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| {{notice|This page describes using Hyak via ''Ikt'' which was the version of Hyak we used from 2014 through May 2020 when it was deprecated and replaced with a new version Hyak called ''Mox''. Up-to-date information on using Hyak is online at [[CommunityData:Hyak]].}}
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| To use Hyak, you must first have a UW NetID, access to Hyak, and a two factor authentication token. Details on getting set up with all three are available at [[CommunityData:Hyak setup]].
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| There are a number of other sources of documentation:
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| * [http://students.washington.edu/hpcc/using-hyak/information-for-beginner-users/slides-from-training-sessions/ Slides from the UW HPC Club]
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| * [http://wiki.hyak.uw.edu Hyak User Documentation]
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| * [[CommunityData:Hyak (Advanced)|Advanced Hyak]]
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| * From Summer 2019: [[CommunityData:Hyak tutorial | Hyak Tutorial]]
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| == Setting up SSH == | | == Setting up SSH == |
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| When you connect to SSH, it will ask you for a key from your token. Typing this in every time you start a connection be a pain. One approach is to create an .ssh config file that will create a "tunnel" the first time you connect and send all subsequent connections to Hyak over that tunnel. Some details [http://wiki.cac.washington.edu/display/hyakusers/Logging+In in the Hyak documentation]. | | When you connect to SSH, it will ask you for a key from your token. Typing this in every time you start a connection be a pain. One approach is to create an .ssh config file that will create a "tunnel" the first time you connect and send all subsequent connections to Hyak over that tunnel. Some details [https://sig.washington.edu/itsigs/Logging_In#SSH_Config_File in the Hyak documentation]. |
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| I've added the following config to the file <code>~/.ssh/config</code> on my laptop (you will want to change the username): | | I've added the following config to the file <code>~/.ssh/config</code> on my laptop (you will want to change the username): |
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| Host ikt hyak | | Host hyak hyak.washington.edu |
| User makohill | | User makohill |
| HostName login2.hyak.washington.edu | | HostName login3.hyak.washington.edu |
| ControlPath ~/.ssh/master-%r@%h:%p | | ControlPath ~/.ssh/master-%r@%h:%p |
| ControlMaster auto | | ControlMaster auto |
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| If you find any, kill them with <code>kill <PROCESSID></code>. Once that is done, you should have no problem connecting to Hyak. | | If you find any, kill them with <code>kill <PROCESSID></code>. Once that is done, you should have no problem connecting to Hyak. |
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| == Connecting to Hyak == | | == Setting Up Hyak == |
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| To connect to Hyak, you now only need to do:
| | When setting up Hyak, you must first add this to your BASHRC file. Generally, you can simply edit the following file on Hyak: <code>~/.bashrc</code> |
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| ssh hyak | | ## hyak specific options |
| | | alias rgrep='grep -r' |
| It will prompt you for your UWNetID's password and your PRN which is the little number that comes from your token.
| | alias big_machine='qsub -W group_list=hyak-mako -l walltime=500:00:00,mem=200gb -I' |
| | | alias any_machine='qsub -W group_list=hyak-mako -l walltime=500:00:00,mem=100gb -I' |
| == Setting up your user's Hyak environment with CDSC tools ==
| | PYTHON_PATH="/com/local/lib/python3.4:$PYTHON_PATH" |
| | | LD_LIBRARY_PATH="/com/local/lib:${LD_LIBRARY_PATH}" |
| When setting up Hyak, you must first add these two stanzas to '''very top''' and the ''very bottom'' of your <code>~/.bashrc</code> file. Generally, you can simply edit the following file on Hyak: <code>~/.bashrc</code>
| | PKG_CONFIG_PATH=/com/local/lib/pkgconfig:/usr/share/pkgconfig |
| | | MC_CORES=16 |
| ## hyak-cdsc specific options -- TOP OF FILE | | PATH="/com/local/bin:$PATH" |
| source /com/gentoo/etc/profile | | module load revolutionr_7.2 |
| ## end hyak-cdsc specific options -- TOP OF FILE | |
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| ## BEGIN hyak-cdsc specific options -- BOTTOM OF FILE | |
| source /etc/profile.d/modules.sh | |
| module load parallel_sql | | module load parallel_sql |
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| alias int_machine='srun -p comdata-int --time=500:00:00 --mem=200G --pty /bin/bash'
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| alias big_machine='srun -p comdata --time=500:00:00 --mem=200G --pty /bin/bash'
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| alias any_machine='srun -p comdata --time=500:00:00 --mem=100G --pty /bin/bash'
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| alias build_machine='srun -p build --time=8:00:00 --mem=10G --pty /bin/bash'
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| alias rgrep='grep -r'
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| MC_CORES=16
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| PATH="/com/local/bin:/sw/local/bin:$PATH"
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| R_LIBS_USER="~/R"
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| umask 007 | | umask 007 |
| ## END hyak-cdsc specific options -- BOTTOM OF FILE
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| These are new as of '''November 30, 2017.''' As a result, '''you must completely remove the old environment variables, and such. They include material that will screw things up.'''
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| The final line is particularly important. If you do not do this, the files you create on Hyak will be able to be read or written by others in the group! | | The final line is particularly important. If you do not do this, the files you create on Hyak will be able to be read or written by others in the group! |
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| These lines will mean that if I have "checked out" an interactive machine, I can ssh from my computer to Hyak and then directly through an addition hop to the machine (like ssh n0652). Those ForwardX11 lines means if I graph things on this window, they will open on my local display. | | These lines will mean that if I have "checked out" an interactive machine, I can ssh from my computer to Hyak and then directly through an addition hop to the machine (like ssh n0652). Those ForwardX11 lines means if I graph things on this window, they will open on my local display. |
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| === Python Packages ===
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| If you need python libraries that are not installed in the shared environment:
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| $ pip3 install --user YOURLIBHERE
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| ...replacing YOURLIBHERE with the name of the library you need, e.g. 'pandas'. The --user option will install it for just you.
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| If you have a lot of dependencies for a specific project, consider using [[#Python Virtual Environments |Python Virtual Environments]]
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| == Set up a password for Jupyter Notebook on Hyak ==
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| Once you have IPython/Jupyter up and running on Hyak and have set up all the port forwarding stuff described above, you might consider adding a password to secure your Jupyter session. Why bother? Anyone with access to Hyak can see that you're forwarding ''something'' via the login node. While unlikely, they may do something to interrupt or otherwise mess with your session.
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| It should work. Keep in mind that anyone with access to your jupyter session can do anything you can do on the command line including access all your data, delete files, etc.
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| Instructions for setting up a password on your Jupyter sessions are available on the [https://sig.washington.edu/itsigs/Hyak_IPython#Set_a_password_on_your_notebook Hyak wiki (UW login required)].
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| Note that you can/should skip the first command that loads the canopy module.
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| == Running Jobs on Hyak == | | == Running Jobs on Hyak == |
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| {{notice|This material is now out of date! It refers to the old version of the Hyak scheduler.}}
| | When you first log in to Hyak, you will be on a "login node". These are nodes that have access to the Internet, and can be used to update code, move files around, etc. They should not be used for computationally intensive tasks. To actually run jobs, there are a few different options, described in detail [https://sig.washington.edu/itsigs/Hyak_Job_Scheduler in the itSigs documentation]. Following are basic instructions for the two most common use cases. |
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| <div style="width: 300px; float: right; border: 1px solid black; background: #DDD; padding: 0.5em;">
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| '''Screencast Examples (Sep, 2019):'''
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| * Using parallel and batch jobs on ikt: [https://communitydata.cc/~mako/hyak_example_day2-20190906.ogv Video]
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| '''Screencast Examples (Feb, 2018, pre-SLURM):'''
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| * Interactive job (ikt): [https://communitydata.cc/~mako/hyak_example_interactive_job-20180215-part_1.ogv Part 1], [https://communitydata.cc/~mako/hyak_example_interactive_job-20180215-part_2.ogv Part 2]
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| * Batch Job (ikt): [https://communitydata.cc/~mako/hyak_example_batch_job-20180517.ogv Video]
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| </div>
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| When you first log in to Hyak, you will be on a "login node". These are nodes that have access to the Internet, and can be used to update code, move files around, etc. They should not be used for computationally intensive tasks. To actually run jobs, there are a few different options, described in detail [https://sig.washington.edu/itsigs/Hyak_Job_Scheduler in the itSigs documentation]. Following are basic instructions for some common use cases. | |
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| === Interactive nodes === | | === Interactive nodes === |
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| === Parallel SQL === | | === Parallel SQL === |
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| For big jobs you will want to use multiple nodes. Hyak has a very cool tool that makes this very easy, called Parallel SQL. Detailed instructions are in [https://sig.washington.edu/itsigs/Hyak_parallel-sql the itsigs parallel-sql documentation]. There is also a [[CommunityData:Hyak walkthrough|full walkthrough example with instructions]]. | | For big jobs you will want to use multiple nodes. Hyak has a very cool tool that makes this very easy, called Parallel SQL. Detailed instructions are in [https://sig.washington.edu/itsigs/Hyak_parallel-sql the itsigs parallel-sql documentation]. There is also a full walkthrough example with instructions in the <code>wikiresearch/hyak_example</code> directory. |
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| The basic workflow is: | | The basic workflow is: |
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| 0. Be empowered to run parallel_sql -- the first time you use parallel_sql, you will need to:
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| login$ module load parallel_sql
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| login$ sudo pssu --initial
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| [sudo] password for USERID: <Enter your UW NetID password>
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| See more information at: [[https://wiki.cac.washington.edu/display/hyakusers/Hyak+parallel-sql]]. If you're not initialized, it'll say "Cannot read database config file '/usr/lusers/<<your username>>/.parallel/db.conf': No such file or directory' when you try.
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| 1. Prepare the code, and test it with a single file (either on your computer, or on an interactive node). | | 1. Prepare the code, and test it with a single file (either on your computer, or on an interactive node). |
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| 2. Write a job_script file. This tells the node what job to run. There is an example on the Parallel SQL wiki page (linked above), and an example in the wikiresearch/hyak_example directory. | | 2. Write a job_script file. This tells the node what job to run. There is an example on the Parallel SQL wiki page (linked above), and an example in the wikiresearch/hyak_example directory. |
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| 3. Create a task_list file. This is a list of commands that should be run, with one line per file that the command should operate on. An example file might look something like: | | 3. Create a task_list file. This is a list of commands that should be run, with one line per file that the command should operate on. An example file might look something like: |
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| $ for job in $(seq 1 N); do qsub job_script; done | | $ for job in $(seq 1 N); do qsub job_script; done |
| # N is the number of nodes | | # N is the number of nodes |
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| You can also use the -t flag, which makes jobs using multiple nodes easier to kill, but is not recommended by "the HYAK people".
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| $ qsub job_script -t 0-N
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| # N is the number of nodes
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| For producing your task_list file, you might find it useful to make a python script that slurps up a list of files from a dir and then inserts those filenames into a command file to be run repeatedly:
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| #!/usr/bin/env python3
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| import glob
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| outfile = "many_Redir_Runs.txt"
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| infileDir = "/com/raw_data/complete_wmf_dumps-20180220/enwiki-20180301/"
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| fileList = glob.glob(infileDir + "enwiki-20180301-pages-meta-history*.7z") #get all the 7z metahistory files
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| with open(outfile, 'w') as outFileHandle:
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| for file in fileList:
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| cleanFile = file.split("/")[-1]
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| commandString = "7za x -so " + file + "| python ./01-extract_redirects.py > output/redir/" + cleanFile + ".tsv \n"
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| outFileHandle.write(commandString)
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| === R Markdown ===
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| [http://rmarkdown.rstudio.com/ R markdown] is a useful way of writing up your analysis as a mix of explanatory text and code. You can, for example, create fancy Tufte-style [https://rstudio.github.io/tufte/ handouts] with code and explanatory text in the [https://raw.githubusercontent.com/rstudio/tufte/master/inst/rmarkdown/templates/tufte_html/skeleton/skeleton.Rmd same file]! In order to use R markdown, in a compute node, run the following command
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| $ Rscript -e "rmarkdown::render('analysis.Rmd')"
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| === Python Virtual Environments ===
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| Python virtual environments are a great way to manage project dependencies, and they seem to work on HYAK in the same way that they do on local machines. First install virtualenv using pip (this only needs to be done once).
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| $ pip install virtualenv --user
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| Initialize a new virtual environment in the current directory. Many people create a new virtual environment for each project.
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| $ # this virtual environment will use python 3
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| $ virtualenv venv -p python3
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| To activate the virtual environment from a login node or an interactive compute node
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| $ source <path_to_venv_parent_dir>/venv/bin/activate
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| To load a virtual environment in parallel sql, add the following to your PBS bash script
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| source <path_to_venv_parent_dir>/venv/bin/activate
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| === Killing jobs on compute nodes ===
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| Torque documentation suggests that you should do this with <tt>qdel</tt>. That might work, but apparently our system runs moab on top of torque and the recommended (by Hyak admins) way to kill a job is to use the <tt>mjobctl</tt> command.
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| For example, you might run <tt>nodestate</tt> from a login node to figure out the ID number for your job (let's say it's 12345), then run <tt>mjobctl -c 12345</tt> to send a SIGTERM signal or <tt>mjobctl -F 12345</tt> to send a SIGKILL signal that will bring job 12345 to an end.
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| Note that only four user accounts at a time can have the bits necessary to kill other people's jobs, so while you can do this on your own jobs, you'll need to bother the IRC channel to find help cancelling other's jobs (we think that Jeremy, Nate, Aaron, and Mako currently have the bits). Also, check out the [http://docs.adaptivecomputing.com/maui/commands/mjobctl.php documentation for mjobctl] for more info.
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