A collection of scripts for Shifter @ NERSC
This script takes one or more executables or libraries (-f flag), determines the libraries that are linked to the file, and copies those libraries into a specified directory (-d flag). This directory should be the VTune results directory. By copying the libraries into this directory, VTune can finalize the results outside of a Shifter container. If the recursive flag (-r) is provided, this script will find and copy the implicitly linked libraries.
-f: executable or library [required]- Accepts 1 or more arguments
-d: output directory [optional]- Accepts only one arguments
- Default: current working directory
-r: enable recursion [optional]- Accepts zero arguments
- Enables copying of implicitly linked libraries
myexelinks to libfoo.so- libfoo.so links to libbar.so
- Within recursion enabled,
shiftercp.pywill copy libbar.so into the output directory
--max-depth=<N>: limits the depth of recursion [optional]- Accepts one integer argument
- Default:
0 N == 0means unlimited, all implicitly linked libraries will be found and copied- Only used in conjunction with
-rflag - Example:
myexelinks to libfoo.so- libfoo.so links to libbar.so (level 1)
- libbar.so links to librt.so (level 2)
- librt.so links to libdc.so (level 3)
- if
N == 0, all above libraries will be copied to output directory - if
N == 1, libfoo.so and libbar.so will be copied to output directory - if
N == 2, libfoo.so, libbar.so, and librt.so will be copied to output directory
-e: regex string [optional]- Accepts one or more strings
- Disabled copying libraries that match the regex string
- See Python re documentation for Regex information
- Uses
re.search(..., <library-name>)
--copy-files: copy the list of files (e.g.-fparameters) to output directory [optional]- Accepts zero arguments
- The list of files provided by
-fflag will also be copied to output directory
- VTune results directory:
vtune-run0001 - Profiled command:
/usr/local/bin/myexewithin Shifter container - Assumes
./shiftercp.pyis in CWD
#!/bin/bash
#SBATCH --qos=debug
#SBATCH -N 1
#SBATCH -t 00:30:00
#SBATCH --image=<username/some-image>
# ... additional sbatch parameters ...
module load vtune
PID_FILE=$(mktemp pid.XXXXXXX)
VTUNE_DIR=${PWD}/vtune-run0001
# run command in shifter, submit to background
shifter /usr/local/bin/myexe & echo $! &> ${PID_FILE}
# attach VTune to process, defer finalization
amplxe-cl -collect <collection-mode> -finalization-mode deferred -r ${VTUNE_DIR} --target-pid=$(cat ${PID_FILE}) ...
# use script to copy libraries linked to myexe into ${VTUNE_DIR}
shifter ./shiftercp.py -d ${VTUNE_DIR} -f /usr/local/bin/myexe
# then, finalize on a login nodeusage: shiftercp.py [-h] [-f [FILES [FILES ...]]] [-d DESTINATION]
[-r] [--max-depth MAX_DEPTH]
[-e [EXCLUDE [EXCLUDE ...]]]
optional arguments:
-h, --help show this help message and exit
-f [FILES [FILES ...]], --files [FILES [FILES ...]]
Get linked targets for this list of files
-d DESTINATION, --destination DESTINATION
Destination directory (default:
'${PWD}')
-r, --recursive Recursive ldd/otool resolution
--max-depth MAX_DEPTH
Max recursive depth (default: 0 == unlimited)
-e [EXCLUDE [EXCLUDE ...]], --exclude [EXCLUDE [EXCLUDE ...]]
List of regex expressions to exclude from copy using
're.search(<str>, <path>)' (default: []), e.g.
'^/usr/lib[6]?[4]?/lib.*\.so\.[0-9]$'$ ./shiftercp.py -r -d example -f $(which python)
Libraries copied to example:
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
/opt/local/Library/Frameworks/Python.framework/Versions/3.6/Python
/opt/local/lib/libiconv.2.dylib
/opt/local/lib/libintl.8.dylib
/usr/lib/closure/libclosured.dylib
/usr/lib/libDiagnosticMessagesClient.dylib
/usr/lib/libSystem.B.dylib
/usr/lib/libc++.1.dylib
/usr/lib/libc++abi.dylib
/usr/lib/libicucore.A.dylib
/usr/lib/libobjc.A.dylib
/usr/lib/libz.1.dylib
/usr/lib/system/libcache.dylib
/usr/lib/system/libcommonCrypto.dylib
/usr/lib/system/libcompiler_rt.dylib
/usr/lib/system/libcopyfile.dylib
/usr/lib/system/libcorecrypto.dylib
/usr/lib/system/libdispatch.dylib
/usr/lib/system/libdyld.dylib
/usr/lib/system/libkeymgr.dylib
/usr/lib/system/liblaunch.dylib
/usr/lib/system/libmacho.dylib
/usr/lib/system/libquarantine.dylib
/usr/lib/system/libremovefile.dylib
/usr/lib/system/libsystem_asl.dylib
/usr/lib/system/libsystem_blocks.dylib
/usr/lib/system/libsystem_c.dylib
/usr/lib/system/libsystem_configuration.dylib
/usr/lib/system/libsystem_coreservices.dylib
/usr/lib/system/libsystem_darwin.dylib
/usr/lib/system/libsystem_dnssd.dylib
/usr/lib/system/libsystem_info.dylib
/usr/lib/system/libsystem_kernel.dylib
/usr/lib/system/libsystem_m.dylib
/usr/lib/system/libsystem_malloc.dylib
/usr/lib/system/libsystem_network.dylib
/usr/lib/system/libsystem_networkextension.dylib
/usr/lib/system/libsystem_notify.dylib
/usr/lib/system/libsystem_platform.dylib
/usr/lib/system/libsystem_pthread.dylib
/usr/lib/system/libsystem_sandbox.dylib
/usr/lib/system/libsystem_secinit.dylib
/usr/lib/system/libsystem_symptoms.dylib
/usr/lib/system/libsystem_trace.dylib
/usr/lib/system/libunwind.dylib
/usr/lib/system/libxpc.dylib
$ ls example/
CoreFoundation libcommonCrypto.dylib libintl.8.dylib
libsystem_blocks.dylib libsystem_m.dylib libsystem_secinit.dylib
Python libcompiler_rt.dylib libkeymgr.dylib
libsystem_c.dylib libsystem_malloc.dylib libsystem_symptoms.dylib
libDiagnosticMessagesClient.dylib libcopyfile.dylib liblaunch.dylib
libsystem_configuration.dylib libsystem_network.dylib libsystem_trace.dylib
libSystem.B.dylib libcorecrypto.dylib libmacho.dylib
libsystem_coreservices.dylib libsystem_networkextension.dylib libunwind.dylib
libc++.1.dylib libdispatch.dylib libobjc.A.dylib
libsystem_darwin.dylib libsystem_notify.dylib libxpc.dylib
libc++abi.dylib libdyld.dylib libquarantine.dylib
libsystem_dnssd.dylib libsystem_platform.dylib libz.1.dylib
libcache.dylib libiconv.2.dylib libremovefile.dylib
libsystem_info.dylib libsystem_pthread.dylib libclosured.dylib
libicucore.A.dylib libsystem_asl.dylib libsystem_kernel.dylib
libsystem_sandbox.dylib
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