[et_pb_section fb_built=”1″ fullwidth=”on” _builder_version=”4.16″ _module_preset=”default” global_colors_info=”{}” theme_builder_area=”post_content”][et_pb_fullwidth_menu menu_id=”15″ menu_style=”centered” fullwidth_menu=”on” active_link_color=”#d80b8c” dropdown_menu_line_color=”#221f72″ _builder_version=”4.16″ _module_preset=”default” menu_font=”|600|||||||” menu_text_color=”#FFFFFF” menu_font_size=”16px” background_color=”#221f72″ background_layout=”dark” sticky_position=”top” global_colors_info=”{}” theme_builder_area=”post_content”][\/et_pb_fullwidth_menu][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.16″ custom_padding=”0px||0px||false|false” global_colors_info=”{}” theme_builder_area=”post_content”][et_pb_row _builder_version=”4.16″ background_size=”initial” background_position=”top_left” background_repeat=”repeat” custom_padding=”||0px||false|false” global_colors_info=”{}” theme_builder_area=”post_content”][et_pb_column type=”4_4″ _builder_version=”4.16″ custom_padding=”|||” global_colors_info=”{}” custom_padding__hover=”|||” theme_builder_area=”post_content”][et_pb_text admin_label=”Breadcrumb” _builder_version=”4.27.4″ _module_preset=”default” global_colors_info=”{}” theme_builder_area=”post_content”]<\/p>\n
Scientific Computing and Data<\/a> \/ High Performance Computing<\/a> \/ Documentation<\/a> \/ Minerva Restricted Cluster<\/p>\n [\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.16″ _module_preset=”default” global_colors_info=”{}” theme_builder_area=”post_content”][et_pb_row _builder_version=”4.27.4″ _module_preset=”default” module_alignment=”center” custom_margin=”|auto||90px||” global_colors_info=”{}” theme_builder_area=”post_content”][et_pb_column type=”4_4″ _builder_version=”4.16″ _module_preset=”default” global_colors_info=”{}” theme_builder_area=”post_content”][et_pb_text admin_label=”conda introduction” _builder_version=”4.27.4″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” global_colors_info=”{}” theme_builder_area=”post_content”]<\/p>\n [\/et_pb_text][et_pb_image src=”https:\/\/scpublic.dmz.hpc.mssm.edu\/HPC\/Minerva_Res\/Minerva_Restricted_Cluster.jpg” _builder_version=”4.27.4″ _module_preset=”default” theme_builder_area=”post_content” hover_enabled=”0″ sticky_enabled=”0″ module_alignment=”center” width=”60%” max_width=”60%” custom_margin=”||30px||false|false”][\/et_pb_image][et_pb_text admin_label=”conda introduction” _builder_version=”4.27.4″ _module_preset=”default” header_font=”|600|||||||” header_text_color=”#221f72″ header_font_size=”26px” header_2_text_color=”#221f72″ header_2_font_size=”24px” custom_margin=”10px||20px||false|false” hover_enabled=”0″ global_colors_info=”{}” theme_builder_area=”post_content” sticky_enabled=”0″]<\/p>\n The <\/span>Minerva Restricted Cluster <\/b>\u00a0(Minerva-Res) is a hardened, high-performance computing (HPC) cluster and shared-use resource for all qualified researchers at Mount Sinai. <\/span>It is designed and operated in accordance with NIST SP 800-171 Rev. 3 security requirements. It is dedicated for genomic data coming from the <\/span>NIH Controlled-Access repository<\/span><\/a>. NIH does not consider controlled access genomic data to be CUI but is using the NIST 800-171 security controls as a best practice for data protection. We reference NIH supported projects involving genomic data sharing as CUI-like data protections. <\/span>\u00a0It is an encrypted, tightly controlled compute environment that includes a variety of standard compute nodes and an encrypted shared filesystem.<\/span><\/p>\n [\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” theme_builder_area=”post_content” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n Access to Minerva-Res is granted strictly on a per-project basis. Principal Investigators (PIs) may manage multiple projects. User accounts can only be created after a project has been formally requested and approved. Continued access to any project requires an active <\/span>Data Use Agreement (DUA) managed by the institution GCO<\/span><\/a>.<\/span><\/p>\n <\/span><\/p>\n [\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” theme_builder_area=”post_content” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n All accounts must be associated with an active, approved project. Users may only access data that is specifically required for your approved research.<\/span><\/p>\n Please Note: We don\u2019t support external collaboration accounts currently due to security requirements.<\/span><\/p>\n Accounts will be deactivated when any of the following occurs:<\/span><\/p>\n <\/span><\/p>\n [\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” theme_builder_area=”post_content” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n Note: <\/b>Access to Minerva-Res requires connection from the campus network or VPN (virtual private network).<\/span><\/p>\n The login nodes are connected to the campus network allowing access only on campus or via tunneling over Mount Sinai\u2019s VPN if off campus.<\/span><\/p>\n There are currently two login nodes available for general use, <\/span>ci06e01<\/b> and <\/span>ci06e02<\/b>. You may connect to one of them through one of two round-robin Domain Name Server (DNS) load balancing names or you may specify one of them explicitly, if you prefer one over the other. For example, if you have a disconnected screen session running on one of the nodes, you will want to log onto that particular node if you want to reconnect.<\/span><\/p>\n The addresses of the nodes are:<\/span><\/p>\n You can login to the Minerva-Res cluster via ssh to minerva-res.hpc.mssm.edu.<\/span><\/span><\/p>\n Authenticate using your institutional (school or hospital) credentials and complete Microsoft Azure MFA (multi-factor authentication) on your mobile device.<\/span><\/p>\n <\/span><\/p>\n [\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” theme_builder_area=”post_content” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n Data may only be transferred to or from Minerva-Res using an approved method. Standard SFTP and routine SSH file transfers are disabled by default. All transfers are logged, and users remain responsible for following restrictions applicable to their data.<\/span><\/p>\n To transfer data into or out of the cluster, a completed and approved DUA is required. Once approved, specific source addresses or subnets will be permitted. Downloading, copying, or transferring data to unauthorized systems is a policy violation.<\/span><\/p>\n Any results or data users generate from source data must be handled with the same security standards as the original source. Treat all derived outputs as sensitive.<\/span><\/p>\n <\/p>\n [\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” theme_builder_area=”post_content” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n Software is available through the read-only module system at <\/span> For complete details, please visit our documentation on Software Environment: Lmod (<\/span>https:\/\/labs.icahn.mssm.edu\/minervalab\/documentation\/software-environment-lmod\/<\/span><\/a>).<\/span><\/p>\n To request additional software, send in an HPC ticket <\/span>hpchelp@hpc.mssm.edu<\/span><\/a>.<\/span><\/p>\n <\/span><\/p>\n [\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” theme_builder_area=”post_content” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n Workloads are managed by the IBM Spectrum LSF scheduler. Do not run computationally intensive tasks directly on the login nodes \u2014 all jobs must be submitted to the scheduler.<\/span><\/p>\n Available queues:<\/span> night<\/span>, <\/span>short<\/span>, <\/span>normal<\/span>, <\/span>interactive<\/span><\/p>\n For interactive work or exploratory analyses, use the <\/span>interactive<\/span> queue. For most batch jobs, use <\/span>normal<\/span> or <\/span>short<\/span> depending on expected runtime.<\/span><\/p>\n For additional information, please visit our documentation on Load Sharing Facility (LSF) Job Scheduler (<\/span>https:\/\/labs.icahn.mssm.edu\/minervalab\/documentation\/lsf-job-scheduler\/<\/span><\/a>).<\/span><\/p>\n <\/p>\n [\/et_pb_text][et_pb_text _builder_version=”4.27.4″ _module_preset=”default” theme_builder_area=”post_content” hover_enabled=”0″ sticky_enabled=”0″]<\/p>\n A dedicated Open OnDemand portal (https:\/\/ondemand-res.hpc.mssm.edu\/<\/a><\/strong>) provides browser-based access to applications including Desktop, SAS, Stata, Jupyter and RStudio.<\/span><\/p>\n Note<\/b>: CMS projects are currently unavailable through File Explorer and will be made available as soon as possible. Data transfer (upload or download) is disabled in Open OnDemand Restricted environment.<\/span><\/p>\nMinerva Restricted Cluster<\/h1>\n
Access the Cluster<\/b><\/h2>\n
Projects<\/b><\/h3>\n
Accounts<\/b><\/h3>\n
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Log In<\/b><\/h3>\n
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ssh yourUserID@minerva-res.hpc.mssm.edu\r\n(yourUserID@minerva.hpc.mssm.edu) Password: <Enter your Sinai School Password Only>\r\nEnter Your Microsoft verification code<609017><\/code><\/pre>\n<\/code><\/p>\n<\/blockquote>\nTransfer Data<\/b><\/h2>\n
Approved Transfers<\/b><\/h3>\n
Derived Data<\/b><\/h3>\n
Software Environment<\/b><\/h2>\n
\/hpc\/packages<\/code>. Use the <\/span>module<\/code> command to load available applications.\u00a0<\/span><\/span><\/p>\n\n
module load <software_name><\/code><\/pre>\n<\/blockquote>\nRunning Jobs (LSF Scheduler)<\/b><\/h2>\n
Open OnDemand<\/b><\/h2>\n