diff --git a/docs.it4i/salomon/storage.md b/docs.it4i/salomon/storage.md index 2496108cf654cbbc481822aa76857c794feba58d..e759db146342105b0617efbdbea8acc273a0268f 100644 --- a/docs.it4i/salomon/storage.md +++ b/docs.it4i/salomon/storage.md @@ -4,9 +4,9 @@ Storage Introduction ------------ -There are two main shared file systems on Salomon cluster, the [HOME](#home)and [SCRATCH](#shared-filesystems). +There are two main shared file systems on Salomon cluster, the [HOME](#home) and [SCRATCH](#shared-filesystems). -All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems. +All login and compute nodes may access same data on shared file systems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp file systems. Policy (in a nutshell) ---------------------- @@ -22,19 +22,19 @@ Policy (in a nutshell) Archiving ------------- -Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use [CESNET storage service](#cesnet-data-storage), which is available via SSHFS. +Please don't use shared file systems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use [CESNET storage service](#cesnet-data-storage), which is available via SSHFS. Shared Filesystems ---------------------- -Salomon computer provides two main shared filesystems, the [ HOME filesystem](#home-filesystem) and the [SCRATCH filesystem](#scratch-filesystem). The SCRATCH filesystem is partitioned to [WORK and TEMP workspaces](#shared-workspaces). The HOME filesystem is realized as a tiered NFS disk storage. The SCRATCH filesystem is realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH filesystems for the purpose of sharing data with other users using fine-grained control. +Salomon computer provides two main shared file systems, the [HOME file system](#home-filesystem) and the [SCRATCH file system](#scratch-filesystem). The SCRATCH file system is partitioned to [WORK and TEMP workspaces](#shared-workspaces). The HOME file system is realized as a tiered NFS disk storage. The SCRATCH file system is realized as a parallel Lustre file system. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH file systems for the purpose of sharing data with other users using fine-grained control. -###HOME filesystem +###HOME file system -The HOME filesystem is realized as a Tiered filesystem, exported via NFS. The first tier has capacity 100 TB, second tier has capacity 400 TB. The filesystem is available on all login and computational nodes. The Home filesystem hosts the [HOME workspace](#home). +The HOME file system is realized as a Tiered file system, exported via NFS. The first tier has capacity 100 TB, second tier has capacity 400 TB. The file system is available on all login and computational nodes. The Home file system hosts the [HOME workspace](#home). -###SCRATCH filesystem +###SCRATCH file system -The architecture of Lustre on Salomon is composed of two metadata servers (MDS) and six data/object storage servers (OSS). Accessible capacity is 1.69 PB, shared among all users. The SCRATCH filesystem hosts the [WORK and TEMP workspaces](#shared-workspaces). +The architecture of Lustre on Salomon is composed of two metadata servers (MDS) and six data/object storage servers (OSS). Accessible capacity is 1.69 PB, shared among all users. The SCRATCH file system hosts the [WORK and TEMP workspaces](#shared-workspaces). Configuration of the SCRATCH Lustre storage @@ -52,16 +52,16 @@ Configuration of the SCRATCH Lustre storage (source <http://www.nas.nasa.gov>) -A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing. +A user file on the Lustre file system can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing. When a client (a compute node from your job) needs to create or access a file, the client queries the metadata server ( MDS) and the metadata target ( MDT) for the layout and location of the [file's stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping). Once the file is opened and the client obtains the striping information, the MDS is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval. If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results. -There is default stripe configuration for Salomon Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance: +There is default stripe configuration for Salomon Lustre file systems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance: -1. stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre filesystems -2. stripe_count the number of OSTs to stripe across; default is 1 for Salomon Lustre filesystems one can specify -1 to use all OSTs in the filesystem. +1. stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre file systems +2. stripe_count the number of OSTs to stripe across; default is 1 for Salomon Lustre file systems one can specify -1 to use all OSTs in the file system. 3. stripe_offset The index of the OST where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended. !!! Note "Note" @@ -89,7 +89,7 @@ stripe_count: -1 stripe_size: 1048576 stripe_offset: -1 In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over all (54) OSTs -Use lfs check OSTs to see the number and status of active OSTs for each filesystem on Salomon. Learn more by reading the man page +Use lfs check OSTs to see the number and status of active OSTs for each file system on Salomon. Learn more by reading the man page ```bash $ lfs check osts @@ -222,10 +222,10 @@ Shared Workspaces ###HOME -Users home directories /home/username reside on HOME filesystem. Accessible capacity is 0.5 PB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250 GB per user. If 250 GB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request. +Users home directories /home/username reside on HOME file system. Accessible capacity is 0.5 PB, shared among all users. Individual users are restricted by file system usage quotas, set to 250 GB per user. If 250 GB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request. !!! Note "Note" - The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects. + The HOME file system is intended for preparation, evaluation, processing and storage of data generated by active Projects. The HOME should not be used to archive data of past Projects or other unrelated data. @@ -243,14 +243,14 @@ The workspace is backed up, such that it can be restored in case of catasthropi ### WORK -The WORK workspace resides on SCRATCH filesystem. Users may create subdirectories and files in directories **/scratch/work/user/username** and **/scratch/work/project/projectid. **The /scratch/work/user/username is private to user, much like the home directory. The /scratch/work/project/projectid is accessible to all users involved in project projectid. +The WORK workspace resides on SCRATCH file system. Users may create subdirectories and files in directories **/scratch/work/user/username** and **/scratch/work/project/projectid. **The /scratch/work/user/username is private to user, much like the home directory. The /scratch/work/project/projectid is accessible to all users involved in project projectid. !!! Note "Note" The WORK workspace is intended to store users project data as well as for high performance access to input and output files. All project data should be removed once the project is finished. The data on the WORK workspace are not backed up. - Files on the WORK filesystem are **persistent** (not automatically deleted) throughout duration of the project. + Files on the WORK file system are **persistent** (not automatically deleted) throughout duration of the project. -The WORK workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as Lustre parallel filesystem and is available from all login and computational nodes. Default stripe size is 1 MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH filesystem. +The WORK workspace is hosted on SCRATCH file system. The SCRATCH is realized as Lustre parallel file system and is available from all login and computational nodes. Default stripe size is 1 MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH file system. !!! Note "Note" Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience. @@ -268,16 +268,16 @@ The WORK workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as L ### TEMP -The TEMP workspace resides on SCRATCH filesystem. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6 PB, shared among all users on TEMP and WORK. Individual users are restricted by filesystem usage quotas, set to 100 TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. >If 100 TB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request. +The TEMP workspace resides on SCRATCH file system. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6 PB, shared among all users on TEMP and WORK. Individual users are restricted by file system usage quotas, set to 100 TB per user. The purpose of this quota is to prevent runaway programs from filling the entire file system and deny service to other users. >If 100 TB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request. !!! Note "Note" The TEMP workspace is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the TEMP workspace as their working directory. Users are advised to save the necessary data from the TEMP workspace to HOME or WORK after the calculations and clean up the scratch files. - Files on the TEMP filesystem that are **not accessed for more than 90 days** will be automatically **deleted**. + Files on the TEMP file system that are **not accessed for more than 90 days** will be automatically **deleted**. -The TEMP workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as Lustre parallel filesystem and is available from all login and computational nodes. Default stripe size is 1 MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH filesystem. +The TEMP workspace is hosted on SCRATCH file system. The SCRATCH is realized as Lustre parallel file system and is available from all login and computational nodes. Default stripe size is 1 MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH file system. !!! Note "Note" Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience. @@ -295,14 +295,14 @@ The TEMP workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as L RAM disk -------- -Every computational node is equipped with filesystem realized in memory, so called RAM disk. +Every computational node is equipped with file system realized in memory, so called RAM disk. !!! Note "Note" - Use RAM disk in case you need really fast access to your data of limited size during your calculation. Be very careful, use of RAM disk filesystem is at the expense of operational memory. + Use RAM disk in case you need really fast access to your data of limited size during your calculation. Be very careful, use of RAM disk file system is at the expense of operational memory. The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory. -The local RAM disk filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk filesystem is limited. Be very careful, use of RAM disk filesystem is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk filesystem at the same time. +The local RAM disk file system is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk file system is limited. Be very careful, use of RAM disk file system is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk file system at the same time. !!! Note "Note" The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript. @@ -328,7 +328,7 @@ Summary CESNET Data Storage ------------ -Do not use shared filesystems at IT4Innovations as a backup for large amount of data or long-term archiving purposes. +Do not use shared file systems at IT4Innovations as a backup for large amount of data or long-term archiving purposes. !!! Note "Note" ../../img/The IT4Innovations does not provide storage capacity for data archiving. Academic staff and students of research institutions in the Czech Republic can use [CESNET Storage service](https://du.cesnet.cz/).