Name already in use
<link crossorigin="anonymous" media="all" rel="stylesheet" href="https://github.githubassets.com/assets/primer-6d48655e42c1.css" />
<link crossorigin="anonymous" media="all" rel="stylesheet" href="https://github.githubassets.com/assets/global-855104497e96.css" />
<link crossorigin="anonymous" media="all" rel="stylesheet" href="https://github.githubassets.com/assets/github-632a8182386b.css" />
<meta name="optimizely-datafile" content="{"groups": [], "environmentKey": "production", "rollouts": [], "typedAudiences": [], "projectId": "16737760170", "variables": [], "featureFlags": [], "experiments": [], "version": "4", "audiences": [{"conditions": "[\"or\", {\"match\": \"exact\", \"name\": \"$opt_dummy_attribute\", \"type\": \"custom_attribute\", \"value\": \"$opt_dummy_value\"}]", "id": "$opt_dummy_audience", "name": "Optimizely-Generated Audience for Backwards Compatibility"}], "anonymizeIP": true, "sdkKey": "WTc6awnGuYDdG98CYRban", "attributes": [{"id": "16822470375", "key": "user_id"}, {"id": "17143601254", "key": "spammy"}, {"id": "18175660309", "key": "organization_plan"}, {"id": "18813001570", "key": "is_logged_in"}, {"id": "19073851829", "key": "geo"}, {"id": "20175462351", "key": "requestedCurrency"}, {"id": "20785470195", "key": "country_code"}, {"id": "21656311196", "key": "opened_downgrade_dialog"}], "botFiltering": false, "accountId": "16737760170", "events": [{"experimentIds": [], "id": "17911811441", "key": "hydro_click.dashboard.teacher_toolbox_cta"}, {"experimentIds": [], "id": "18124116703", "key": "submit.organizations.complete_sign_up"}, {"experimentIds": [], "id": "18145892387", "key": "no_metric.tracked_outside_of_optimizely"}, {"experimentIds": [], "id": "18178755568", "key": "click.org_onboarding_checklist.add_repo"}, {"experimentIds": [], "id": "18180553241", "key": "submit.repository_imports.create"}, {"experimentIds": [], "id": "18186103728", "key": "click.help.learn_more_about_repository_creation"}, {"experimentIds": [], "id": "18188530140", "key": "test_event"}, {"experimentIds": [], "id": "18191963644", "key": "click.empty_org_repo_cta.transfer_repository"}, {"experimentIds": [], "id": "18195612788", "key": "click.empty_org_repo_cta.import_repository"}, {"experimentIds": [], "id": "18210945499", "key": "click.org_onboarding_checklist.invite_members"}, {"experimentIds": [], "id": "18211063248", "key": "click.empty_org_repo_cta.create_repository"}, {"experimentIds": [], "id": "18215721889", "key": "click.org_onboarding_checklist.update_profile"}, {"experimentIds": [], "id": "18224360785", "key": "click.org_onboarding_checklist.dismiss"}, {"experimentIds": [], "id": "18234832286", "key": "submit.organization_activation.complete"}, {"experimentIds": [], "id": "18252392383", "key": "submit.org_repository.create"}, {"experimentIds": [], "id": "18257551537", "key": "submit.org_member_invitation.create"}, {"experimentIds": [], "id": "18259522260", "key": "submit.organization_profile.update"}, {"experimentIds": [], "id": "18564603625", "key": "view.classroom_select_organization"}, {"experimentIds": [], "id": "18568612016", "key": "click.classroom_sign_in_click"}, {"experimentIds": [], "id": "18572592540", "key": "view.classroom_name"}, {"experimentIds": [], "id": "18574203855", "key": "click.classroom_create_organization"}, {"experimentIds": [], "id": "18582053415", "key": "click.classroom_select_organization"}, {"experimentIds": [], "id": "18589463420", "key": "click.classroom_create_classroom"}, {"experimentIds": [], "id": "18591323364", "key": "click.classroom_create_first_classroom"}, {"experimentIds": [], "id": "18591652321", "key": "click.classroom_grant_access"}, {"experimentIds": [], "id": "18607131425", "key": "view.classroom_creation"}, {"experimentIds": [], "id": "18831680583", "key": "upgrade_account_plan"}, {"experimentIds": [], "id": "19064064515", "key": "click.signup"}, {"experimentIds": [], "id": "19075373687", "key": "click.view_account_billing_page"}, {"experimentIds": [], "id": "19077355841", "key": "click.dismiss_signup_prompt"}, {"experimentIds": [], "id": "19079713938", "key": "click.contact_sales"}, {"experimentIds": [], "id": "19120963070", "key": "click.compare_account_plans"}, {"experimentIds": [], "id": "19151690317", "key": "click.upgrade_account_cta"}, {"experimentIds": [], "id": "19424193129", "key": "click.open_account_switcher"}, {"experimentIds": [], "id": "19520330825", "key": "click.visit_account_profile"}, {"experimentIds": [], "id": "19540970635", "key": "click.switch_account_context"}, {"experimentIds": [], "id": "19730198868", "key": "submit.homepage_signup"}, {"experimentIds": [], "id": "19820830627", "key": "click.homepage_signup"}, {"experimentIds": [], "id": "19988571001", "key": "click.create_enterprise_trial"}, {"experimentIds": [], "id": "20036538294", "key": "click.create_organization_team"}, {"experimentIds": [], "id": "20040653299", "key": "click.input_enterprise_trial_form"}, {"experimentIds": [], "id": "20062030003", "key": "click.continue_with_team"}, {"experimentIds": [], "id": "20068947153", "key": "click.create_organization_free"}, {"experimentIds": [], "id": "20086636658", "key": "click.signup_continue.username"}, {"experimentIds": [], "id": "20091648988", "key": "click.signup_continue.create_account"}, {"experimentIds": [], "id": "20103637615", "key": "click.signup_continue.email"}, {"experimentIds": [], "id": "20111574253", "key": "click.signup_continue.password"}, {"experimentIds": [], "id": "20120044111", "key": "view.pricing_page"}, {"experimentIds": [], "id": "20152062109", "key": "submit.create_account"}, {"experimentIds": [], "id": "20165800992", "key": "submit.upgrade_payment_form"}, {"experimentIds": [], "id": "20171520319", "key": "submit.create_organization"}, {"experimentIds": [], "id": "20222645674", "key": "click.recommended_plan_in_signup.discuss_your_needs"}, {"experimentIds": [], "id": "20227443657", "key": "submit.verify_primary_user_email"}, {"experimentIds": [], "id": "20234607160", "key": "click.recommended_plan_in_signup.try_enterprise"}, {"experimentIds": [], "id": "20238175784", "key": "click.recommended_plan_in_signup.team"}, {"experimentIds": [], "id": "20239847212", "key": "click.recommended_plan_in_signup.continue_free"}, {"experimentIds": [], "id": "20251097193", "key": "recommended_plan"}, {"experimentIds": [], "id": "20438619534", "key": "click.pricing_calculator.1_member"}, {"experimentIds": [], "id": "20456699683", "key": "click.pricing_calculator.15_members"}, {"experimentIds": [], "id": "20467868331", "key": "click.pricing_calculator.10_members"}, {"experimentIds": [], "id": "20476267432", "key": "click.trial_days_remaining"}, {"experimentIds": [], "id": "20476357660", "key": "click.discover_feature"}, {"experimentIds": [], "id": "20479287901", "key": "click.pricing_calculator.custom_members"}, {"experimentIds": [], "id": "20481107083", "key": "click.recommended_plan_in_signup.apply_teacher_benefits"}, {"experimentIds": [], "id": "20483089392", "key": "click.pricing_calculator.5_members"}, {"experimentIds": [], "id": "20484283944", "key": "click.onboarding_task"}, {"experimentIds": [], "id": "20484996281", "key": "click.recommended_plan_in_signup.apply_student_benefits"}, {"experimentIds": [], "id": "20486713726", "key": "click.onboarding_task_breadcrumb"}, {"experimentIds": [], "id": "20490791319", "key": "click.upgrade_to_enterprise"}, {"experimentIds": [], "id": "20491786766", "key": "click.talk_to_us"}, {"experimentIds": [], "id": "20494144087", "key": "click.dismiss_enterprise_trial"}, {"experimentIds": [], "id": "20499722759", "key": "completed_all_tasks"}, {"experimentIds": [], "id": "20500710104", "key": "completed_onboarding_tasks"}, {"experimentIds": [], "id": "20513160672", "key": "click.read_doc"}, {"experimentIds": [], "id": "20516196762", "key": "actions_enabled"}, {"experimentIds": [], "id": "20518980986", "key": "click.dismiss_trial_banner"}, {"experimentIds": [], "id": "20535446721", "key": "click.issue_actions_prompt.dismiss_prompt"}, {"experimentIds": [], "id": "20557002247", "key": "click.issue_actions_prompt.setup_workflow"}, {"experimentIds": [], "id": "20595070227", "key": "click.pull_request_setup_workflow"}, {"experimentIds": [], "id": "20626600314", "key": "click.seats_input"}, {"experimentIds": [], "id": "20642310305", "key": "click.decrease_seats_number"}, {"experimentIds": [], "id": "20662990045", "key": "click.increase_seats_number"}, {"experimentIds": [], "id": "20679620969", "key": "click.public_product_roadmap"}, {"experimentIds": [], "id": "20761240940", "key": "click.dismiss_survey_banner"}, {"experimentIds": [], "id": "20767210721", "key": "click.take_survey"}, {"experimentIds": [], "id": "20795281201", "key": "click.archive_list"}, {"experimentIds": [], "id": "20966790249", "key": "contact_sales.submit"}, {"experimentIds": [], "id": "20996500333", "key": "contact_sales.existing_customer"}, {"experimentIds": [], "id": "20996890162", "key": "contact_sales.blank_message_field"}, {"experimentIds": [], "id": "21000470317", "key": "contact_sales.personal_email"}, {"experimentIds": [], "id": "21002790172", "key": "contact_sales.blank_phone_field"}, {"experimentIds": [], "id": "21354412592", "key": "click.dismiss_create_readme"}, {"experimentIds": [], "id": "21366102546", "key": "click.dismiss_zero_user_content"}, {"experimentIds": [], "id": "21370252505", "key": "account_did_downgrade"}, {"experimentIds": [], "id": "21370840408", "key": "click.cta_create_readme"}, {"experimentIds": [], "id": "21375451068", "key": "click.cta_create_new_repository"}, {"experimentIds": [], "id": "21385390948", "key": "click.zero_user_content"}, {"experimentIds": [], "id": "21467712175", "key": "click.downgrade_keep"}, {"experimentIds": [], "id": "21484112202", "key": "click.downgrade"}, {"experimentIds": [], "id": "21495292213", "key": "click.downgrade_survey_exit"}, {"experimentIds": [], "id": "21508241468", "key": "click.downgrade_survey_submit"}, {"experimentIds": [], "id": "21512030356", "key": "click.downgrade_support"}, {"experimentIds": [], "id": "21539090022", "key": "click.downgrade_exit"}, {"experimentIds": [], "id": "21543640644", "key": "click_fetch_upstream"}, {"experimentIds": [], "id": "21646510300", "key": "click.move_your_work"}, {"experimentIds": [], "id": "21656151116", "key": "click.add_branch_protection_rule"}, {"experimentIds": [], "id": "21663860599", "key": "click.downgrade_dialog_open"}, {"experimentIds": [], "id": "21687860483", "key": "click.learn_about_protected_branches"}, {"experimentIds": [], "id": "21689050333", "key": "click.dismiss_protect_this_branch"}, {"experimentIds": [], "id": "21864370109", "key": "click.sign_in"}], "revision": "1367"}" />
<meta name="hovercard-subject-tag" content="repository:44996115" data-turbo-transient>
<meta name="google-site-verification" content="c1kuD-K2HIVF635lypcsWPoD4kilo5-jA_wBFyT4uMY">
<meta name="user-login" content="">
<meta name="viewport" content="width=device-width">
<meta name="description" content="Contribute to fasrc/User_Codes development by creating an account on GitHub.">
<link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
<link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub">
<meta property="fb:app_id" content="1401488693436528">
<meta name="apple-itunes-app" content="app-id=1477376905" />
<meta name="twitter:image:src" content="https://opengraph.githubassets.com/74119eb60a1d67944ae582280a7621e00c4839dd3f4632ec5b6af2054f6515b2/fasrc/User_Codes" /><meta name="twitter:site" content="@github" /><meta name="twitter:card" content="summary_large_image" /><meta name="twitter:title" content="User_Codes/README.md at master · fasrc/User_Codes" /><meta name="twitter:description" content="Contribute to fasrc/User_Codes development by creating an account on GitHub." />
<meta property="og:image" content="https://opengraph.githubassets.com/74119eb60a1d67944ae582280a7621e00c4839dd3f4632ec5b6af2054f6515b2/fasrc/User_Codes" /><meta property="og:image:alt" content="Contribute to fasrc/User_Codes development by creating an account on GitHub." /><meta property="og:image:width" content="1200" /><meta property="og:image:height" content="600" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="User_Codes/README.md at master · fasrc/User_Codes" /><meta property="og:url" content="https://github.com/fasrc/User_Codes" /><meta property="og:description" content="Contribute to fasrc/User_Codes development by creating an account on GitHub." />
<link rel="assets" href="https://github.githubassets.com/">
<meta name="hostname" content="github.com">
<meta name="expected-hostname" content="github.com">
<meta name="enabled-features" content="TURBO_EXPERIMENT_RISKY,IMAGE_METRIC_TRACKING,GEOJSON_AZURE_MAPS">
<meta data-hydrostats="publish">
<link rel="canonical" href="https://github.com/fasrc/User_Codes/blob/master/Applications/AlphaFold/README.md" data-turbo-transient>
<div class="position-relative js-header-wrapper ">
<a href="#start-of-content" class="px-2 py-4 color-bg-accent-emphasis color-fg-on-emphasis show-on-focus js-skip-to-content">Skip to content</a>
<span data-view-component="true" class="progress-pjax-loader Progress position-fixed width-full">
<span style="width: 0%;" data-view-component="true" class="Progress-item progress-pjax-loader-bar left-0 top-0 color-bg-accent-emphasis"></span>
<script crossorigin="anonymous" defer="defer" type="application/javascript" src="https://github.githubassets.com/assets/vendors-node_modules_github_remote-form_dist_index_js-node_modules_delegated-events_dist_inde-94fd67-53c5902c854f.js"></script>
</div>
<div id="js-flash-container" data-turbo-replace>
{{ message }}
A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
User_Codes/Applications/AlphaFold/README.md
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Cannot retrieve contributors at this time
78 lines (56 sloc)
3.06 KB
AlphaFold
Note: currently (Dec/2022) this documentation is in testing phase.
What is AlphaFold?
AlphaFold in the FASRC Cannon cluster
Alphafold runs within a Docker container. However, Docker containers are not
allowed in high performance computing (HPC) systems such as Cannon because
Docker requires root/sudo privileges, which poses a security concern in HPC
systems.
Instead, we use Singularity
containers
which was specifically designed for HPC systems. We build a Singularity
container based on the Singularity definition file from
https://github.com/prehensilecode/alphafold_singularity, At the time of the
first deployment (Dec 2022), this refers to version 2.2.4 of AlphaFold. The
Singularity image is tagged with the AlphaFold version.
The AlphaFold database is stored in a cluster-wide location, meaning that
individual users do not have to download the AlphaFold database to run their
simulations. The database is stored in SSD as recommended by the developers.
Running AlphaFold
We recommend running AlphaFold on GPU partitions because it runs much faster
than solely using CPUs — due to AlphaFold’s GPU optimization. See slurm
partitions
for the specifics of each partition.
Below you will find a slurm script example
run_alphafold.sh that uses the fasta file
5ZE6_1.fasta.
This example assumes that run_alphafold.sh and my_fasta are located in the
same directory. If they are located in different directories, you will have to
edit my_fasta_path.
You will have to edit in the run_alphafold.sh script:
SBATCHdirectives to suit your needs (e.g. time-t, number of cores-c,
amount of memory--mem)my_fastato suit to your own fasta file- (optional)
my_output_dirif you would like your output to go somewhere else - (optional)
my_fasta_path
Note: AlphaFold screen output goes to the stderr file (.err) rather than the
stdout file (.out).
Slurm script
User_Codes/Applications/AlphaFold/run_alphafold.sh
Lines 1 to 35
in
d0114e5
Fasta file
User_Codes/Applications/AlphaFold/5ZE6_1.fasta
Lines 1 to 2
in
f15ac0e
Submitting a slurm batch job that runs AlphaFold
Log in to Cannon (see login
instructions). Go to the
directory where run_alphafold.sh is located. Then submit a slurm batch job
with the command:
sbatch run_alphafold.sh
This example takes about 1-2 hours to run on Cannon in the gpu partition with
8 cores (-c 8).
Resources
- AlphaFold GitHub
- University of Virginia AlphaFold docs
- AlphaFold discussion about Singularity implementation
<footer class="footer width-full container-xl p-responsive">
Footer
You can’t perform that action at this time.
<template id="site-details-dialog">
<div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
<template id="snippet-clipboard-copy-button">
</div>
<div id="js-global-screen-reader-notice" class="sr-only" aria-live="polite" ></div>