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This shows you the differences between two versions of the page.

--- lab:computing_resources [2018/02/21 13:09]
alexskr
+++ lab:computing_resources [2019/01/29 13:50] (current)
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 ====== Computing resources ======
-Lab has a number of computing resources - general purpose computing node, a database server, a VM environment,  and a small cluster. For most things, BMIR IT team ( Alex Skrenchuk and Graham Freeman) and can grant you access. In order to get access, email bmir-it-team@lists.stanford.edu, cc me asking to deny if inappropriate.
+Lab has a number of computing resources - general purpose computing node, rstudio pro server, a database server, a VM environment, and a small cluster. For most things, BMIR IT team (Alex Skrenchuk) and can grant you access. In order to get access, email bmir-it-team@lists.stanford.edu, cc me asking to deny if inappropriate.
-Access to most of the resources requires connecting to the VPN (https://vpn.stanford.edu).  As a general rule you should use SUNet ID credentials for authentication.  A notable exception is MySQL.  MySQL user name as the same as your SUNet ID and password is stored in the ~/my.cnf file on your server home directory.
+Access to most of the resources requires connecting to the VPN ([[https://vpn.stanford.edu|https://vpn.stanford.edu]]). As a general rule you should use SUNet ID credentials for authentication. A notable exception is MySQL. MySQL user name as the same as your SUNet ID and password is stored in the ~/my.cnf file on your server home directory.
+Please note that none of the computing resources are HIPAA compliant so it should not be used for processing PHI or High risk data unless it is de-identified.
 ===== General Purpose Server =====
-**khatrialb-dev1.stanford.edu  ** is the server that you can use for most of your work.  If you have a project requiring high CPU/Memory needs consider using cluster.
+**khatrialb-dev1.stanford.edu ** is the server that you can use for most of your work. If you have a project requiring high CPU/Memory needs consider using cluster.
+===== Filesystem overview =====
+^Name^Type^Purpose^ Backup/Snapshot ^ Quota ^
+| Home Directory |NFS | Small, important files (source code, executables, configuration files...) | Y/Y |20G |
+| /labs/khatrilab | NFS | Project data, large datasets | Y/N | 55Tb|
+| /labs/khatrilab/users/<SUNetID> | NFS | Individual Lab member Projects | Y/N | |
+| /scratch/labs/khatrilab | NFS | | |
+| /scratch/users/<SUNetID>| NFS | Large, temporary files, raw application output | N/N | |
+| /scratch/labs/khatrilab | NFS | Large, temporary files, raw application output | N/N | |
+| /local-scratch | local | temporary files requiring high I/O |N/N | |
+=== Where should I store my files? ===
+  * personal scripts, configuration files and software installations → home
+  * group-shared scripts, software installations, and large datasets → /labs/khatrilab/users/<SUNetID>
+  * temporary output of jobs, large checkpoint files → /scratch/users/<SUNetID>
+  * Temproray files created by Rstduio (~/.rstudio)→ Create a sym link ~./rstudio to /scratch/users/<SUNetID>/rstuido
 ===== Database server =====
 **khatrilab-db1.stanford.edu** is our database server.
 Login Info
   * login: Your SUNet
-  * Password:  Your initial password is stored in ~/my.cnf
+  * Password: Your initial password is stored in ~/my.cnf
 ===== Rstudio Pro Server =====
-[[https://rstudio.khatrilab.stanford.edu| https://rstudio.khatrilab.stanford.edu]]
+[[https://rstudio.khatrilab.stanford.edu|https://rstudio.khatrilab.stanford.edu]]
 ===== Cluster =====
-We have a BMIR owned cluster (10 nodes) shared with the Shah lab. Access is via khatrilab-dev1.stanford.edu. See [[lab:bmir_cluster|here ]] for details and some usage instructions.
-  *For complete code samples see Parallel processing for tips on how to access from khatrilab-dev1
+We have a BMIR owned cluster (10 nodes) shared with the Shah lab. Access is via khatrilab-dev1.stanford.edu. See [[:lab:bmir_cluster|here ]] for details and some usage instructions.
-  *[[http://slurm.schedmd.com/pdfs/summary.pdf| Cheat sheet]] for SLURM commands
+  * For complete code samples see Parallel processing for tips on how to access from khatrilab-dev1
+  * [[http://slurm.schedmd.com/pdfs/summary.pdf|Cheat sheet]] for SLURM commands