" -name "$(basename "$l")")
if [ -n "$file_found" ]; then
DEBUG "skipping $l"
continue
fi
enqueue_file "$l"
file_dir=$(dirname "$l")
# Avoid duplicates.
if [ "$(echo "$ld_conf" | grep -c "$file_dir")" -eq 0 ]; then
enqueue_ldconf "$file_dir"
fi
done
fi
if [ -n "$lib_found" ]; then
# We want to put the libraries in the first directory that ldconfig
# searches, so that we can override (or overwrite) any of the same library
# that may already be in the image.
VERBOSE "asking ldconfig for inferred shared library destination"
# "ldconfig -Nv" gives pointless warnings on stderr even if successful; we
# don't want to show those to users (unless -vv or higher). However, we
# don't want to simply pipe stderr to /dev/null because this hides real
# errors. Thus, use the following abomination to pipe stdout and stderr to
# *separate grep commands*. See: https://stackoverflow.com/a/31151808
if [ "$log_level" -lt 2 ]; then # VERBOSE or lower
stderr_filter='(^|dynamic linker, ignoring|given more than once|No such file or directory)$'
else # DEBUG or higher
stderr_filter=weird_al_yankovic_will_not_appear_in_ldconfig_output
fi
lib_dest=$( { "${ch_bin}/ch-run" "$image" -- /sbin/ldconfig -Nv \
2>&1 1>&3 3>&- | grep -Ev "$stderr_filter" ; } \
3>&1 1>&2 | grep -E '^/' | cut -d: -f1 | head -1 )
[ -n "$lib_dest" ] || FATAL 'empty path from ldconfig'
[ -z "${lib_dest%%/*}" ] || FATAL "bad path from ldconfig: ${lib_dest}"
VERBOSE "inferred shared library destination: ${image}/${lib_dest}"
fi
if [ -n "$fi_prov_found" ]; then
# The libfabric provider can be specified with FI_PROVIDER. The path the
# search for shared providers at can be specified with FI_PROVIDER_PATH
# (undocumented). This complicates the inferred destination because these
# variables can be inherited from the host or explicitly set in the
# image's /ch/environment file.
#
# For simplicity, the inferred injection destination is the always the
# 'libfabric' directory at the path where libfabric.so is found. If it
# does not exist, create it. Warn if FI_PROVIDER_PATH or FI_PROVIDER is
# found in the the image's /ch/environment file.
VERBOSE "searching ${image} for libfabric shared provider destination"
ch_env_p=$(grep -E '^FI_PROVIDER_PATH=' "${image}/ch/environment") \
|| true # avoid -e exit
ch_env_p=${ch_env_p##*=}
if [ -n "$ch_env_p" ]; then
warn "FI_PROVIDER_PATH in ${image}/ch/environment; consider --dest"
fi
img_libfabric=$(find "$image" -name 'libfabric.so')
img_libfabric_path=$(echo "$img_libfabric" | sed "s@$image@@")
DEBUG "found: ${image}${img_libfabric_path}"
fi_prov_dest=$(dirname "/${img_libfabric_path}")
fi_prov_dest="${fi_prov_dest}/libfabric"
queue_mkdir "$fi_prov_dest"
VERBOSE "inferred provider destination: $fi_prov_dest"
fi
if [ -n "$print_lib_dest" ]; then
echo "$lib_dest"
exit 0
fi
if [ -n "$print_fi_dest" ]; then
echo "$fi_prov_dest"
fi
if [ -n "$print_cray_fi_dest" ]; then
echo "$cray_fi_dest"
fi
if [ -f /etc/opt/cray/release/cle-release ]; then
# Cray needs a pile of hugetlbfs filesystems mounted at
# /var/lib/hugetlbfs/global. Create mount point for ch-run.
queue_mkdir /var/lib/hugetlbfs
# UGNI
if [ ! -L /etc/opt/cray/release/cle-release ]; then
# ALPS libraries require the contents of this directory to be present
# at the same path as the host. Create the mount point here, then
# ch-run bind-mounts it later.
queue_mkdir /var/opt/cray/alps/spool
# The cray-ugni provider will link against cray’s libwlm_detect so.
# Create the mount point for ch-run.
queue_mkdir /opt/cray/wlm_detect
# libwlm_detect.so requires file(s) to present at the same path as the
# host. Create mount point for ch-run.
queue_mkdir /etc/opt/cray/wlm_detect
# OFI uGNI provider, libgnix-fi.so, links against the Cray host’s
# libxpmem, libudreg, libalpsutil, libalpslli, and libugni; create
# mount points for ch-run to use later.
queue_mkdir /opt/cray/udreg
queue_mkdir /opt/cray/xpmem
queue_mkdir /opt/cray/ugni
queue_mkdir /opt/cray/alps
fi
# CXI (slingshot)
if [ -f /opt/cray/etc/release/cos ]; then
# Newer Cray Shasta environments require the contents of this
# directory to be present at the same path as the host. Create mount
# points for ch-run to use later.
queue_mkdir /var/spool/slurmd
fi
fi
[ "$inject_files" ] || FATAL "empty file list"
VERBOSE "injecting into image: ${image}"
old_ifs="$IFS"
IFS="$newline"
# Process unlink list.
for u in $inject_unlinks; do
DEBUG "deleting: ${image}${u}"
rm -f "${image}${u}"
done
# Process bind-mount destination targets.
for d in $inject_mkdirs; do
DEBUG "mkdir: ${image}${d}"
mkdir -p "${image}${d}"
done
# Process ldconfig targets.
if [ "$fi_prov_found" ] || [ "$cray_fi_found" ]; then
if [ ! -f "${image}/etc/ld.so.conf" ]; then
DEBUG "creating empty ld.so.conf"
touch "${image}/etc/ld.so.conf"
fi
if ! grep -F 'include ld.so.conf.d/*.conf' "${image}/etc/ld.so.conf" \
> /dev/null 2>&1; then
DEBUG "ld.so.conf: adding 'include ld.so.conf.d/*.conf'"
echo 'include ld.so.conf.d/*.conf' >> "${image}/etc/ld.so.conf"
fi
# Prepare image ch-ofi.conf.
printf '' > "${image}/etc/ld.so.conf.d/ch-ofi.conf"
# add ofi dso provider ld library dirs.
for c in $ld_conf; do
DEBUG "ld.so.conf: adding ${c}"
echo "$c" >> "${image}/etc/ld.so.conf.d/ch-ofi.conf"
done
fi
for file in $inject_files; do
f="${file%%:*}"
d="${file#*:}"
infer=
if is_bin "$f" && [ -z "$d" ]; then
d=/usr/bin
infer=" (inferred)"
elif is_so "$f" && [ -z "$d" ]; then
case "$f" in
*libfabric.so)
d=$lib_dest
if ldd "$f" | grep libcxi > /dev/null 2>&1; then
d=$cray_fi_dest
fi
;;
*-fi.so)
d=$fi_prov_dest
;;
*)
d=$lib_dest
;;
esac
infer=" (inferred)"
fi
VERBOSE "${f} -> ${d}${infer}"
[ "$d" ] || FATAL "no destination for: ${f}"
[ -z "${d%%/*}" ] || FATAL "not an absolute path: ${d}"
[ -d "${image}${d}" ] || FATAL "not a directory: ${image}${d}"
if [ ! -w "${image}${d}" ]; then
# Some images unpack with unwriteable directories; fix. This seems
# like a bit of a kludge to me, so I'd like to remove this special
# case in the future if possible. (#323)
INFO "${image}${d} not writeable; fixing"
chmod u+w "${image}${d}" || FATAL "can't chmod u+w: ${image}${d}"
fi
cp --dereference --preserve=all "$f" "${image}${d}" \
|| FATAL "cannot inject: ${f}"
done
IFS="$old_ifs"
if [ -z "$no_ldconfig" ] \
&& { [ "$lib_found" ] \
|| [ "$fi_prov_found" ] \
|| [ "$cray_fi_found" ] ;} then
VERBOSE "running ldconfig"
"${ch_bin}/ch-run" -w "$image" -- /sbin/ldconfig 2> /dev/null \
|| FATAL 'ldconfig error'
if [ -n "$fi_prov_found" ] || [ -n "$cray_fi_found" ]; then
VERBOSE "validating ldconfig cache"
for file in $inject_files; do
f="$(basename "${file%%:*}")"
f=$( "${ch_bin}/ch-run" "$image" \
-- find / \
-not \( -path /proc -prune \) \
-not \( -path /dev -prune \) \
-not \( -path /tmp -prune \) \
-not \( -path /sys -prune \) \
-not \( -path /var/opt/cray -prune \) \
-not \( -path /etc/opt/cray -prune \) \
-name "$f")
if [ "$("${ch_bin}/ch-run" "$image" -- ldd "$f" | grep -c 'not found ')" -ne 0 ]; then
FATAL "ldconfig: '${ch_bin}/ch-run $image -- ldd $f' failed"
fi
done
fi
else
VERBOSE "not running ldconfig"
fi
echo 'done'
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