NEMO/Hardware: Difference between revisions

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== System Architecture ==
== System Architecture ==


The bwForCluster [https://www.hpc.uni-freiburg.de/ NEMO] is a high-performance compute resource with high speed interconnect. It is intended for compute activities related to research in for researchers from the fields '''N'''euroscience, '''E'''lementary Particle Physics and '''M'''icrosystems Engineering (NEMO).
The bwForCluster [https://www.hpc.uni-freiburg.de/ NEMO] is a high-performance compute resource with high speed interconnect. It is intended for compute activities related to research in for researchers from the fields '''N'''euroscience, '''E'''lementary Particle Physics, '''M'''icrosystems Engineering and '''M'''aterials Science (NEMO).


{| style="width: 100%; border-spacing: 5px;"
{| style="width: 100%; border-spacing: 5px;"
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|-
|-
!scope="column" | Queuing System
!scope="column" | Queuing System
| [http://docs.adaptivecomputing.com MOAB / Torque] (see [[Batch Jobs]] for help)
| [http://docs.adaptivecomputing.com MOAB / Torque] (see [[NEMO/Moab]] for help)
|-
|-
!scope="column" | (Scientific) Libraries and Software
!scope="column" | (Scientific) Libraries and Software
Line 29: Line 29:


* Operating System: [https://en.wikipedia.org/wiki/CentOS CentOS] Linux 7 (similar to RHEL 7)
* Operating System: [https://en.wikipedia.org/wiki/CentOS CentOS] Linux 7 (similar to RHEL 7)
* Queuing System: [http://docs.adaptivecomputing.com MOAB / Torque] (see [[Batch Jobs]] for help)
* Queuing System: [http://docs.adaptivecomputing.com MOAB / Torque] (see [[NEMO/Moab]] for help)
* (Scientific) Libraries and Software: [[Environment Modules]]
* (Scientific) Libraries and Software: [[Environment Modules]]
* Own Python Environments: [[Conda]]


=== Compute and Special Purpose Nodes ===


For researchers from the scientific fields '''N'''euroscience, '''E'''lementary Particle Physics, '''M'''icrosystems Engineering and '''M'''aterials Science the bwForCluster '''NEMO''' offers 908 compute nodes plus several special purpose nodes for login, interactive jobs, visualization and machine learning.
=== Compute Nodes ===


See [[bwForCluster NEMO Specific Batch Features]] for queuing gpu nodes!
For researchers from the scientific fields '''N'''euroscience, '''E'''lementary Particle Physics and '''M'''icrosystems Engineering the bwFor Cluster '''NEMO''' offers 888 compute nodes plus several special purpose nodes for login, interactive jobs, etc.


Compute node specification:
Node specification:
{| class="wikitable" style="text-align:center;"
{| class="wikitable" style="text-align:center;"
|-
|-
! style="width:10%"|
! style="width:10%"|
! style="width:10%"| Compute Nodes
! style="width:10%"| Compute Nodes / Interactive Nodes
! style="width:10%"| Login / Interactive Nodes
! style="width:10%"| Memory Nodes
! style="width:10%"| Memory Nodes
! style="width:10%"| Special Purpose Nodes
! style="width:10%"| Login
! style="width:10%"| Visualization Nodes
! style="width:10%"| AMD + T4 Nodes
! style="width:10%"| GPU Node
|-
|-
!scope="column"| Quantity
!scope="column"| Quantity
| 900 / 4 interactive
| 888
| 2 login / 4 interactive
| 4 med mem / 4 high mem
| 2 login
| 4 med / 4 high
| 2
| 2 vis
| 4
| 1
|-
|-
!scope="column" | Processors
!scope="column" | Processors
|colspan="3" style="text-align:center;" | 2 x [http://ark.intel.com/products/92981/Intel-Xeon-Processor-E5-2630-v4-25M-Cache-2_20-GHz Intel Xeon E5-2630v4 (Broadwell)]
|colspan="4" style="text-align:center;" | 2 x [http://ark.intel.com/products/92981/Intel-Xeon-Processor-E5-2630-v4-25M-Cache-2_20-GHz Intel Xeon E5-2630v4 (Broadwell)]
| 2 x [https://www.amd.com/de/products/cpu/amd-epyc-7742 AMD EPYC2 7742]
| 2 x visulization nodes with Nvidia P4 / P4000 ]
| 1 x [https://www.amd.com/de/products/cpu/amd-epyc-7551p AMD EPYC 7551P]
|-
|-
!scope="column" | Processor Frequency (GHz)
!scope="column" | Processor Base Frequency/Boost Frequency (all-cores) (GHz)
|colspan="3" | 2,2
|colspan="4" | 2,2/2,4
| 2,6
| 2,25/TBD
| 2,0/TBD
|-
|-
!scope="column" | Number of Cores per Node
!scope="column" | Number of Cores per Node
|colspan="3" | 20
|colspan="4" | 20
| 16
| 128
| 64 (32 phys cores /w enabled SMT)
|-
!scope="column" | Accelerator
|colspan="3" | ---
|colspan="2" | 1 x [https://www.nvidia.com/en-us/data-center/tesla-t4/ Nvidia T4]
| 8 x [https://www.nvidia.com/en-us/data-center/tesla-v100/ Nvidia V100 32GiB]
|-
|-
!scope="column" | Working Memory DDR4 (GB)
!scope="column" | Working Memory DDR4 (GB)
| 128
| | 256 / 512
|colspan="2" | 128
|colspan="2" | 128
| | 256 / 512
| 512
| 128
| 256
|-
|-
!scope="column" | Local Disk (GB)
!scope="column" | Local SSD (GB)
|colspan="4" | 240 (SSD)
|colspan="4" | 240
| 480
| 960
|-
|-
!scope="column" | Interconnect
!scope="column" | Interconnect
|colspan="4" | Omni-Path 100
|colspan="3" | Omni-Path 100
| ---
|colspan="2" | Omni-Path 100
|-
!scope="column" | Job examples
|colspan="2" | -l nodes=x:ppn=20:pmem=6gb
| ssh login.nemo.uni-freiburg.de (*)
| ssh vis.nemo.uni-freiburg.de (*)
| -l nodes=1:ppn=128:pmem=3800mb(:gpus=1)
| -l nodes=1:ppn=8:pmem=3gb:gpus=1 -q gpu
|-
|-
|}
|}
(*) No job necessary, just ssh to these machines. Available host names: login1 (and alias login), login2, vis1 (and alias vis), vis2.


NOTE:
NOTE:
The OS needs memory as well. Only about 120 / 250 / 500 GB RAM are available for jobs.
The OS needs memory as well. Only about 120 / 250 / 500 GB RAM are available for jobs.
Maximum memory specification for standard nodes therefore is '-l pmem=6GB'.
Maximum memory specification for standard nodes therefore is '-l pmem=6GB'.

=== Special Purpose Nodes ===

Besides the classical compute node several nodes serve as login and preprocessing nodes, nodes for interactive jobs and nodes for creating virtual environments providing a virtual service environment.

[[Category:bwForCluster NEMO]]
[[Category:Hardware and Architecture|bwForCluster NEMO]]



== Storage Architecture ==
== Storage Architecture ==
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!scope="column" | Capacity
!scope="column" | Capacity
| 45 TB
| 45 TB
| 768 TB
| 960 TB
| 200 GB per node
| 200 GB per node
|-
|-
!scope="column" | [https://en.wikipedia.org/wiki/Disk_quota#Quotas Quotas]
!scope="column" | [https://en.wikipedia.org/wiki/Disk_quota#Quotas Quotas]
| 100 GB per user
| 100 GB per user
| 20 TB / 1 Million files per user
| 10 TB / 4 Million chunks per user (~1 Million files)
| none
| none
|-
|-
Line 173: Line 193:
-->
-->



==== Snapshots ====

For data stored in your $HOME directory, snapshots are being created. These are copies or states of your $HOME at the time when the snapshot was taken. That way you can restore old states of files and directories. To see the snapshots you have to change into the '.snapshot' directory in any of your directories in $HOME. The '.snapshot' directory is not a real directory, so you won't be able to list (eg. 'ls -la') or see it from the outside.

<pre>
fr_xyz0000@login2 ~> cd .snapshot
fr_xyz0000@login2 ~/.snapshot>
fr_xyz0000@login2 ~/.snapshot> cd
fr_xyz0000@login2 ~> cd test/.snapshot
fr_xyz0000@login2 ~/test/.snapshot>
</pre>


=== Workspaces ===
=== Workspaces ===
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|<tt>ws_release my_workspace</tt>
|<tt>ws_release my_workspace</tt>
|Manually erase your workspace "my_workspace" and release used space on storage (remove data first for immediate deletion of the data).
|Manually erase your workspace "my_workspace" and release used space on storage (remove data first for immediate deletion of the data).
|-
|<tt>ws_unlock my_workspace</tt>
|Unlock expired workspace "my_workspace" few days after expiration (grace period depends on storage capacity, see <tt>ws_list</tt> for expired workspaces).
|-
|-
|}
|}
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* Use a single set of rules at the level of a workspace
* Use a single set of rules at the level of a workspace
* Make the entire workspace either readonly or readwrite for individual co-workers
* Make the entire workspace either readonly or readwrite for individual co-workers
* Optional: Make the entire workspace readonly for your Rechenvorhaben (group bwYYMNNN), e.g. for large input data
* Optional: Make the entire workspace readonly for your project/Rechenvorhaben (group bwYYMNNN), e.g. for large input data
* If a more granular set of rules is necessary, consider using additional workspaces
* If a more granular set of rules is necessary, consider using additional workspaces
* The owner of a workspace is responsible for its content and management
* The owner of a workspace is responsible for its content and management
* <font color=green>'''If setting ACLs for individual co-workers, set ACLs for your user first, otherwise you won't be able to access the files of your co-workers!'''</font>




Please note that <pre>ls</pre> (List directory contents) shows ACLs on directories and files only when run as <pre>ls -l</pre> as in long format, as "plus" sign after the standard unix access rights.
Please note that <tt>ls</tt> (List directory contents) shows ACLs on directories and files only when run as <tt>ls -l</tt> as in long format, as "plus" sign after the standard unix access rights. Use <tt>getfacl</tt> to see ACLs for directories and files.


Examples with regard to workspace <pre>my_workspace</pre>:
Examples with regard to "my_workspace":
{| class="wikitable"
{| class="wikitable"
|-
|-
!style="width:30%" | Command
!style="width:45%" | Command
!style="width:70%" | Action
!style="width:55%" | Action
|-
|-
|<tt>getfacl $(ws_find my_workspace)</tt>
|<tt>getfacl $(ws_find my_workspace)</tt>
Line 243: Line 279:
|Grant user "fr_xy1001" read-only access to the workspace named "my_workspace"
|Grant user "fr_xy1001" read-only access to the workspace named "my_workspace"
|-
|-
|<tt>setfacl -Rm u:fr_xy1001:rwX,d:u:fr_xy1001:rwX $(ws_find my_workspace)</tt>
|<tt>setfacl -Rm u:fr_me0000:rwX,d:u:fr_me0000:rwX $(ws_find my_workspace)</tt>
|Grant user "fr_xy1001" read and write access to the workspace named "my_workspace"
<tt>setfacl -Rm u:fr_xy1001:rwX,d:u:fr_xy1001:rwX $(ws_find my_workspace)</tt>
|Grant user your user "fr_me0000" and "fr_xy1001" read and write access to the workspace named "my_workspace" (see explanation above)
|-
|-
|<tt>setfacl -Rm g:bw16e001:rX,d:g:bw16e001:rX $(ws_find my_workspace)</tt>
|<tt>setfacl -Rm g:bw16e001:rX,d:g:bw16e001:rX $(ws_find my_workspace)</tt>
|Grant group (Rechenvorhaben) "bw16e001" read-only access to the workspace named "my_workspace"
|Grant group (project/Rechenvorhaben) "bw16e001" read-only access to the workspace named "my_workspace"
|-
|<tt>setfacl -Rm g:bw16e001:rwX,d:g:bw16e001:rwX $(ws_find my_workspace)</tt>
|Grant group (project/Rechenvorhaben) "bw16e001" read and write access to the workspace named "my_workspace"
|-
|-
|<tt>setfacl -Rb $(ws_find my_workspace)</tt>
|<tt>setfacl -Rb $(ws_find my_workspace)</tt>
Line 254: Line 294:
|}
|}


=== Local Disk Space ===
=== Local Disk Space <code>$TMPDIR</code> ===


All compute nodes are equipped with a local SSD with 240 GB capacity (usable 200 GB). During computation the environment variable <tt>$TMPDIR</tt> points to this local disk space. The data will become unavailable as soon as the job has finished.
All compute nodes are equipped with a local SSD with 240 GB capacity (usable 200 GB). During computation the environment variable <code>$TMPDIR</code> points to this local disk space. The data will become unavailable as soon as the job has finished.


=== Limits and best practices ===
=== Limits and best practices ===
Line 264: Line 304:
Per user, the following restrictions apply:
Per user, the following restrictions apply:


* Restriction on size: 20 Terabytes
* Restriction on size: 10 Terabytes


* Restriction on of files chunks: 4.000.000
* Restriction on of files chunks: 4.000.000
Line 270: Line 310:
You can check your current usage in the workspaces with the following command:
You can check your current usage in the workspaces with the following command:


nemoquota
beegfs-ctl --getquota --uid $USER


Note that "chunk files" roughly translates to 4 times number of files.
Note that "chunk files" roughly translates to 4 times number of files.


If you are over quota, please start deleting files or free workspaces using:
If you are over quota, please start '''deleting''' files. Just deleting the workspace (with ws_release) or abandoning it (by not extending) '''will not''' reduce your quota: The files in there still exist for a grace period of several days.

ws_release <workspace_name>


Please note the following best practice using the parallel filesystem (i.e. workspaces):
Please note the following best practice using the parallel filesystem (i.e. workspaces):
Line 289: Line 327:


The compute nodes all are interconnected through the high performance network Omni-Path which offers a very small latency and 100 Gbit/s throughput. The parallel storage for the workspaces is attached via Omni-Path to all cluster nodes. For non-blocking communication 17 islands with 44 nodes and 880 cores each are available. The islands are connected with a blocking factor of 1:11 (or 400 Gbit/s for 44 nodes).
The compute nodes all are interconnected through the high performance network Omni-Path which offers a very small latency and 100 Gbit/s throughput. The parallel storage for the workspaces is attached via Omni-Path to all cluster nodes. For non-blocking communication 17 islands with 44 nodes and 880 cores each are available. The islands are connected with a blocking factor of 1:11 (or 400 Gbit/s for 44 nodes).

[[Category:BwForCluster NEMO]]
[[Category:Hardware and Architecture|bwForCluster NEMO]]
[[Category:BwForCluster NEMO|Hardware and Architecture]]

Latest revision as of 15:00, 22 June 2023

System Architecture

The bwForCluster NEMO is a high-performance compute resource with high speed interconnect. It is intended for compute activities related to research in for researchers from the fields Neuroscience, Elementary Particle Physics, Microsystems Engineering and Materials Science (NEMO).

Figure: bwForCluster NEMO Schematic

Figure: bwForCluster NEMO Schematic

Operating System and Software

Compute and Special Purpose Nodes

For researchers from the scientific fields Neuroscience, Elementary Particle Physics, Microsystems Engineering and Materials Science the bwForCluster NEMO offers 908 compute nodes plus several special purpose nodes for login, interactive jobs, visualization and machine learning.

See bwForCluster NEMO Specific Batch Features for queuing gpu nodes!

Node specification:

Compute Nodes / Interactive Nodes Memory Nodes Login Visualization Nodes AMD + T4 Nodes GPU Node
Quantity 900 / 4 interactive 4 med mem / 4 high mem 2 login 2 vis 4 1
Processors 2 x Intel Xeon E5-2630v4 (Broadwell) 2 x AMD EPYC2 7742 1 x AMD EPYC 7551P
Processor Base Frequency/Boost Frequency (all-cores) (GHz) 2,2/2,4 2,25/TBD 2,0/TBD
Number of Cores per Node 20 128 64 (32 phys cores /w enabled SMT)
Accelerator --- 1 x Nvidia T4 8 x Nvidia V100 32GiB
Working Memory DDR4 (GB) 128 256 / 512 128 512 256
Local SSD (GB) 240 480 960
Interconnect Omni-Path 100 --- Omni-Path 100
Job examples -l nodes=x:ppn=20:pmem=6gb ssh login.nemo.uni-freiburg.de (*) ssh vis.nemo.uni-freiburg.de (*) -l nodes=1:ppn=128:pmem=3800mb(:gpus=1) -l nodes=1:ppn=8:pmem=3gb:gpus=1 -q gpu

(*) No job necessary, just ssh to these machines. Available host names: login1 (and alias login), login2, vis1 (and alias vis), vis2.

 NOTE:
 The OS needs memory as well. Only about 120 / 250 / 500 GB RAM are available for jobs.
 Maximum memory specification for standard nodes therefore is '-l pmem=6GB'.

Storage Architecture

The bwForCluster NEMO consists of two separate storage systems, one for the user's home directory $HOME and one serving as a workspace. The home directory is limited in space and parallel access but offers snapshots of your files and Backup. The workspace is a parallel file system which offers fast and parallel file access and a bigger capacity than the home directory. This storage is based on BeeGFS and can be accessed parallel from many nodes. Additionally, each compute node provides high-speed temporary storage (SSD) on the node-local solid state disk via the $TMPDIR environment variable.

$HOME Workspace $TMPDIR
Visibility global (GbE) global (Omni-Path) node local
Lifetime permanent workspace lifetime (max. 100 days, extension possible) batch job walltime
Capacity 45 TB 960 TB 200 GB per node
Quotas 100 GB per user 10 TB / 4 Million chunks per user (~1 Million files) none
Backup snapshots + tape backup no no
 global             : all nodes access the same file system
 local              : each node has its own file system
 permanent          : files are stored permanently
 batch job walltime : files are removed at end of the batch job


$HOME

Home directories are meant for permanent file storage of files that are keep being used like source codes, configuration files, executable programs etc.; the content of home directories will be backed up on a regular basis. The files in $HOME are stored on a Isilon OneFS and provided via NFS to all nodes.


 NOTE:
 Compute jobs on nodes must not write temporary data to $HOME.
 Instead they should use the local $TMPDIR directory for I/O-heavy use cases
 and workspaces for less I/O intense multinode-jobs.



Snapshots

For data stored in your $HOME directory, snapshots are being created. These are copies or states of your $HOME at the time when the snapshot was taken. That way you can restore old states of files and directories. To see the snapshots you have to change into the '.snapshot' directory in any of your directories in $HOME. The '.snapshot' directory is not a real directory, so you won't be able to list (eg. 'ls -la') or see it from the outside.

fr_xyz0000@login2 ~> cd .snapshot
fr_xyz0000@login2 ~/.snapshot>
fr_xyz0000@login2 ~/.snapshot> cd
fr_xyz0000@login2 ~> cd test/.snapshot
fr_xyz0000@login2 ~/test/.snapshot> 

Workspaces

Workspaces can be generated through the workspace tools. This will generate a directory on the parallel storage with a limited lifetime. When this lifetime is reached the workspace will be deleted automatically after a grace period. Workspaces can be extended to prevent deletion. You can create reminders and calendar entries to prevent accidental removal.

To create a workspace you'll need to supply a name for your workspace area and a lifetime in days. For more information read the corresponding help, e.g: ws_allocate -h.

Defaults and maximum values:

Default and maximum lifetime (days) 100
Maximum extensions 99

Examples:

Command Action
ws_allocate my_workspace 100 Allocate a workspace named "my_workspace" for 100 days.
ws_list List all your workspaces.
ws_find my_workspace Get absolute path of workspace "my_workspace".
ws_extend my_workspace 100 Set expiration date of workspace "my_workspace" to 100 days (regardless of remaining days).
ws_release my_workspace Manually erase your workspace "my_workspace" and release used space on storage (remove data first for immediate deletion of the data).
ws_unlock my_workspace Unlock expired workspace "my_workspace" few days after expiration (grace period depends on storage capacity, see ws_list for expired workspaces).

Sharing Workspace Data within your Workgroup

Data in workspaces can be shared with colleagues. Making workspaces world readable/writable using standard unix access rights is strongly discouraged. It is recommended to use ACL (Access Control Lists).

Best practices with respect to ACL usage:

  • Take into account that ACL take precedence over standard unix access rights
  • Use a single set of rules at the level of a workspace
  • Make the entire workspace either readonly or readwrite for individual co-workers
  • Optional: Make the entire workspace readonly for your project/Rechenvorhaben (group bwYYMNNN), e.g. for large input data
  • If a more granular set of rules is necessary, consider using additional workspaces
  • The owner of a workspace is responsible for its content and management
  • If setting ACLs for individual co-workers, set ACLs for your user first, otherwise you won't be able to access the files of your co-workers!


Please note that ls (List directory contents) shows ACLs on directories and files only when run as ls -l as in long format, as "plus" sign after the standard unix access rights. Use getfacl to see ACLs for directories and files.

Examples with regard to "my_workspace":

Command Action
getfacl $(ws_find my_workspace) List access rights on the workspace named "my_workspace"
setfacl -Rm u:fr_xy1001:rX,d:u:fr_xy1001:rX $(ws_find my_workspace) Grant user "fr_xy1001" read-only access to the workspace named "my_workspace"
setfacl -Rm u:fr_me0000:rwX,d:u:fr_me0000:rwX $(ws_find my_workspace)

setfacl -Rm u:fr_xy1001:rwX,d:u:fr_xy1001:rwX $(ws_find my_workspace)

Grant user your user "fr_me0000" and "fr_xy1001" read and write access to the workspace named "my_workspace" (see explanation above)
setfacl -Rm g:bw16e001:rX,d:g:bw16e001:rX $(ws_find my_workspace) Grant group (project/Rechenvorhaben) "bw16e001" read-only access to the workspace named "my_workspace"
setfacl -Rm g:bw16e001:rwX,d:g:bw16e001:rwX $(ws_find my_workspace) Grant group (project/Rechenvorhaben) "bw16e001" read and write access to the workspace named "my_workspace"
setfacl -Rb $(ws_find my_workspace) Remove all ACL rights. Standard Unix access rights apply again.

Local Disk Space $TMPDIR

All compute nodes are equipped with a local SSD with 240 GB capacity (usable 200 GB). During computation the environment variable $TMPDIR points to this local disk space. The data will become unavailable as soon as the job has finished.

Limits and best practices

To keep the system in a working state for all users, users are asked to respect the limits ("quotas") on the the parallel filesystem, i.e. on workspaces.

Per user, the following restrictions apply:

  • Restriction on size: 10 Terabytes
  • Restriction on of files chunks: 4.000.000

You can check your current usage in the workspaces with the following command:

 nemoquota

Note that "chunk files" roughly translates to 4 times number of files.

If you are over quota, please start deleting files. Just deleting the workspace (with ws_release) or abandoning it (by not extending) will not reduce your quota: The files in there still exist for a grace period of several days.

Please note the following best practice using the parallel filesystem (i.e. workspaces):

  • The parallel file system works optimal with medium to large files, large quantities of very small files significantly reduce performance and should be avoided
  • Temporary files should not be kept there. Consider using $TMPDIR for these. This is the SSD local to the compute node. Additional benefit: It's faster...
  • There is no backup for workspaces. Final results you cannot afford to loose should go to your home-directory or (better yet) be archived outside NEMO

High Performance Network

The compute nodes all are interconnected through the high performance network Omni-Path which offers a very small latency and 100 Gbit/s throughput. The parallel storage for the workspaces is attached via Omni-Path to all cluster nodes. For non-blocking communication 17 islands with 44 nodes and 880 cores each are available. The islands are connected with a blocking factor of 1:11 (or 400 Gbit/s for 44 nodes).