What Disks to Use
Disk Quotas
Disk Configuration
Disk Usage Monitoring
NetApp Snapshots: How to Recover Old or Deleted Files
SSD and Local Disk Space

(this is still a draft, some items need to be fixed)

1. What Disks to Use

All the useful disk space available on the cluster is mounted off a dedicated device (aka appliance or server), a NetApp filer.

The available disk space is divided in several area (aka partitions):

a small partition for basic configuration files and small storage, the /home partition,
a set of medium size partitions, one for SAO users, one for non-SAO users, the /data partitions,
a set of large partitions, one for SAO users, one for non-SAO users, the /pool partitions,
a second set of large partitionsfor temporary storage, the /scratch partitions.

Note that:

we impose quotas: limit on how much can be stored on each partition by each user, and
we monitor disk usage;
/home should not be used to keep large files, use /pool instead;
/scratch is for temporary storage (i.e., while a job is running) if you need more than what you can store under /pool.
We will implement an automatic scrubber: old stuff will be deleted to make space, using a FIFO model.
None of the disks on the cluster are for long term storage, please copy your results back to your "home" computer and
delete what you don't need any longer.
Once you reach your quota you won't be able to write anything on that partition until you delete stuff.
We are in the process of adding local SSDs (solid state disks) to some compute nodes (not all - stay tuned), and
for special cases it may be OK to use disk space local to the compute node.

Contact us if your jobs can benefit for either SSDs or local disk space (missing link).

2. Disk Quotas

To prevent the disks to fill up and hose the cluster, there is a limit (aka quota) on

how much disk space and
how many files (in fact "inodes": the sum of number of files and number of directories)
each user can keep.

Each quota type has a soft limit (warning) and a hard limit (error) and is specific to each partition. In other words exceeding the soft limit produces warnings; while exceeding the hard limit is not allowed, and results in errors.

3. Disk Configuration

	Maximum	Quotas per user		NetApp
	disk	disk space	`no. of files`	snapshots
Disk name	capacity	soft/hard	soft/hard	enabled?	Purpose
`/home`	`8TB`	50/`100GB`	`1.8/2M`	`yes: 4 weeks`	For your basic configuration files, scripts and job files - your limit is low but you can recover old stuff up to 4 weeks.
`/data/sao`	`20TB`	`2.8/3.0TB`	`1/2M`	`yes: 2 weeks`	For important but relatively small files like final results, etc. - your limit is medium, you can recover old stuff, but disk space is not released right away. For SAO users.
`/data/genomics`	`10TB`	`1.0/2.0TB`	`1/2M`	`yes: 2 weeks`	For important but relatively small files like final results, etc. - your limit is medium, you can recover old stuff, but disk space is not released right away. For non-SAO users.
/`pool/sao`	`60TB`	`1.8/2.0TB`	`4/5M`	`no`	For the bulk of your storage - your limit is high, and disk space is released right away, for SAO users.
`/pool/genomics`	`50TB`	`1.8/2.0TB`	`1.8/2M`	`no`	For the bulk of your storage - your limit is high, and disk space is released right away, for non-SAO users.
`/scratch`	`50TB`	`2.8/3.0TB`	`1/1M`	`no, FIFO model`	For temporary storage, if you need more than what you can keep in `/pool` - SAO/non-SAO user should use `/scratch/sao` or `/scratch/genomics`, respectively. The FIFO model (first in first out) purging has yet to be implemented as we tune the system.

Notes

The notation

2.8/3.0TB means that the soft limit is 2.8TB and the hard limit is 3.0TB of disk space, while
4/5M means that the soft limit is 4 millions inodes and the hard limit is 5 millions.

It is inefficient to store a slew of small files and if you do you may reach your inodes quota before you space quota.

While some of the tool(s) you use may force you to be inefficient while jobs are running, you should remember to

remove useless files when jobs have completed,
compress file that can benefit from compression, and
archive a slew of file into a tar-ball or a zip, as follow
   % zip archive.zip dir/
or
   % tar czf archibe.tgz dir/
both examples archive the content of the directory dir/ into a single zip or a tgz file. You can then delete the content of dir/ with
   % rm -rf dir/
You can unpack each type of archive with
% unzip archive.zip
or
% tar xf archive.tgz

The sizes of the partitions (aka the various disks) on the NetApp will "auto-grow" until they reach the listed maximum capacity, so the size shown by the traditional Un*x command, like df does necessarily not reflect the maximum size.

Once we secure more space for /scratch, we will implement a FIFO (first in first out) model, where old files are deleted without warning to make space.

There will be a minimum age limit, meaning that only files older that (let's say) 3 months will be deleted.
Older files will be deleted before the newer ones (FIFO),
We will run a scrubber an a regular interval

4. Disk Monitoring

The following tools can be used to monitor your disk usage.

You can use the following Un*x commands:

`du`	show disk use
`df`	show disk free

or you can use Hydra-specific home-grown tools, (these require that you load the tool/local-hpc module)

`dus-report.pl`	run `du` and parse its output in a more user friendly format
`disk-usage.pl`	run `df` and parse its output in a more user friendly format

Disk usage

The output of du can be very long and confusing. It is best used with the option "-hs" to show the sum ("-s") and to print it in a human readable format ("-h").

If there is a lot of files/directory, du can take a while to complete.

For example:

% du -sh dir/
136M    dir/

The output of df can be very long and confusing.

You can use it to query a specific partition and get the output in a human readable format ("-h"), for example:

% df -h /pool/sao
Filesystem           Size  Used Avail Use% Mounted on
10.61.10.1:/vol_sao   20T   15T  5.1T  75% /pool/sao

You can compile the output of du into a more useful report with the dus-report.pl tool. This tool will run du for you (can take a while) and parse its output to produce a more concise/useful report.

For example, to see the directories that hold the most stuff in /pool/sao/hpc:

% dus-report.pl /pool/sao/hpc
 612.372 GB            /pool/sao/hpc
                       capac.   20.000 TB (75% full), avail.    5.088 TB
 447.026 GB  73.00 %   /pool/sao/hpc/rtdc
 308.076 GB  50.31 %   /pool/sao/hpc/rtdc/v4.4.0
 138.950 GB  22.69 %   /pool/sao/hpc/rtdc/vX
 137.051 GB  22.38 %   /pool/sao/hpc/rtdc/vX/M100-test-oob-2
 120.198 GB  19.63 %   /pool/sao/hpc/rtdc/v4.4.0/test2
 120.198 GB  19.63 %   /pool/sao/hpc/rtdc/v4.4.0/test2-2-9
  83.229 GB  13.59 %   /pool/sao/hpc/c7
  83.229 GB  13.59 %   /pool/sao/hpc/c7/hpc
  65.280 GB  10.66 %   /pool/sao/hpc/sw
  64.235 GB  10.49 %   /pool/sao/hpc/rtdc/v4.4.0/test1
  49.594 GB   8.10 %   /pool/sao/hpc/sw/intel-cluster-studio
  46.851 GB   7.65 %   /pool/sao/hpc/rtdc/vX/M100-test-oob-2/X54.ms
  46.851 GB   7.65 %   /pool/sao/hpc/rtdc/vX/M100-test-oob-2/X54.ms/SUBMSS
  43.047 GB   7.03 %   /pool/sao/hpc/rtdc/vX/M100-test-oob-2/X220.ms
  43.047 GB   7.03 %   /pool/sao/hpc/rtdc/vX/M100-test-oob-2/X220.ms/SUBMSS
  42.261 GB   6.90 %   /pool/sao/hpc/c7/hpc/sw
  36.409 GB   5.95 %   /pool/sao/hpc/c7/hpc/tests
  30.965 GB   5.06 %   /pool/sao/hpc/c7/hpc/sw/intel-cluster-studio
  23.576 GB   3.85 %   /pool/sao/hpc/rtdc/v4.4.0/test2/X54.ms
  23.576 GB   3.85 %   /pool/sao/hpc/rtdc/v4.4.0/test2-2-9/X54.ms
  23.576 GB   3.85 %   /pool/sao/hpc/rtdc/v4.4.0/test2/X54.ms/SUBMSS
  23.576 GB   3.85 %   /pool/sao/hpc/rtdc/v4.4.0/test2-2-9/X54.ms/SUBMSS
  22.931 GB   3.74 %   /pool/sao/hpc/rtdc/v4.4.0/test2/X220.ms
  22.931 GB   3.74 %   /pool/sao/hpc/rtdc/v4.4.0/test2-2-9/X220.ms
report in /tmp/dus.pool.sao.hpc.hpc

You can rerun dus-report.pl with different options on the same intermediate file, like

% dus-report.pl -n 999 -pc 1 /tmp/dus.pool.sao.hpc.hpc

to get a different report, to see the list down to 1%. Use

% dus-report.pl -help

to see how else you can use it.

The tool disk-usage.pl runs df and presents its output in a more friendly format:

% disk-usage.pl 
Filesystem                              Size     Used    Avail Capacity  Mounted on
NetApp.1:/vol_home/hpc                 2.70T    1.02T    1.68T  38%/17%  /home/hpc
NetApp.1:/vol_sao                     20.00T   14.91T    5.09T  75%/34%  /pool/sao
NetApp.1:/vol_sao_atmos               18.00T   13.80T    4.20T  77%/7%   /pool/sao_atmos
NetApp.1:/vol_sao_rtdc                 1.00T  167.51G  856.49G  17%/1%   /pool/sao_rtdc
NetApp.1:/vol_genomics                20.00T   17.12T    2.88T  86%/57%  /pool/genomics
NetApp.1:/vol_data_genomics            1.90T   10.78G    1.89T   1%/3%   /data/genomics
NetApp.1:/vol_data/sao                 3.60T    3.27T  336.17G  91%/37%  /data/sao
NetApp.1:/vol_data/admin               3.60T    3.27T  336.17G  91%/37%  /data/admin
NetApp.1:/vol_old_pools/cluster0      17.00T   15.60T    1.40T  92%/22%  /pool/cluster0
NetApp.1:/vol_old_pools/cluster1      17.00T   15.60T    1.40T  92%/22%  /pool/cluster1
NetApp.1:/vol_old_pools/cluster2      17.00T   15.60T    1.40T  92%/22%  /pool/cluster2
NetApp.1:/vol_old_pools/cluster3      17.00T   15.60T    1.40T  92%/22%  /pool/cluster3
NetApp.1:/vol_old_pools/cluster4      17.00T   15.60T    1.40T  92%/22%  /pool/cluster4
NetApp.1:/vol_old_pools/cluster5      17.00T   15.60T    1.40T  92%/22%  /pool/cluster5
NetApp.1:/vol_old_pools/cluster7      17.00T   15.60T    1.40T  92%/22%  /pool/cluster7
NetApp.1:/vol_sylvain                 14.18T   12.75T    1.43T  90%/51%  /pool/sylvain
NetApp.1:/vol_scratch/genomics        25.00T   19.53T    5.47T  79%/5%   /scratch/genomics
NetApp.1:/vol_scratch/sao             25.00T   19.53T    5.47T  79%/5%   /scratch/sao
NetApp.5:/vol/a2v1/genomics01         20.00T    0.05G   20.00T   1%/1%   /scratch/genomics01
NetApp.5:/vol/a2v1/sao01              20.00T    0.05G   20.00T   1%/1%   /scratch/sao01

Use

% disk-usage.pl -help

to see how else to use it. You can, for instance, get the disk quotas and the max size with:

% disk-usage.pl -quotas
                                                                 quotas: disk usage #(inodes)  max 
Filesystem                              Size     Used    Avail Capacity  soft/hard  soft/hard size Mounted on
NetApp.1:/vol_home/hpc                 2.70T    1.02T    1.68T  38%/17%   50G/100G  1.8M/2.0M   8T /home/hpc
NetApp.1:/vol_sao                     20.00T   14.91T    5.09T  75%/34%  1.8T/2.0T  4.0M/5.0M  60T /pool/sao
NetApp.1:/vol_sao_atmos               18.00T   13.80T    4.20T  77%/7%   8.0T/10.T  9.0M/10.M  22T /pool/sao_atmos
NetApp.1:/vol_sao_rtdc                 1.00T  167.51G  856.49G  17%/1%   2.8T/3.0T  2.5M/3.0M  11T /pool/sao_rtdc
NetApp.1:/vol_genomics                20.00T   17.12T    2.88T  86%/57%  1.8T/2.0T  1.8M/2.0M  50T /pool/genomics
NetApp.1:/vol_data_genomics            1.90T   10.78G    1.89T   1%/3%   1.0T/2.0T  1.0M/2.0M  10T /data/genomics
NetApp.1:/vol_data/*                   3.60T    3.27T  336.17G  91%/37%  2.8T/3.0T  35.M/40.M  20T /data/sao:admin
NetApp.1:/vol_old_pools/cluster*      17.00T   15.60T    1.40T  92%/22%                            /pool/cluster0:1:2:3:4:5:7
NetApp.1:/vol_sylvain                 14.18T   12.75T    1.43T  90%/51%  14.T/15.T  63.M/65.M  15T /pool/sylvain
NetApp.1:/vol_scratch/*               25.00T   19.53T    5.47T  79%/5%   2.8T/3.0T  1.0M/1.0M  50T /scratch/genomics:sao
NetApp.5:/vol/a2v1/*                  20.00T    0.05G   20.00T   1%/1%   14.T/15.T  2.0M/2.0M  20T /scratch/genomics01:sao01

Monitoring Quota Usage

The Linux command quota is not (yet) working with the NetApp filer.

We compile a daily quota report and provide tools to parse the quota report. (need to insert links to these tools)

5. NetApp Snapshots: How to Recover Old or Deleted Files.

Some of the disks on the NetApp filer have the so called "snapshot mechanism" enabled:

This allow users to recover deleted files or access an older version of a file.
Indeed, the NetApp filer makes a "snapshot" copy of the file system (the content of the disk) every so often and keeps these snapshots up to a given age.
So if we enable hourly snapshot and set a two weeks retention, you can recover a file as it was hours ago, days ago or weeks ago, but only up to two weeks ago.
The drawback of the snapshot is that when files are deleted, the disk space is not freed until the deleted files age-out. like 2 or 4 weeks later.

How to Use the NetApp Snapshots:

To recover an old version or a deleted file, foo.dat, that was (for example) in /data/genomics/frandsen/important/results/:

If the file was deleted:

 cd /data/genomics/.snapshot/XXXX/frandsen/important/results
 cp -pi foo.dat /data/genomics/frandsen/important/results/foo.dat

If you want to recover an old version:

 cd /data/genomics/.snapshot/XXXX/frandsen/important/results
 cp -pi foo.dat /data/genomics/frandsen/important/results/old-foo.dat

The -p will preserve the file creation date and the -i will prevent overwriting an existing file.
The XXXX is to be replaced by either:
- hourly.YYYY-MM-DD_HHMM
- daily.YYYY-MM-DD_0010
- weekly.YYYY-MM-DD_0015
  where YYY-MM-DD is a date specification (i.e., 2015-11-01)
The files under .snapshot are read-only:
- they be recovered using cp, tar or rsync; but
- they cannot be moved (mv) or deleted (rm).

6. SSD and Local Disk Space

We are in the process of adding local SSDs (solid state disks) to some compute nodes (not all - stay tuned), and
for special cases it may be OK to use disk space local to the compute node.

Until we post here detailed instruction, you should contact us if your jobs can benefit for either SSDs or local disk space (missing link).

Last Updated 19 Jan 2016 SGK.

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