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Added a new option --volume in run-*_container.sh
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Shuwei Ye authored and Shuwei Ye committed Oct 26, 2023
1 parent 3fb83e5 commit 3253b58
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Showing 2 changed files with 83 additions and 37 deletions.
67 changes: 44 additions & 23 deletions run-atlas_container.sh
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/bin/bash
# coding: utf-8
# version=2023-10-26-beta01
# version=2023-10-26-beta02
# author: Shuwei Ye <yesw@bnl.gov>
"true" '''\'
myScript="${BASH_SOURCE:-$0}"
Expand Down Expand Up @@ -67,7 +67,7 @@ from urllib.request import urlopen, Request
URL_MYSELF = "https://raw.githubusercontent.com/usatlas/ML-Containers/main/run-atlas_container.sh"
CONTAINER_CMDS = ['podman', 'docker', 'singularity']
ATLAS_PROJECTS = ['athena', 'analysisbase', 'athanalysis', 'analysistop', 'athanalysis']
ATLAS_PROJECTS = ['athena', 'analysisbase', 'athanalysis', 'analysistop']
DOCKERHUB_REPO = "https://hub.docker.com/v2/repositories/atlas"
Expand Down Expand Up @@ -299,7 +299,7 @@ def build_sandbox(sandboxPath, dockerPath, force=False):
# write setup for Singularity sandbox
def write_sandboxSetup(filename, inputArgs, imageInfo, sandboxPath, runOpt):
def write_sandboxSetup(filename, inputArgs, imageInfo, sandboxPath, bindOpt):
imageSize = imageInfo["imageCompressedSize"]
dockerPath = imageInfo["dockerPath"]
lastUpdate = imageInfo["lastUpdate"]
Expand All @@ -312,20 +312,20 @@ dockerPath=%s
imageCompressedSize=%s
imageLastUpdate=%s
sandboxPath=%s
runOpt="%s"
bindOpt="%s"
releaseSetup1="/release_setup.sh"
releaseSetup2="/home/atlas/release_setup.sh"
if [ -e $sandboxPath$releaseSetup1 -o $sandboxPath$releaseSetup2 ]; then
if [[ $# -eq 1 && "$1" =~ ^[Jj]upyter$ ]]; then
runCmd="echo Jupyter is not ready yet"
# runCmd="singularity exec $runOpt $sandboxPath /bin/bash -c "'"source $releaseSetup; jupyter lab"'
# runCmd="singularity exec $bindOpt $sandboxPath /bin/bash -c "'"source $releaseSetup; jupyter lab"'
else
if [ -e $releaseSetup1 ]; then
releaseSetup=$releaseSetup1
else
releaseSetup=$releaseSetup2
fi
runCmd="singularity run $runOpt $sandboxPath /bin/bash --init-file $releaseSetup"
runCmd="singularity run $bindOpt $sandboxPath /bin/bash --init-file $releaseSetup"
fi
echo -e "\\n$runCmd\\n"
eval $runCmd
Expand All @@ -334,12 +334,12 @@ else
echo "Please rebuild the Singularity sandbox by running the following"
echo -e "\n\t source %s $imageName"
fi
""" % (' '.join(inputArgs), dockerPath, imageSize, lastUpdate, sandboxPath, runOpt, myScript) )
""" % (' '.join(inputArgs), dockerPath, imageSize, lastUpdate, sandboxPath, bindOpt, myScript) )
shellFile.close()
# create docker/podman container
def create_container(contCmd, contName, imageInfo, force=False):
def create_container(contCmd, contName, imageInfo, bindOpt, force=False):
dockerPath = imageInfo['dockerPath']
pullCmd = "%s pull %s" % (contCmd, dockerPath)
retCode = subprocess.call(pullCmd.split())
Expand All @@ -363,7 +363,7 @@ def create_container(contCmd, contName, imageInfo, force=False):
sys.exit(1)
pwd = os.getcwd()
createOpt = "-it -v %s:%s -w %s %s" % (pwd, pwd, pwd, jupyterOpt)
createOpt = "-it -v %s:%s -w %s %s %s" % (pwd, pwd, pwd, jupyterOpt, bindOpt)
createCmd = "%s create %s --name %s %s" % \
(contCmd, createOpt, contName, dockerPath)
out = run_shellCmd(createCmd)
Expand All @@ -373,7 +373,7 @@ def create_container(contCmd, contName, imageInfo, force=False):
# write setup for Docker/Podman container
def write_dockerSetup(filename, inputArgs, contCmd, contName, imageInfo, override=False):
def write_dockerSetup(filename, inputArgs, contCmd, contName, imageInfo, bindOpt, override=False):
imageSize = imageInfo["imageCompressedSize"]
dockerPath = imageInfo["dockerPath"]
lastUpdate = imageInfo["lastUpdate"]
Expand All @@ -398,10 +398,9 @@ dockerPath=%s
imageCompressedSize=%s
imageLastUpdate=%s
contName=%s
# releaseSetup1="/release_setup.sh"
bindOpt="%s"
releaseSetup="/home/atlas/release_setup.sh"
jupyterOpt="-p 8888:8888 -e NB_USER=$USER -e HOME=$HOME -v ${HOME}:${HOME}"
jupyterOpt="$jupyterOpt -v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro"
re_exited="ago[\ ]+Exited"
re_up="ago[\ ]+Up"

Expand All @@ -418,7 +417,7 @@ elif [[ "$listOut" =~ $re_up ]]; then
eval $unpauseCmd >/dev/null
fi
else
createCmd="$contCmd create -it -v $PWD:$PWD -w $PWD $jupyterOpt --name $contName $dockerPath"
createCmd="$contCmd create -it $bindOpt -v $PWD:$PWD -w $PWD $jupyterOpt --name $contName $dockerPath"
echo -e "\\n$createCmd"
eval $createCmd >/dev/null
startCmd="$contCmd start $contName"
Expand Down Expand Up @@ -449,7 +448,7 @@ fi
stopCmd="$contCmd stop $contName"
echo -e "\\n$stopCmd"
eval $stopCmd
""" % (' '.join(inputArgs), contCmd, dockerPath, imageSize, lastUpdate, contName) )
""" % (' '.join(inputArgs), contCmd, dockerPath, imageSize, lastUpdate, contName, bindOpt) )
shellFile.close()
Expand Down Expand Up @@ -485,15 +484,15 @@ def cleanLast(filename):
contCmd = myImageInfo['contCmd']
if contCmd == 'singularity' or contCmd == 'apptainer':
sandboxPath = myImageInfo['sandboxPath']
print("Removing the last sandbox=", sandboxPath)
print("\nRemoving the last sandbox=%s\n" % sandboxPath)
try:
rmtree(sandboxPath)
except:
pass
os.rename(filename, filename + '.last')
else:
contName = myImageInfo['contName']
print("Removing the last container=", contName)
print("\nRemoving the last container=%s\n" % contName)
rmCmd = "%s rm -f %s" % (contCmd, contName)
run_shellCmd(rmCmd, exitOnFailure=False)
os.rename(filename, filename + '.last')
Expand All @@ -519,8 +518,6 @@ def setup(args):
print("Please install one of the above tool first")
sys.exit(1)
cleanLast(args.shellFilename)
contCmd = contCmds[0]
if args.contCmd is not None:
if args.contCmd in contCmds:
Expand All @@ -531,21 +528,44 @@ def setup(args):
print("\t",contCmds)
sys,exit(1)
cleanLast(args.shellFilename)
paths = args.volume
volumes = []
if paths is not None:
pwd = os.getcwd()
home = os.path.expanduser("~")
for path in paths.split(','):
if os.path.samefile(pwd, path):
continue
elif contCmd == "singularity" and os.path.samefile(home, path):
continue
volumes += [path]
if contCmd == "singularity":
if not os.path.exists("singularity"):
os.mkdir("singularity")
sandboxPath = "singularity/%s-%s" % (project, release)
build_sandbox(sandboxPath, dockerPath, args.force)
runOpt = ''
write_sandboxSetup(args.shellFilename, args.tags, imageInfo, sandboxPath, runOpt)
bindOpt = ''
for path in volumes:
bindOpt += " -B %s" % path
write_sandboxSetup(args.shellFilename, args.tags, imageInfo, sandboxPath, bindOpt)
elif contCmd == "podman" or contCmd == "docker":
testCmd = "%s info" % contCmd
run_shellCmd(testCmd)
contName = '_'.join([getpass.getuser(), project, release])
create_container(contCmd, contName, imageInfo, args.force)
write_dockerSetup(args.shellFilename, args.tags, contCmd, contName, imageInfo, args.force)
bindOpt = ''
for path in volumes:
if path.find(':') > 0:
bindOpt += " -v %s" % path
else:
bindOpt += " -v %s:%s" % (path, path)
create_container(contCmd, contName, imageInfo, bindOpt, args.force)
write_dockerSetup(args.shellFilename, args.tags, contCmd, contName, imageInfo, bindOpt, args.force)
sleep(1)
Expand All @@ -566,7 +586,7 @@ def main():

source %s listReleases AthAnalysis
source %s listReleases AthAnalysis,"21.2.2*"
source %s AnalysisBase:21.2.132
source %s AnalysisBase:latest
source %s # Empty arg to rerun the already setup container
source %s setup AnalysisBase,21.2.132""" % ((myScript,)*5)
Expand Down Expand Up @@ -604,6 +624,7 @@ def main():
action="store_const", const="%s" % cmd,
help="Use %s to the container" % cmd)
sp_setup.add_argument('-f', '--force', action='store_true', default=False, help="Force to override the existing container/sandbox")
sp_setup.add_argument('--volume', nargs='?', metavar='path[,srcPath:targePath]', help="Additional path(s) delimited by comma, to be mounted into the container")
sp_setup.add_argument('tags', nargs='+', metavar='<ReleaseTags>', help='A release to run')
sp_setup.set_defaults(func=setup)
set_default_subparser(parser, 'setup', 3)
Expand Down
53 changes: 39 additions & 14 deletions run-ml_container.sh
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/bin/bash
# coding: utf-8
# version=2023-10-26-r01
# version=2023-10-26-r02
"true" '''\'
myScript="${BASH_SOURCE:-$0}"
ret=0
Expand Down Expand Up @@ -410,7 +410,7 @@ fi
# create docker/podman container
def create_container(contCmd, contName, dockerPath, force=False):
def create_container(contCmd, contName, dockerPath, bindOpt, force=False):
pullCmd = "%s pull %s" % (contCmd, dockerPath)
retCode = subprocess.call(pullCmd.split())
username = getpass.getuser()
Expand All @@ -432,7 +432,7 @@ def create_container(contCmd, contName, dockerPath, force=False):
sys.exit(1)
pwd = os.getcwd()
createOpt = "-it -v %s:%s -w %s %s" % (pwd, pwd, pwd, jupyterOpt)
createOpt = "-it -v %s:%s -w %s %s %s" % (pwd, pwd, pwd, jupyterOpt, bindOpt)
createCmd = "%s create %s --name %s %s" % \
(contCmd, createOpt, contName, dockerPath)
out = run_shellCmd(createCmd)
Expand All @@ -442,7 +442,7 @@ def create_container(contCmd, contName, dockerPath, force=False):
# write setup for Docker/Podman container
def write_dockerSetup(filename, imageName, dockerPath, contCmd, contName, override=False):
def write_dockerSetup(filename, imageName, dockerPath, contCmd, contName, bindOpt, override=False):
imageInfo = getImageInfo(None, imageName, printOut=False)
imageSize = imageInfo["imageSize"]
lastUpdate = imageInfo["lastUpdate"]
Expand All @@ -462,6 +462,7 @@ imageDigest=%s
dockerPath=%s
linesCondaHistory=%s
contName=%s
runOpt="%s"
jupyterOpt="-p 8888:8888 -e NB_USER=$USER -e HOME=$HOME -v ${HOME}:${HOME}"
jupyterOpt="$jupyterOpt -v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro"
re_exited="ago[\ ]+Exited"
Expand Down Expand Up @@ -499,7 +500,7 @@ fi
echo -e "\\n$runCmd\\n"
eval $runCmd
""" % (contCmd, imageName, imageSize, lastUpdate, imageDigest,
dockerPath, linesCondaHistory, contName) )
dockerPath, linesCondaHistory, contName, bindOpt) )
shellFile.close()
Expand Down Expand Up @@ -547,15 +548,15 @@ def cleanLast(filename):
contCmd = myImageInfo['contCmd']
if contCmd == 'singularity' or contCmd == 'apptainer':
sandboxPath = myImageInfo['sandboxPath']
print("Removing the last sandbox=", sandboxPath)
print("\nRemoving the last sandbox=%s\n" % sandboxPath)
try:
rmtree(sandboxPath)
except:
pass
os.rename(filename, filename + '.last')
else:
contName = myImageInfo['contName']
print("Removing the last container=", contName)
print("\nRemoving the last container=%s\n" % contName)
rmCmd = "%s rm -f %s" % (contCmd, contName)
run_shellCmd(rmCmd, exitOnFailure=False)
os.rename(filename, filename + '.last')
Expand Down Expand Up @@ -589,8 +590,6 @@ def setup(args):
print("Please install one of the above tool first")
sys.exit(1)
cleanLast(args.shellFilename)
contCmd = contCmds[0]
if args.contCmd is not None:
if args.contCmd in contCmds:
Expand All @@ -601,6 +600,20 @@ def setup(args):
print("\t",contCmds)
sys,exit(1)
cleanLast(args.shellFilename)
paths = args.volume
volumes = []
if paths is not None:
pwd = os.getcwd()
home = os.path.expanduser("~")
for path in paths.split(','):
if os.path.samefile(pwd, path):
continue
elif contCmd == "singularity" and os.path.samefile(home, path):
continue
volumes += [path]
if contCmd == "singularity":
if not os.path.exists("singularity"):
os.mkdir("singularity")
Expand All @@ -611,6 +624,9 @@ def setup(args):
runCmd = "singularity run -w %s" % imageFullPath
runOpt = '-w'
for path in volumes:
runOpt += " -B %s" % path
# Check if Home bind-mount works with --writable mode
# if not, add the option --no-home
testCmd = runCmd + " ls /dev/null >/dev/null 2>&1"
Expand All @@ -624,9 +640,16 @@ def setup(args):
run_shellCmd(testCmd)
contName = '_'.join([getpass.getuser(), imageName, tagName])
create_container(contCmd, contName, dockerPath, args.force)
bindOpt = ''
for path in volumes:
if path.find(':') > 0:
bindOpt += " -v %s" % path
else:
bindOpt += " -v %s:%s" % (path, path)
create_container(contCmd, contName, dockerPath, bindOpt, args.force)
write_dockerSetup(args.shellFilename, imageFullName, dockerPath,
contCmd, contName, args.force)
contCmd, contName, bindOpt, args.force)
sleep(1)
Expand Down Expand Up @@ -678,6 +701,7 @@ def update(args):
latestImageInfo = getImageInfo(None, myImageName, printOut=False)
latestUpdate = latestImageInfo["lastUpdate"]
latestDigest = latestImageInfo["imageDigest"]
runOpt = myImageInfo["runOpt"].strip('"')
if latestUpdate > myImageUpdate and myImageDigest != latestDigest:
print("Update is available with the last update date=%s" % latestUpdate)
print("\twith the corresponding image digest =", latestDigest)
Expand All @@ -701,11 +725,11 @@ def update(args):
if contCmd == 'singularity':
build_sandbox(contNamePath, dockerPath, force=True)
write_sandboxSetup(args.shellFilename, myImageName, dockerPath, \
contNamePath, myImageInfo["runOpt"].strip('"'))
contNamePath, runOpt)
else:
create_container(contCmd, contNamePath, dockerPath, force=True)
create_container(contCmd, contNamePath, dockerPath, runOpt, force=True)
write_dockerSetup(args.shellFilename, myImageName, dockerPath, \
contCmd, contNamePath, override=True)
contCmd, contNamePath, runOpt, override=True)
if len(pkgs) > 0:
install_newPkgs(contCmd, contNamePath, pkgs, channels)
Expand Down Expand Up @@ -798,6 +822,7 @@ def main():
action="store_const", const="%s" % cmd,
help="Use %s to the container" % cmd)
sp_setup.add_argument('-f', '--force', action='store_true', default=False, help="Force to override the existing container/sandbox")
sp_setup.add_argument('--volume', nargs='?', metavar='path[,srcPath:targePath]', help="Additional path(s) delimited by comma, to be mounted into the container")
sp_setup.add_argument('name', metavar='<ImageName>', help='image name to run')
sp_setup.set_defaults(func=setup)
set_default_subparser(parser, 'setup', 3)
Expand Down

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