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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 file systems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp file systems.
\* Use [HOME](#home) for your most valuable data and programs.
\* Use [WORK](#work) for your large project files.
\* Use [TEMP](#temp) for large scratch data.
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.
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.
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).
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
* Disk array SFA12KX
* 540 x 4 TB SAS 7.2krpm disk
* 54 x OST of 10 disks in RAID6 (8+2)
* 15 x hot-spare disk
* 4 x 400 GB SSD cache
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 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 file systems
1. 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.
1. 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.
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns.
$ lfs getstripe dir | filename
$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir | filename
$ lfs getstripe /scratch/work/user/username
/scratch/work/user/username
stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
$ lfs setstripe -c -1 /scratch/work/user/username/
$ lfs getstripe /scratch/work/user/username/
/scratch/work/user/username/
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 file system on Salomon. Learn more by reading the man page
$ lfs check osts
$ man lfs
```
### Hints on Lustre Stripping
When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.
Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.
Using a large stripe size can improve performance when accessing very large files
Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.
Read more on <http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
Disk usage and user quotas can be checked and reviewed using following command:
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$ it4i-disk-usage -h
# Using human-readable format
# Using power of 1024 for space
# Using power of 1000 for entries
Filesystem: /home
Space used: 110G
Space limit: 238G
Entries: 40k
Entries limit: 500k
# based on filesystem quota
Filesystem: /scratch
Space used: 377G
Space limit: 93T
Entries: 14k
Entries limit: 0
# based on Lustre quota
Filesystem: /scratch
Space used: 377G
Entries: 14k
# based on Robinhood
Filesystem: /scratch/work
Space used: 377G
Entries: 14k
# based on Robinhood
Filesystem: /scratch/temp
Space used: 12K
Entries: 6
# based on Robinhood
In this example, we view current size limits and space occupied on the /home and /scratch filesystem, for a particular user executing the command.
Note that limits are imposed also on number of objects (files, directories, links, etc...) that are allowed to create.
To have a better understanding of where the space is exactly used, you can use following command to find out.
$ du -hs dir
```
Example for your HOME directory:
$ cd /home
$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr
258M cuda-samples
15M .cache
13M .mozilla
5,5M .eclipse
2,7M .idb_13.0_linux_intel64_app
```
This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.
To have a better understanding of previous commands, you can read manpages.
Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.
ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.
[vop999@login1.salomon ~]$ umask 027
[vop999@login1.salomon ~]$ mkdir test
[vop999@login1.salomon ~]$ ls -ld test
[vop999@login1.salomon ~]$ getfacl test
# file: test
# owner: vop999
# group: vop999
user::rwx
group::r-x
other::---
[vop999@login1.salomon ~]$ setfacl -m user:johnsm:rwx test
[vop999@login1.salomon ~]$ ls -ld test
[vop999@login1.salomon ~]$ getfacl test
# file: test
# owner: vop999
# group: vop999
user::rwx
user:johnsm:rwx
group::r-x
mask::rwx
other::---
```
Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:
[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
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.
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.
The files on HOME will not be deleted until end of the [users lifecycle](../general/obtaining-login-credentials/obtaining-login-credentials/).
The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files.
| Accesspoint | /home/username |
| Capacity | 0.5 PB |
| Throughput | 6 GB/s |
| User quota | 250 GB |
| Protocol | NFS, 2-Tier |
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.
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 file system are **persistent** (not automatically deleted) throughout duration of the project.
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.
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
| -------------------- | --------------------------------------------------------- |
| Accesspoints | /scratch/work/user/username, /scratch/work/user/projectid |
| Capacity | 1.6 PB |
| Throughput | 30 GB/s |
| User quota | 100 TB |
| Default stripe size | 1 MB |
| Default stripe count | 1 |
| Number of OSTs | 54 |
| Protocol | Lustre |
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.
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 file system that are **not accessed for more than 90 days** will be automatically **deleted**.
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.
Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.
| Accesspoint | /scratch/temp |
| Capacity | 1.6 PB |
| Throughput | 30 GB/s |
| User quota | 100 TB |
| Default stripe size | 1 MB |
| Default stripe count | 1 |
| Number of OSTs | 54 |
| Protocol | Lustre |
Every computational node is equipped with file system realized in memory, so called RAM disk.
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/$PBS_JOBID directory.
The local RAM disk file system is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk file system is limited. Be very careful, use of RAM disk file system is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk file system at the same time.
The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.
| ----------- | ------------------------------------------------------------------------------------------------------- |
| Mountpoint | /ramdisk |
| Accesspoint | /ramdisk/$PBS_JOBID |
| Capacity | 120 GB |
| Throughput | over 1.5 GB/s write, over 5 GB/s read, single thread, over 10 GB/s write, over 50 GB/s read, 16 threads |
| User quota | none |
| Mountpoint | Usage | Protocol | Net | Capacity | Throughput | Limitations | Access |
| ------------- | ------------------------------ | ----------- | ------- | -------- | ------------ | ----------------------- | --------------------------- |
| /home | home directory | NFS, 2-Tier | 0.5 PB | 6 GB/s | Quota 250GB | Compute and login nodes | backed up |
| /scratch/work | large project files | Lustre | 1.69 PB | 30 GB/s | Quota | Compute and login nodes | none |
| /scratch/temp | job temporary data | Lustre | 1.69 PB | 30 GB/s | Quota 100 TB | Compute and login nodes | files older 90 days removed |
| /ramdisk | job temporary data, node local | local | 120GB | 90 GB/s | none | Compute nodes | purged after job ends |
Do not use shared file systems at IT4Innovations as a backup for large amount of data or long-term archiving purposes.
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/).
The CESNET Storage service can be used for research purposes, mainly by academic staff and students of research institutions in the Czech Republic.
User of data storage CESNET (DU) association can become organizations or an individual person who is either in the current employment relationship (employees) or the current study relationship (students) to a legal entity (organization) that meets the “Principles for access to CESNET Large infrastructure (Access Policy)”.
User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.
The service is documented [here](https://du.cesnet.cz/en/start). For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The procedure to obtain the CESNET access is quick and trouble-free.
(source [https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
It is very important to understand the CESNET storage before uploading data. [Please read](https://du.cesnet.cz/en/navody/home-migrace-plzen/start) first.
Once registered for CESNET Storage, you may [access the storage](https://du.cesnet.cz/en/navody/faq/start) in number of ways. We recommend the SSHFS and RSYNC methods.
### SSHFS Access
The SSHFS provides a very convenient way to access the CESNET Storage. The storage will be mounted onto a local directory, exposing the vast CESNET Storage as if it was a local removable hard drive. Files can be than copied in and out in a usual fashion.
```
Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz (Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno) Mount tier1_home **(only 5120M !)**:
```console
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
```
For easy future access from Anselm, install your public key
```console
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
```
Mount tier1_cache_tape for the Storage VO:
```console
$ sshfs username@ssh.du1.cesnet.cz:/cache_tape/VO_storage/home/username cesnet/
```
View the archive, copy the files and directories in and out
```console
$ ls cesnet/
$ cp -a mydir cesnet/.
$ cp cesnet/myfile .
```
Once done, please remember to unmount the storage
Rsync provides delta transfer for best performance, can resume interrupted transfers
Rsync is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. Rsync is widely used for backups and mirroring and as an improved copy command for everyday use.
Rsync finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated.
More about Rsync at [here](https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele)
Transfer large files to/from CESNET storage, assuming membership in the Storage VO
```console
$ rsync --progress datafile username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.
$ rsync --progress username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafile .
Transfer large directories to/from CESNET storage, assuming membership in the Storage VO
```console
$ rsync --progress -av datafolder username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.
$ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .