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namespace:doc-mach:soroban [2020/05/19 02:26] mickey [Directory organization for shared data] |
namespace:doc-mach:soroban [2020/05/19 02:34] (current) mickey |
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===== Directories for data shared among members of project MACH ===== | ===== Directories for data shared among members of project MACH ===== | ||
- | ====== Internal page for MACH project members ====== | + | ==== Directory organization for shared data ==== |
- | ====== ====== | + | * /bio/db |
+ | * Public biological sequence and related data. | ||
+ | * /data/mach/<user> | ||
+ | * Data by project MACH will be kept under | ||
+ | * <user> is a person who put the data / did the analysis. | ||
+ | * How MiSeq raw read data and analyzed data are organized will be desided among the users of the project. | ||
- | [[:namespace:doc-mach:installed-software|List of software installed on soroban]] | ||
- | [[:namespace:doc-mach:usage-soroban|Usage of 'soroban' server for non-MACH users]] | + | ==== Procedure to use /data/mach/<user> ==== |
- | + | ||
- | ===== Directories for data shared among members of project MACH ===== | + | |
- | + | ||
- | ==== Directory organization for shared data ==== * /bio/db ** Public biological sequence and related data. * Data by project MACH will be kept under /data/mach/* is a person who put the data / did the analysis. * How MiSeq raw read data and analyzed data are organized will be desided among the users of the project. | + | |
- | + | ||
- | ==== Procedure to start the use ==== | + | |
+ | <code> | ||
cd /data/mach | cd /data/mach | ||
+ | mkdir <user> #e.g. mkdir mickey | ||
+ | </code> | ||
- | mkdir <user> (e.g. mkdir mickey) | ||
- | ==== Note about priviledges of users ==== | ||
- | |||
- | Highest priority: Usage for MACH project by the project members. | ||
- | |||
- | ===== List of users ===== | ||
- | |||
- | |**User** |**Family name** |**First name** |**Secondary groups** |**Note** | | ||
- | |bioadmin| | | |to install bioinformatic tools without using root by using su/sudo| | ||
- | |joaquin|Rilling|Joaquin|fuse, machanal|| | ||
- | |so|Fujiyoshi|So|fuse, machanal|| | ||
- | |mickey|Kawai|Mikihiko|fuse, machanal|| | ||
- | |fumito|Maruyama|Fumito|machanal| | | ||
- | |satoshi|Nagai|Satoshi|machanal| | | ||
- | |kyoko|Yarimizu|Kyoko|machanal| | | ||
- | |shoko|Ueki|Shoko|machanal| | | ||
- | |||
- | ===== List of groups ===== | ||
- | |||
- | |**Date created** |**Group name** |**Purpose** |Note| | ||
- | |20191001?|fuse|To mount basemount for getting raw gigabase-order raw sequence files of Illumina MiSeq from Illumina's BaseSpace|probably set by default setting of os| | ||
- | |20191001?|machanal|To share analyzed data among members of project MACH (e.g. at /data/mach/)|| | ||
- | |not yet|machdb| | | | ||
- | |not yet|machweb| | | | ||
- | |not yet|machmodel| | | | ||
- | |||
- | ==== Assignment of users to a group ==== | ||
- | |||
- | |**Group** |**Assigned user** | | ||
- | |machanal|joaquin| | ||
- | |machanal|so| | ||
- | |machanal|mickey| | ||
- | |machanal|fumito| | ||
- | |machanal|satoshi| | ||
- | |machanal|kyoko| | ||
- | |machanal|shoko| | ||
- | | | | | ||
- | |fuse|joaquin| | ||
- | |fuse|so| | ||
- | |fuse|mickey| | ||
- | |||
- | ===== Directory organization ===== | ||
- | |||
- | ==== For sharing data among project members ==== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/data/|775 (root-research)| |20TB| | ||
- | |/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| | | ||
- | |/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| | | ||
- | |||
- | * /data can be other path, for example, /home/proj | ||
- | * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different. | ||
- | |||
- | === List of projects === | ||
- | |||
- | |**Project** |**Group** |**User** |**Last name** |**First name** | | ||
- | |mach|machanal|joaquin|Joaqui|Rilling| | ||
- | |mach|machanal|so|So|Fujiyoshi| | ||
- | |mach|machanal|mickey|Mikihiko|Kawai| | ||
- | |ao|name_ao|kei|Kei|Yoshimura| | ||
- | |ao|name_ao|fumiaki|Fumiaki|Morimoto| | ||
- | |ao|name_ao|xiaojun|Xiaojun|name| | ||
- | |||
- | ===== For directories of tools and public databases of biological data ===== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/bio|775 (bioadmin-bioadmin)| |25TB| | ||
- | |/bio/bin| | | | | ||
- | |/bio/package| | | | | ||
- | |/bio/package/<tool>/<version>| | | | | ||
- | |/bio/db| | | | | ||
- | |||
- | ===== Queues / Groups of user priviledge (SLURM) ===== | ||
- | |||
- | See belows for basic usage of SLURM at UFRO-CEMCC servers [[https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages|https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages]] | ||
- | |||
- | ===== ===== | ||
- | |||
- | ===== ===== | ||
- | |||
- | ==== Assignment of users to a group ==== | ||
- | |||
- | |**Group** |**Assigned user** | | ||
- | |machanal|joaquin| | ||
- | |machanal|so| | ||
- | |machanal|mickey| | ||
- | |machanal|fumito| | ||
- | |machanal|satoshi| | ||
- | |machanal|kyoko| | ||
- | |machanal|shoko| | ||
- | |fuse|joaquin| | ||
- | |fuse|so| | ||
- | |fuse|mickey| | ||
- | |||
- | ===== Directory organization ===== | ||
- | |||
- | ==== For sharing data among project members ==== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** | | ||
- | |/data/|775 (root-research)| | | ||
- | |/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| | ||
- | |/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| | ||
- | |||
- | * /data can be other path, for example, /home/proj * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different. | ||
- | |||
- | === List of projects === | ||
- | |||
- | |**Project** |**Group** |**User** | | ||
- | |mach|machanal|joaquin| | ||
- | |mach|machanal|so| | ||
- | |mach|machanal|mickey| | ||
- | |||
- | ===== For directories of tools and public databases of biological data ===== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/bio|775 (bioadmin-bioadmin)| |25TB| | ||
- | |/bio/bin| | | | | ||
- | |/bio/db| | | | | ||
- | |/bio/package| | | | | ||
- | |/bio/package/<tool>/<version>| | | | | ||
- | |||
- | ===== Queues / Groups of user priviledge (SLURM) ===== | ||
- | |||
- | See belows for basic usage of SLURM at UFRO-CEMCC servers [[https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages|https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages]] | ||
- | |||
- | ==== Groups of priviledges ==== | ||
- | |||
- | |**Priority** |**Group name of priviledge** |**Purpose** |**Note** | | | ||
- | |High|mach|Usage for MACH project by the project members.|Distribute evenly among users (e.g. for biological analysis and for simulation) (by ticket, nice value etc. on SLURM)| | | ||
- | |machcolab|Coollaborative studies by MACH members| | | | | ||
- | |ufro-internal||Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | | | ||
- | |Low|external|Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | | | ||
- | |||
- | ===== Limitation of initial resources for default user account ===== | ||
- | |||
- | |**Queue name** |**Duration of one job** |**Memory per job** | | | | ||
- | |small|6hr| |medium|72hr| | ||
- | |||
- | |**Group of priviledge** |**Number of simultaneous jobs** | | | | | ||
- | |default|e.g. 30?| | | | | ||
- | |||
- | Submit an application form if one wants to request large resources, say, storage, memory per queue, number of similutaneously running queues/cpu. | ||
- | |||
- | ====== Internal page for MACH project members ====== | ||
- | |||
- | ====== ====== | ||
- | |||
- | ===== General note about data that are/will be managed by members of project MACH ===== | ||
- | |||
- | Roughly speaking, three types of data will be kept, public biological sequence and related data, MiSeq data and Analized data. | ||
- | |||
- | * Public biological sequence and related data will be kept under /bio/db. | ||
- | * Data by project MACH will be kept under /data/mach/<user>, where <user> is a person who did the analysis. | ||
- | * How MiSeq raw read data and analyzed data are organized will be desided amont the users of the project. | ||
- | |||
- | ==== Note about priviledges of users ==== | ||
- | |||
- | Highest priority: Usage for MACH project by the project members. | ||
- | |||
- | ===== List of users ===== | ||
- | |||
- | |**User** |**Family name** |**First name** |**Secondary groups** |**Note** | | ||
- | |bioadmin| | | |to install bioinformatic tools without using root by using su/sudo| | ||
- | |joaquin|Rilling|Joaquin|fuse, machanal|| | ||
- | |so|Fujiyoshi|So|fuse, machanal|| | ||
- | |mickey|Kawai|Mikihiko|fuse, machanal|| | ||
- | |fumito|Maruyama|Fumito|machanal| | | ||
- | |satoshi|Nagai|Satoshi|machanal| | | ||
- | |kyoko|Yarimizu|Kyoko|machanal| | | ||
- | |shoko|Ueki|Shoko|machanal| | | ||
- | |||
- | ===== List of groups ===== | ||
- | |||
- | |**Date created** |**Group name** |**Purpose** |Note| | ||
- | |20191001?|fuse|To mount basemount for getting raw gigabase-order raw sequence files of Illumina MiSeq from Illumina's BaseSpace|probably set by default setting of os| | ||
- | |20191001?|machanal|To share analyzed data among members of project MACH (e.g. at /data/mach/)|| | ||
- | |not yet|machdb| | | | ||
- | |not yet|machweb| | | | ||
- | |not yet|machmodel| | | | ||
- | |||
- | ==== Assignment of users to a group ==== | ||
- | |||
- | |**Group** |**Assigned user** | | ||
- | |machanal|joaquin| | ||
- | |machanal|so| | ||
- | |machanal|mickey| | ||
- | |machanal|fumito| | ||
- | |machanal|satoshi| | ||
- | |machanal|kyoko| | ||
- | |machanal|shoko| | ||
- | | | | | ||
- | |fuse|joaquin| | ||
- | |fuse|so| | ||
- | |fuse|mickey| | ||
- | |||
- | ===== Directory organization ===== | ||
- | |||
- | ==== For sharing data among project members ==== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/data/|775 (root-research)| |20TB| | ||
- | |/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| | | ||
- | |/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| | | ||
- | |||
- | * /data can be other path, for example, /home/proj | ||
- | * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different. | ||
- | |||
- | === List of projects === | ||
- | |||
- | |**Project** |**Group** |**User** |**Last name** |**First name** | | ||
- | |mach|machanal|joaquin|Joaqui|Rilling| | ||
- | |mach|machanal|so|So|Fujiyoshi| | ||
- | |mach|machanal|mickey|Mikihiko|Kawai| | ||
- | |ao|name_ao|kei|Kei|Yoshimura| | ||
- | |ao|name_ao|fumiaki|Fumiaki|Morimoto| | ||
- | |ao|name_ao|xiaojun|Xiaojun|name| | ||
- | |||
- | ===== For directories of tools and public databases of biological data ===== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/bio|775 (bioadmin-bioadmin)| |25TB| | ||
- | |/bio/bin| | | | | ||
- | |/bio/package| | | | | ||
- | |/bio/package/<tool>/<version>| | | | | ||
- | |/bio/db| | | | | ||
- | |||
- | ===== Queues / Groups of user priviledge (SLURM) ===== | ||
- | |||
- | See belows for basic usage of SLURM at UFRO-CEMCC servers [[https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages|https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages]] | ||
- | |||
- | ===== ===== | ||
- | |||
- | ===== ===== | ||
- | |||
- | ==== Assignment of users to a group ==== | ||
- | |||
- | |**Group** |**Assigned user** | | ||
- | |machanal|joaquin| | ||
- | |machanal|so| | ||
- | |machanal|mickey| | ||
- | |machanal|fumito| | ||
- | |machanal|satoshi| | ||
- | |machanal|kyoko| | ||
- | |machanal|shoko| | ||
- | |fuse|joaquin| | ||
- | |fuse|so| | ||
- | |fuse|mickey| | ||
- | |||
- | ===== Directory organization ===== | ||
- | |||
- | ==== For sharing data among project members ==== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** | | ||
- | |/data/|775 (root-research)| | | ||
- | |/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| | ||
- | |/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| | ||
- | |||
- | * /data can be other path, for example, /home/proj * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different. | ||
- | |||
- | === List of projects === | ||
- | |||
- | |**Project** |**Group** |**User** | | ||
- | |mach|machanal|joaquin| | ||
- | |mach|machanal|so| | ||
- | |mach|machanal|mickey| | ||
- | |||
- | ===== For directories of tools and public databases of biological data ===== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/bio|775 (bioadmin-bioadmin)| |25TB| | ||
- | |/bio/bin| | | | | ||
- | |/bio/db| | | | | ||
- | |/bio/package| | | | | ||
- | |/bio/package/<tool>/<version>| | | | | ||
- | |||
- | ===== Queues / Groups of user priviledge (SLURM) ===== | ||
- | |||
- | See belows for basic usage of SLURM at UFRO-CEMCC servers [[https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages|https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages]] | ||
- | |||
- | ==== Groups of priviledges ==== | ||
- | |||
- | |**Priority** |**Group name of priviledge** |**Purpose** |**Note** | | | ||
- | |High|mach|Usage for MACH project by the project members.|Distribute evenly among users (e.g. for biological analysis and for simulation) (by ticket, nice value etc. on SLURM)| | | ||
- | |machcolab|Coollaborative studies by MACH members| | | | | ||
- | |ufro-internal||Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | | | ||
- | |Low|external|Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | | | ||
- | |||
- | ===== Limitation of initial resources for default user account ===== | ||
- | |||
- | | |**Disk quote per user** | | ||
- | |default|500GB| | ||
- | |||
- | |**Queue name** |**Duration of one job** |**Memory per job** | | | | ||
- | |small|6hr| |medium|72hr| | ||
- | |||
- | |**Group of priviledge** |**Number of simultaneous jobs** | | | | | ||
- | |default|e.g. 30?| | | | | ||
- | |||
- | Submit an application form if one wants to request large resources, say, storage, memory per queue, number of similutaneously running queues/cpu. | ||
- | |||
- | [[:namespace:doc-mach:meeting|MACH Meeting about soroban]] | ||
- | |||
- | \\ | ||
- | |||
- | |||
- | ==== Procedure to start the use ==== | ||
- | |||
- | cd /data/mach | ||
- | |||
- | mkdir <user> (e.g. mkdir mickey) | ||
- | |||
- | |||
- | ==== Note about priviledges of users ==== | ||
- | |||
- | Highest priority: Usage for MACH project by the project members. | ||
- | |||
- | ===== List of users ===== | ||
- | |||
- | |**User** |**Family name** |**First name** |**Secondary groups** |**Note** | | ||
- | |bioadmin| | | |to install bioinformatic tools without using root by using su/sudo| | ||
- | |joaquin|Rilling|Joaquin|fuse, machanal|| | ||
- | |so|Fujiyoshi|So|fuse, machanal|| | ||
- | |mickey|Kawai|Mikihiko|fuse, machanal|| | ||
- | |fumito|Maruyama|Fumito|machanal| | | ||
- | |satoshi|Nagai|Satoshi|machanal| | | ||
- | |kyoko|Yarimizu|Kyoko|machanal| | | ||
- | |shoko|Ueki|Shoko|machanal| | | ||
- | |||
- | ===== List of groups ===== | ||
- | |||
- | |**Date created** |**Group name** |**Purpose** |Note| | ||
- | |20191001?|fuse|To mount basemount for getting raw gigabase-order raw sequence files of Illumina MiSeq from Illumina's BaseSpace|probably set by default setting of os| | ||
- | |20191001?|machanal|To share analyzed data among members of project MACH (e.g. at /data/mach/)|| | ||
- | |not yet|machdb| | | | ||
- | |not yet|machweb| | | | ||
- | |not yet|machmodel| | | | ||
- | |||
- | ==== Assignment of users to a group ==== | ||
- | |||
- | |**Group** |**Assigned user** | | ||
- | |machanal|joaquin| | ||
- | |machanal|so| | ||
- | |machanal|mickey| | ||
- | |machanal|fumito| | ||
- | |machanal|satoshi| | ||
- | |machanal|kyoko| | ||
- | |machanal|shoko| | ||
- | | | | | ||
- | |fuse|joaquin| | ||
- | |fuse|so| | ||
- | |fuse|mickey| | ||
- | |||
- | ===== Directory organization ===== | ||
- | |||
- | ==== For sharing data among project members ==== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/data/|775 (root-research)| |20TB| | ||
- | |/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| | | ||
- | |/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| | | ||
- | |||
- | * /data can be other path, for example, /home/proj | ||
- | * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different. | ||
- | |||
- | === List of projects === | ||
- | |||
- | |**Project** |**Group** |**User** |**Last name** |**First name** | | ||
- | |mach|machanal|joaquin|Joaqui|Rilling| | ||
- | |mach|machanal|so|So|Fujiyoshi| | ||
- | |mach|machanal|mickey|Mikihiko|Kawai| | ||
- | |ao|name_ao|kei|Kei|Yoshimura| | ||
- | |ao|name_ao|fumiaki|Fumiaki|Morimoto| | ||
- | |ao|name_ao|xiaojun|Xiaojun|name| | ||
- | |||
- | |||
- | ===== For directories of tools and public databases of biological data ===== | ||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/bio|775 (bioadmin-bioadmin)| |25TB| | ||
- | |/bio/bin| | | | | ||
- | |/bio/package| | | | | ||
- | |/bio/package/<tool>/<version>| | | | | ||
- | |/bio/db| | | | | ||
- | |||
- | ===== Queues / Groups of user priviledge (SLURM) ===== | ||
- | See belows for basic usage of SLURM at UFRO-CEMCC servers | ||
- | https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages | ||
- | ===== ===== | ||
- | |||
- | |||
- | ===== ===== | ||
- | |||
- | |||
- | ==== Assignment of users to a group ==== | ||
- | |**Group** |**Assigned user**| | ||
- | |machanal|joaquin| | ||
- | |machanal|so| | ||
- | |machanal|mickey| | ||
- | |machanal|fumito| | ||
- | |machanal|satoshi| | ||
- | |machanal|kyoko| | ||
- | |machanal|shoko| | ||
- | |fuse|joaquin| | ||
- | |fuse|so| | ||
- | |fuse|mickey| | ||
- | |||
- | ===== Directory organization ===== | ||
- | ==== For sharing data among project members ==== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** | | ||
- | |/data/|775 (root-research)| | ||
- | |/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| | ||
- | |/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| | ||
- | |||
- | * /data can be other path, for example, /home/proj | ||
- | * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different. | ||
- | |||
- | === List of projects === | ||
- | |**Project** |**Group** |**User** | | ||
- | |mach|machanal|joaquin| | ||
- | |mach|machanal|so| | ||
- | |mach|machanal|mickey| | ||
- | |||
- | |||
- | ===== For directories of tools and public databases of biological data ===== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/bio|775 (bioadmin-bioadmin)| |25TB | | ||
- | |/bio/bin| | | | | ||
- | |/bio/db| | | | | ||
- | |/bio/package| | | | | ||
- | |/bio/package/<tool>/<version>| | | | | ||
- | |||
- | ===== Queues / Groups of user priviledge (SLURM) ===== | ||
- | See belows for basic usage of SLURM at UFRO-CEMCC servers | ||
- | https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages | ||
==== Groups of priviledges ==== | ==== Groups of priviledges ==== | ||
Line 483: | Line 49: | ||
- | ====== Internal page for MACH project members ====== | ||
- | |||
- | ====== ====== | ||
- | |||
- | ===== General note about data that are/will be managed by members of project MACH ===== | ||
- | |||
- | Roughly speaking, three types of data will be kept, public biological sequence and related data, MiSeq data and Analized data. | ||
- | |||
- | * Public biological sequence and related data will be kept under /bio/db. | ||
- | * Data by project MACH will be kept under /data/mach/<user>, where <user> is a person who did the analysis. | ||
- | * How MiSeq raw read data and analyzed data are organized will be desided amont the users of the project. | ||
- | |||
- | ==== Note about priviledges of users ==== | ||
- | |||
- | Highest priority: Usage for MACH project by the project members. | ||
- | |||
- | ===== List of users ===== | ||
- | |||
- | |**User** |**Family name** |**First name** |**Secondary groups** |**Note** | | ||
- | |bioadmin| | | |to install bioinformatic tools without using root by using su/sudo| | ||
- | |joaquin|Rilling|Joaquin|fuse, machanal|| | ||
- | |so|Fujiyoshi|So|fuse, machanal|| | ||
- | |mickey|Kawai|Mikihiko|fuse, machanal|| | ||
- | |fumito|Maruyama|Fumito|machanal| | | ||
- | |satoshi|Nagai|Satoshi|machanal| | | ||
- | |kyoko|Yarimizu|Kyoko|machanal| | | ||
- | |shoko|Ueki|Shoko|machanal| | | ||
- | |||
- | ===== List of groups ===== | ||
- | |||
- | |**Date created** |**Group name** |**Purpose** |Note| | ||
- | |20191001?|fuse|To mount basemount for getting raw gigabase-order raw sequence files of Illumina MiSeq from Illumina's BaseSpace|probably set by default setting of os| | ||
- | |20191001?|machanal|To share analyzed data among members of project MACH (e.g. at /data/mach/)|| | ||
- | |not yet|machdb| | | | ||
- | |not yet|machweb| | | | ||
- | |not yet|machmodel| | | | ||
- | |||
- | ==== Assignment of users to a group ==== | ||
- | |||
- | |**Group** |**Assigned user** | | ||
- | |machanal|joaquin| | ||
- | |machanal|so| | ||
- | |machanal|mickey| | ||
- | |machanal|fumito| | ||
- | |machanal|satoshi| | ||
- | |machanal|kyoko| | ||
- | |machanal|shoko| | ||
- | | | | | ||
- | |fuse|joaquin| | ||
- | |fuse|so| | ||
- | |fuse|mickey| | ||
- | |||
- | ===== Directory organization ===== | ||
- | |||
- | ==== For sharing data among project members ==== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/data/|775 (root-research)| |20TB| | ||
- | |/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| | | ||
- | |/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| | | ||
- | |||
- | * /data can be other path, for example, /home/proj | ||
- | * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different. | ||
- | |||
- | === List of projects === | ||
- | |||
- | |**Project** |**Group** |**User** |**Last name** |**First name** | | ||
- | |mach|machanal|joaquin|Joaqui|Rilling| | ||
- | |mach|machanal|so|So|Fujiyoshi| | ||
- | |mach|machanal|mickey|Mikihiko|Kawai| | ||
- | |ao|name_ao|kei|Kei|Yoshimura| | ||
- | |ao|name_ao|fumiaki|Fumiaki|Morimoto| | ||
- | |ao|name_ao|xiaojun|Xiaojun|name| | ||
- | |||
- | ===== For directories of tools and public databases of biological data ===== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/bio|775 (bioadmin-bioadmin)| |25TB| | ||
- | |/bio/bin| | | | | ||
- | |/bio/package| | | | | ||
- | |/bio/package/<tool>/<version>| | | | | ||
- | |/bio/db| | | | | ||
- | |||
- | ===== Queues / Groups of user priviledge (SLURM) ===== | ||
- | |||
- | See belows for basic usage of SLURM at UFRO-CEMCC servers [[https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages|https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages]] | ||
- | |||
- | ===== ===== | ||
- | |||
- | ===== ===== | ||
- | |||
- | ==== Assignment of users to a group ==== | ||
- | |||
- | |**Group** |**Assigned user** | | ||
- | |machanal|joaquin| | ||
- | |machanal|so| | ||
- | |machanal|mickey| | ||
- | |machanal|fumito| | ||
- | |machanal|satoshi| | ||
- | |machanal|kyoko| | ||
- | |machanal|shoko| | ||
- | |fuse|joaquin| | ||
- | |fuse|so| | ||
- | |fuse|mickey| | ||
- | |||
- | ===== Directory organization ===== | ||
- | |||
- | ==== For sharing data among project members ==== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** | | ||
- | |/data/|775 (root-research)| | | ||
- | |/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| | ||
- | |/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| | ||
- | |||
- | * /data can be other path, for example, /home/proj * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different. | ||
- | |||
- | === List of projects === | ||
- | |||
- | |**Project** |**Group** |**User** | | ||
- | |mach|machanal|joaquin| | ||
- | |mach|machanal|so| | ||
- | |mach|machanal|mickey| | ||
- | |||
- | ===== For directories of tools and public databases of biological data ===== | ||
- | |||
- | |**Path** |**Permission** |**Purpose** |**Size** | | ||
- | |/bio|775 (bioadmin-bioadmin)| |25TB| | ||
- | |/bio/bin| | | | | ||
- | |/bio/db| | | | | ||
- | |/bio/package| | | | | ||
- | |/bio/package/<tool>/<version>| | | | | ||
- | |||
- | ===== Queues / Groups of user priviledge (SLURM) ===== | ||
- | |||
- | See belows for basic usage of SLURM at UFRO-CEMCC servers [[https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages|https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages]] | ||
- | |||
- | ==== Groups of priviledges ==== | ||
- | |||
- | |**Priority** |**Group name of priviledge** |**Purpose** |**Note** | | | ||
- | |High|mach|Usage for MACH project by the project members.|Distribute evenly among users (e.g. for biological analysis and for simulation) (by ticket, nice value etc. on SLURM)| | | ||
- | |machcolab|Coollaborative studies by MACH members| | | | | ||
- | |ufro-internal||Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | | | ||
- | |Low|external|Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | | | ||
- | |||
- | ===== Limitation of initial resources for default user account ===== | ||
- | |||
- | | |**Disk quote per user** | | ||
- | |default|500GB| | ||
- | |||
- | |**Queue name** |**Duration of one job** |**Memory per job** | | | | ||
- | |small|6hr| |medium|72hr| | ||
- | |||
- | |**Group of priviledge** |**Number of simultaneous jobs** | | | | | ||
- | |default|e.g. 30?| | | | | ||
- | |||
- | Submit an application form if one wants to request large resources, say, storage, memory per queue, number of similutaneously running queues/cpu. | ||
- | |||
- | [[:namespace:doc-mach:meeting|MACH Meeting about soroban]] | ||
- | |||
- | \\ | ||