Teraflops of Jupyter: A Notebook Based Analysis Portal at BNL

Transcription

1 Teraflops of Jupyter: A Notebook Based Analysis Portal at BNL Ofer Rind Spring HEPiX, Madison, WI May 17,2018 In collaboration with: Doug Benjamin, Costin Caramarcu, Zhihua Dong, Will Strecker-Kellogg, Thomas Throwe

2 BNL SDCC Serves an increasingly diverse, multi-disciplinary user community: RHIC Tier-0, US ATLAS Tier-1 and Tier-3, Belle2 Tier-1, Neutrino, Astro, LQCD, CFN,. Large HTC infrastructure accessed via HTCondor (plus experiment-specific job management layers) Growing HPC infrastructure, currently with two production clusters accessed via Slurm Limited interactive resources accessed via ssh gateways

3 Interactive Data Analysis Wish list for running effective, interactive data analysis in an era of large-scale computing, with complex software stacks.? Lower the barrier to entry for using data analysis resources at BNL Minimize or eliminate software setup and installation Need flexible, easy-to-follow examples/tutorials Simple way to document and share results and code Reproducibility, adaptability Straightforward way to make use of software methods and ecosystems being developed in non-hep communities (e.g. machine learning) And make our resources more easily available to non-hep communities

4 Data Analysis As A Service Jupyter Notebooks (ipython) Provide a flexible, standardized, platform independent interface through a web browser No local software to install Many language extensions (kernels) and tools available Easy to share, reproduce, document results and create tutorials From the facility point of view: Can we implement this by leveraging existing resources? Would prefer to avoid building new dedicated infrastructure, such as a specialized cluster (cf. CERN Swan)

5 Some terminology Jupyter notebook: web-based application suitable for capturing the whole computation process: developing, documenting, and executing code, as well as communicating the results Jupyterlab: nextgeneration webbased user interface

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7 Some terminology Jupyterhub: multi-user hub, spawns, manages, and proxies multiple instances of the single-user Jupyter notebook server

8 Current Test Setup at BNL Jupyterhub servers deployed on RHEV Anaconda3 install Varying environments/networks depending on function: HTC/ Condor or HPC/Slurm Access via ssh tunnel through firewall to Jupyterhub https proxy Kerberos auth to Jupyterhub server Transparent setup leverages PAM stack Working on OAuth implementation Jira, confluence, etc. for documentation Temporary two node slurm reservation on Institutional Cluster (Broadwell/Nvidia) for testing How to connect users to the batch resources?

9 One approach: slurm_magic Execute usual CLI batch commands through notebook interface. Easily adapted for HTCondor as well. But not so satisfying could just open a terminal to do this anyway

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11 More useful approach: HTCondor API Provide access to distributed computing through familiar APIs (python s threading, multiprocessing, asyncio, etc ) I d like to submit and manage a job or cluster of jobs

12 More useful approach: HTCondor API At a higher level, abstract away the batch job layer I d like to run over a dataset Serialize function, ship off to jobs, serialize output, gather Early stage of development - see Will Strecker-Kellogg for details

13 Yet another approach: batchspawner Spawn ipython notebook itself within a single node batch job Notebook can be spawned locally or onto batch system, with connection established back to hub and to browser through the http proxy batchspawner.py with hooks for slurm, HTCondor, torque, etc. Also, wrapspawner.py, which allows for selection between multiple profile setups at startup. github.com/jupyterhub/wrapspawner Anaconda installation for batch users on shared gpfs volume

14 Slurm jupyterhub_config.py HTCondor + Profiles # # BatchSpawner(Spawner) configuration # Using Slurm to Spawn user to IC # c.jupyterhub.spawner_class = 'batchspawner.slurmspawner' # # BatchSpawnerBase configuration # These are simply setting parameters used in the job script template below # c.batchspawnerbase.req_nprocs = '1' c.batchspawnerbase.req_partition = 'long' c.batchspawnerbase.req_runtime = '120:00' c.batchspawnerbase.req_account = 'pq302951' c.slurmspawner.batch_script = '''#!/bin/sh #SBATCH --partition={partition} #SBATCH --time={runtime} #SBATCH --job-name=spawner-jupyterhub #SBATCH --workdir={homedir} #SBATCH --export={keepvars} #SBATCH --get-user-env=l #SBATCH --account={account} #SBATCH --reservation=racf_32 #SBATCH {options} {cmd} ''' # # ProfilesSpawner configuration # # List of profiles to offer for selection. Signature is: # List(Tuple( Unicode, Unicode, Type(Spawner), Dict )) # corresponding to profile display name, unique key, Spawner class, # dictionary of spawner config options. # # The first three values will be exposed in the input_template as {display}, # {key}, and {type} # c.jupyterhub.spawner_class = 'wrapspawner.profilesspawner' c.profilesspawner.profiles = [ ( "Local server", 'local', 'jupyterhub.spawner.localprocessspawner', {'ip':' '} ), ('Condor Shared Queue', 'CondorDefault', 'batchspawner.condorspawner', dict(req_nprocs='20', req_memory='18g', req_options='+job_type = "jupyter"')), ] c.condorspawner.batch_script = ''' Executable = /bin/sh RequestMemory = {memory} RequestCpus = {nprocs} Arguments = \"-c 'export PATH=/u0b/software/anaconda3/bin:$PATH; exec {cmd}'\" Remote_Initialdir = {homedir} Output = {homedir}/.jupyterhub.$(clusterid).condor.out Error = {homedir}/.jupyterhub.$(clusterid).condor.err ShouldTransferFiles = False GetEnv = True PeriodicRemove = (JobStatus == 1 && NumJobStarts > 1) {options} Queue '''

15 Jupyterhub Server Compute Cluster (Slurm, HTCondor) HTTP Proxy Spawner Shared Storage Resources (GPFS, dcache, BNL Box)

16 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) HTTP Proxy Spawner Shared Storage Resources (GPFS, dcache, BNL Box)

17 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) LocalProcessSpawner HTTP Proxy Spawner Shared Storage Resources (GPFS, dcache, BNL Box)

18 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) LocalProcessSpawner HTTP Proxy Spawner Shared Storage Resources (GPFS, dcache, BNL Box)

19 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) LocalProcessSpawner HTTP Proxy Spawner Slurm_magic HTCondor API Batch Scheduler Shared Storage Resources (GPFS, dcache, BNL Box)

20 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) LocalProcessSpawner HTTP Proxy Spawner Slurm_magic HTCondor API Batch Scheduler sbatch, condor_submit Shared Storage Resources (GPFS, dcache, BNL Box)

21 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) HTTP Proxy Spawner Batch Scheduler Shared Storage Resources (GPFS, dcache, BNL Box)

22 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) HTTP Proxy Spawner BatchSpawner Batch Scheduler Shared Storage Resources (GPFS, dcache, BNL Box)

23 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) HTTP Proxy Spawner BatchSpawner Batch Scheduler sbatch, condor_submit Shared Storage Resources (GPFS, dcache, BNL Box)

24 Auth (krb, oauth, sso) Jupyterhub Server Compute Cluster (Slurm, HTCondor) HTTP Proxy Spawner BatchSpawner Batch Scheduler sbatch, condor_submit Shared Storage Resources (GPFS, dcache, BNL Box)

25 The Interface

26 The Interface

27 The Interface

28 The Interface

29 The Interface

30 The Interface

31 The Interface

32 The Interface

33 Example: ML Applications for ATLAS Tensorflow/Keras

34 Example: ML Applications for ATLAS Tensorflow/Keras :00: : I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA [ ] :00: : I tensorflow/core/common_runtime/gpu/gpu_device.cc:1344] Found device 0 with properties: name: Tesla P100-PCIE-16GB major: 6 minor: 0 memoryclockrate(ghz): pcibusid: 0000:07:00.0 totalmemory: 15.89GiB freememory: 15.60GiB :00: : I tensorflow/core/common_runtime/gpu/gpu_device.cc:1344] Found device 1 with properties: name: Tesla P100-PCIE-16GB major: 6 minor: 0 memoryclockrate(ghz): pcibusid: 0000:81:00.0 totalmemory: 15.89GiB freememory: 15.60GiB [ ] :00: : I tensorflow/core/common_runtime/gpu/gpu_device.cc:1041] Created TensorFlow device (/ job:localhost/replica:0/task:0/device:gpu:0 with MB memory) -> physical GPU (device: 0, name: Tesla P100- PCIE-16GB, pci bus id: 0000:07:00.0, compute capability: 6.0) :00: : I tensorflow/core/common_runtime/gpu/gpu_device.cc:1041] Created TensorFlow device (/ job:localhost/replica:0/task:0/device:gpu:1 with MB memory) -> physical GPU (device: 1, name: Tesla P100- PCIE-16GB, pci bus id: 0000:81:00.0, compute capability: 6.0)

35 Open Issues Authentication (implementing oauth) Eliminate need for tunneling Allocation of resources Interactive users won t be patient with batch system latency - how do we handle scheduling on an oversubscribed cluster? What are appropriate time/resource limitations on the notebooks? How to handle idle notebooks taking up job slots? External connectivity requirements (esp. on HPC) Management of software environment (is anaconda the way to go?) Who are the users? HEP inreach and outreach (e.g. notebooks already heavily used at NSLS2)

36 Conclusions We have begun to overlay a flexible, Jupyter notebook-based analysis portal atop existing batch resources at BNL Providing the tools that users want for the new ways they work now Technical and policy issues remain Looking for users from the diverse communities we serve and other interested admins/developers to collaborate with

37 Let s discuss Must a question have answer? Can t there be another way? Would you like to talk about it?