https://www.bsc.es/supportkc/assets/js/2dad56ed.8075ad6f.js

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1function m(e){let{components:t,...n}=e;return(0,r.kt)(d,(0,a.Z)({},p,n,{components:t,mdxType:"MDXLayout"}),(0,r.kt)("h1",{id:"quick-guides"},"Quick Guides"),(0,r.kt)(o.ZP,{mdxType:"Quick"}))}m.isMDXComponent=!0},43422:(e,t,n)=>{n.d(t,{ZP:()=>i});var a=n(87462),r=(n(67294),n(3905));const o={toc:[{value:"Index",id:"index",level:2},{value:"Log in to the cluster \u21a9",id:"log-in-to-the-cluster-",level:2},{value:"Login nodes \u21a9",id:"login-nodes-",level:3},{value:"Password change \u21a9",id:"password-change-",level:3},{value:"Access from/to the outside \u21a9",id:"access-fromto-the-outside-",level:3},{value:"Example to copy files or directories from MN4 to an external machine:",id:"example-to-copy-files-or-directories-from-mn4-to-an-external-machine",level:5},{value:"Example to copy files or directories from an external machine to MN4:",id:"example-to-copy-files-or-directories-from-an-external-machine-to-mn4",level:5},{value:"Directories and file systems \u21a9",id:"directories-and-file-systems-",level:2},{value:"Basic directories under GPFS \u21a9",id:"basic-directories-under-gpfs-",level:3},{value:"Storage space limits/quotas \u21a9",id:"storage-space-limitsquotas-",level:3},{value:"Running jobs \u21a9",id:"running-jobs-",level:2},{value:"Submit to queues \u21a9",id:"submit-to-queues-",level:3},{value:"To submit a job:",id:"to-submit-a-job",level:5},{value:"To show all the submitted jobs:",id:"to-show-all-the-submitted-jobs",level:5},{value:"To cancel a job:",id:"to-cancel-a-job",level:5},{value:"Queue limits \u21a9",id:"queue-limits-",level:3},{value:"Interactive jobs \u21a9",id:"interactive-jobs-",level:3},{value:"Interactive sessions",id:"interactive-sessions",level:4},{value:"To request an interactive session on a compute node:",id:"to-request-an-interactive-session-on-a-compute-node",level:5},{value:"To request an interactive session on a non-shared (exclusive) compute node:",id:"to-request-an-interactive-session-on-a-non-shared-exclusive-compute-node",level:5},{value:"To request an interactive session on a compute node using GPUs:",id:"to-request-an-interactive-session-on-a-compute-node-using-gpus",level:5}]},s="wrapper";function i(e){let{components:t,...n}=e;return(0,r.kt)(s,(0,a.Z)({},o,n,{components:t,mdxType:"MDXLayout"}),(0,r.kt)("h1",{id:"english"},"English"),(0,r.kt)("h2",{id:"index"},"Index"),(0,r.kt)("ol",null,(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#connectingto"},"Log in to the cluster"),(0,r.kt)("ol",{parentName:"li"},(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#loginnodes"},"Login nodes (logins)")),(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#passwordchange"},"Password change")),(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#outsideconnect"},"Access from/to the outside")))),(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#filesystems"},"Directories and file systems"),(0,r.kt)("ol",{parentName:"li"},(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#gpfsdirectories"},"Basic directories under GPFS")),(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#bscquota"},"Storage space limits/quotas")))),(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#runningjobs"},"Running jobs"),(0,r.kt)("ol",{parentName:"li"},(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#submittingjobs"},"Submit to queues")),(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#bscqueues"},"Queue limits")),(0,r.kt)("li",{parentName:"ol"},(0,r.kt)("a",{parentName:"li",href:"#interactive"},"Interactive jobs"))))),(0,r.kt)("h2",{id:"log-in-to-the-cluster-"},"Log in to the cluster",(0,r.kt)("a",{parentName:"h2",href:"#ToC-connectingto"}," \u21a9")),(0,r.kt)("admonition",{title:"IMPORTANT",type:"caution"},(0,r.kt)("p",{parentName:"admonition"},(0,r.kt)("strong",{parentName:"p"},"The accounts are for personal and non-transferable usage.")," If the project\nrequires someone else's access to the machine or any increase\nin the assigned resources, the project manager will be in charge\nto make this type of request.")),(0,r.kt)("h3",{id:"login-nodes-"},"Login nodes",(0,r.kt)("a",{parentName:"h3",href:"#ToC-loginnodes"}," \u21a9")),(0,r.kt)("table",null,(0,r.kt)("thead",{parentName:"table"},(0,r.kt)("tr",{parentName:"thead"},(0,r.kt)("th",{parentName:"tr",align:null},"Cluster"),(0,r.kt)("th",{parentName:"tr",align:null}))),(0,r.kt)("tbody",{parentName:"table"},(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},"MareNostrum 4 (GP)"),(0,r.kt)("td",{parentName:"tr",align:null},"mn1.bsc.es",(0,r.kt)("br",null),"mn2.bsc.es",(0,r.kt)("br",null),"mn3.bsc.es")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},"CTE-AMD"),(0,r.kt)("td",{parentName:"tr",align:null},"amdlogin1.bsc.es")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},"CTE-POWER"),(0,r.kt)("td",{parentName:"tr",align:null},"plogin1.bsc.es",(0,r.kt)("br",null),"plogin2.bsc.es")),(0,r.kt)("tr",{parentName:"tbody"},(0,r.kt)("td",{parentName:"tr",align:null},"MinoTauro"),(0,r.kt)("td",{parentName:"tr",align:null},"mt1.bsc.es")))),(0,r.kt)("p",null,"All connections must be done through SSH (Secure SHell), for example:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"mylaptop$> ssh {username}@mn1.bsc.es\n")),(0,r.kt)("h3",{id:"password-change-"},"Password change",(0,r.kt)("a",{parentName:"h3",href:"#ToC-passwordchange"}," \u21a9")),(0,r.kt)("p",null,"For security reasons, you must change the first password."),(0,r.kt)("p",null,"To change your password, you have to login at Storage (Data Transfer machine):"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"mylaptop$> ssh {username}@dt01.bsc.es\n")),(0,r.kt)("p",null,"using the same username and password than in the cluster. Then, you have to\nuse the 'passwd' command."),(0,r.kt)("p",null,"The new password will become effective after about 10 minutes."),(0,r.kt)("h3",{id:"access-fromto-the-outside-"},"Access from/to the outside",(0,r.kt)("a",{parentName:"h3",href:"#ToC-outsideconnect"}," \u21a9")),(0,r.kt)("p",null,"The login nodes are the only nodes accessible from the outside, but no connections\nare allowed from the cluster to the outside world for security reasons."),(0,r.kt)("p",null,"All file transfers from/to the outside must be executed from your local machine\nand not within the cluster:"),(0,r.kt)("h5",{id:"example-to-copy-files-or-directories-from-mn4-to-an-external-machine"},"Example to copy files or directories from MN4 to an external machine:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},' mylaptop$> scp -r {username}@dt01.bsc.es:"MN4_SOURCE_dir" "mylaptop_DEST_dir"\n')),(0,r.kt)("h5",{id:"example-to-copy-files-or-directories-from-an-external-machine-to-mn4"},"Example to copy files or directories from an external machine to MN4:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},' mylaptop$> scp -r "mylaptop_SOURCE_dir" {username}@dt01.bsc.es:"MN4_DEST_dir"\n')),(0,r.kt)("h2",{id:"directories-and-file-systems-"},"Directories and file systems",(0,r.kt)("a",{parentName:"h2",href:"#ToC-filesystems"}," \u21a9")),(0,r.kt)("p",null,"There are different partitions of disk space. Each area may have specific size limits and usage policies."),(0,r.kt)("h3",{id:"basic-directories-under-gpfs-"},"Basic directories under GPFS",(0,r.kt)("a",{parentName:"h3",href:"#ToC-gpfsdirectories"}," \u21a9")),(0,r.kt)("p",null,"GPFS (General Parallel File System, a distributed networked filesystem) can be accessed from all the nodes and Data Transfer Machine 

1(dt01.bsc.es)."),(0,r.kt)("p",null,"The available GPFS directories and file systems are:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},(0,r.kt)("inlineCode",{parentName:"p"},"/apps"),": over this filesystem reside applications and libraries already installed on the machine for everyday use. Users cannot write to it.")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},(0,r.kt)("inlineCode",{parentName:"p"},"/gpfs/home"),": after login, it is the default work area where users can save source codes, scripts, and other personal data. The space quota is individual (with a relatively lessened capacity). ",(0,r.kt)("strong",{parentName:"p"},"Not recommended for run jobs; please run your jobs on your group\u2019s /gpfs/projects or /gpfs/scratch instead"),".")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},(0,r.kt)("inlineCode",{parentName:"p"},"/gpfs/projects"),": it's intended for data sharing between users of the same group or project. All members of the group share the space quota.")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},(0,r.kt)("inlineCode",{parentName:"p"},"/gpfs/scratch"),": each user has their directory under this partition, for example, to store temporary job files during execution. All members of the group share the space quota."))),(0,r.kt)("h3",{id:"storage-space-limitsquotas-"},"Storage space limits/quotas",(0,r.kt)("a",{parentName:"h3",href:"#ToC-bscquota"}," \u21a9")),(0,r.kt)("p",null,"To check the limits of disk space, as well as the quotas of current use for each file system:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"}," $> bsc_quota\n")),(0,r.kt)("h2",{id:"running-jobs-"},"Running jobs",(0,r.kt)("a",{parentName:"h2",href:"#ToC-runningjobs"}," \u21a9")),(0,r.kt)("h3",{id:"submit-to-queues-"},"Submit to queues",(0,r.kt)("a",{parentName:"h3",href:"#ToC-submittingjobs"}," \u21a9")),(0,r.kt)("p",null,"Jobs submission to the queue system have to be done through the Slurm directives,\nfor example:"),(0,r.kt)("h5",{id:"to-submit-a-job"},"To submit a job:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"}," $> sbatch {job_script}\n")),(0,r.kt)("h5",{id:"to-show-all-the-submitted-jobs"},"To show all the submitted jobs:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"}," $> squeue\n")),(0,r.kt)("h5",{id:"to-cancel-a-job"},"To cancel a job:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"}," $> scancel {job_id}\n")),(0,r.kt)("h3",{id:"queue-limits-"},"Queue limits",(0,r.kt)("a",{parentName:"h3",href:"#ToC-bscqueues"}," \u21a9")),(0,r.kt)("p",null,"To check the limits for the queues (QoS) assigned to the project, you can do:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"}," $> bsc_queues\n")),(0,r.kt)("h3",{id:"interactive-jobs-"},"Interactive jobs",(0,r.kt)("a",{parentName:"h3",href:"#ToC-interactive"}," \u21a9")),(0,r.kt)("h4",{id:"interactive-sessions"},"Interactive sessions"),(0,r.kt)("p",null,"Allocation of an interactive session has to be done through Slurm, for example:"),(0,r.kt)("h5",{id:"to-request-an-interactive-session-on-a-compute-node"},"To request an interactive session on a compute node:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"}," $> salloc -n 1 -c 4  # example to request 1 task, 4 CPUs (cores) per task\n")),(0,r.kt)("h5",{id:"to-request-an-interactive-session-on-a-non-shared-exclusive-compute-node"},"To request an interactive session on a non-shared (exclusive) compute node:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"}," $> salloc --exclusive\n")),(0,r.kt)("h5",{id:"to-request-an-interactive-session-on-a-compute-node-using-gpus"},"To request an interactive session on a compute node using GPUs:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"}," $> salloc -c 80 --gres=gpu:2  # example to request 80 CPUs (cores) + 2 GPUs\n")))}i.isMDXComponent=!0}}]);