Skip to content
Snippets Groups Projects
Commit 9538bfea authored by Lubomir Prda's avatar Lubomir Prda
Browse files

Merge branch 'master' into 'soft_consolidation' 

# Conflicts:
#   mkdocs.yml
parents 2ac17e4b bd4f62ad
No related branches found
No related tags found
5 merge requests!368Update prace.md to document the change from qprace to qprod as the default...,!367Update prace.md to document the change from qprace to qprod as the default...,!366Update prace.md to document the change from qprace to qprod as the default...,!323extended-acls-storage-section,!25Soft consolidation
Pipeline #
Hide whitespace changes
Inline Side-by-side
Showing
with 142 additions and 249 deletions
docs.it4i/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md → docs.it4i/salomon/job-submission-and-execution.md
+ 2
− 2
View file @ 9538bfea
...@@ -402,7 +402,7 @@ exit ...@@ -402,7 +402,7 @@ exit
In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes. In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.
!!! Note "Note" !!! Note "Note"
Consider preloading inputs and executables onto [shared scratch](../storage/storage/) before the calculation starts. Consider preloading inputs and executables onto [shared scratch](storage/) before the calculation starts.
In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished. In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.
...@@ -441,7 +441,7 @@ HTML commented section #2 (examples need to be reworked) ...@@ -441,7 +441,7 @@ HTML commented section #2 (examples need to be reworked)
!!! Note "Note" !!! Note "Note"
Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends. Be very careful, use of RAM disk filesystem is at the expense of operational memory. Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends. Be very careful, use of RAM disk filesystem is at the expense of operational memory.
Example jobscript for single node calculation, using [local scratch](../storage/storage/) on the node: Example jobscript for single node calculation, using [local scratch](storage/) on the node:
```bash ```bash
#!/bin/bash #!/bin/bash
......
docs.it4i/salomon/network/network.md → docs.it4i/salomon/network.md
+ 0
− 0
View file @ 9538bfea
File moved
docs.it4i/salomon/outgoing-connections.md deleted 100644 → 0
+ 0
− 83
View file @ 2ac17e4b
Outgoing connections
====================
Connection restrictions
-----------------------
Outgoing connections, from Salomon Cluster login nodes to the outside world, are restricted to following ports:
|Port|Protocol|
|---|---|
|22|ssh|
|80|http|
|443|https|
|9418|git|
!!! Note "Note"
Please use **ssh port forwarding** and proxy servers to connect from Salomon to all other remote ports.
Outgoing connections, from Salomon Cluster compute nodes are restricted to the internal network. Direct connections form compute nodes to outside world are cut.
Port forwarding
---------------
### Port forwarding from login nodes
!!! Note "Note"
Port forwarding allows an application running on Salomon to connect to arbitrary remote host and port.
It works by tunneling the connection from Salomon back to users workstation and forwarding from the workstation to the remote host.
Pick some unused port on Salomon login node (for example 6000) and establish the port forwarding:
```bash
local $ ssh -R 6000:remote.host.com:1234 salomon.it4i.cz
```
In this example, we establish port forwarding between port 6000 on Salomon and port 1234 on the remote.host.com. By accessing localhost:6000 on Salomon, an application will see response of remote.host.com:1234. The traffic will run via users local workstation.
Port forwarding may be done **using PuTTY** as well. On the PuTTY Configuration screen, load your Salomon configuration first. Then go to Connection->SSH->Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However, this requires that user has ssh access to remote.host.com
```bash
$ ssh -L 6000:localhost:1234 remote.host.com
```
Note: Port number 6000 is chosen as an example only. Pick any free port.
### Port forwarding from compute nodes
Remote port forwarding from compute nodes allows applications running on the compute nodes to access hosts outside Salomon Cluster.
First, establish the remote port forwarding form the login node, as [described above](outgoing-connections/#port-forwarding-from-login-nodes).
Second, invoke port forwarding from the compute node to the login node. Insert following line into your jobscript or interactive shell
```bash
$ ssh -TN -f -L 6000:localhost:6000 login1
```
In this example, we assume that port forwarding from login1:6000 to remote.host.com:1234 has been established beforehand. By accessing localhost:6000, an application running on a compute node will see response of remote.host.com:1234
### Using proxy servers
Port forwarding is static, each single port is mapped to a particular port on remote host. Connection to other remote host, requires new forward.
!!! Note "Note"
Applications with inbuilt proxy support, experience unlimited access to remote hosts, via single proxy server.
To establish local proxy server on your workstation, install and run SOCKS proxy server software. On Linux, sshd demon provides the functionality. To establish SOCKS proxy server listening on port 1080 run:
```bash
local $ ssh -D 1080 localhost
```
On Windows, install and run the free, open source [Sock Puppet](http://sockspuppet.com/) server.
Once the proxy server is running, establish ssh port forwarding from Salomon to the proxy server, port 1080, exactly as [described above](outgoing-connections/#port-forwarding-from-login-nodes).
```bash
local $ ssh -R 6000:localhost:1080 salomon.it4i.cz
```
Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding to access the [proxy server from compute nodes](outgoing-connections/#port-forwarding-from-compute-nodes) as well .
docs.it4i/salomon/prace.md
+ 5
− 5
View file @ 9538bfea
...@@ -119,11 +119,11 @@ If the user uses GSI SSH based access, then the procedure is similar to the SSH ...@@ -119,11 +119,11 @@ If the user uses GSI SSH based access, then the procedure is similar to the SSH
### Access with SSH ### Access with SSH
After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the [section in general documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access/). After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the [section in general documentation](shell-and-data-access/).
File transfers File transfers
------------------ ------------------
PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see [the section in the general documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access/). PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see [the section in the general documentation](shell-and-data-access/).
Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners). Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
...@@ -215,7 +215,7 @@ Usage of the cluster ...@@ -215,7 +215,7 @@ Usage of the cluster
-------------------- --------------------
There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses. There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.
For production runs always use scratch file systems. The available file systems are described [here](storage/storage/). For production runs always use scratch file systems. The available file systems are described [here](storage/).
### Software, Modules and PRACE Common Production Environment ### Software, Modules and PRACE Common Production Environment
...@@ -229,7 +229,7 @@ PRACE users can use the "prace" module to use the [PRACE Common Production Envir ...@@ -229,7 +229,7 @@ PRACE users can use the "prace" module to use the [PRACE Common Production Envir
### Resource Allocation and Job Execution ### Resource Allocation and Job Execution
General information about the resource allocation, job queuing and job execution is in this [section of general documentation](resource-allocation-and-job-execution/introduction/). General information about the resource allocation, job queuing and job execution is in this [section of general documentation](resource-allocation-and-job-execution/).
For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree". For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".
...@@ -244,7 +244,7 @@ For PRACE users, the default production run queue is "qprace". PRACE users can a ...@@ -244,7 +244,7 @@ For PRACE users, the default production run queue is "qprace". PRACE users can a
### Accounting & Quota ### Accounting & Quota
The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See [example in the general documentation](resource-allocation-and-job-execution/resources-allocation-policy/). The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See [example in the general documentation](resources-allocation-policy/).
PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)](http://www.prace-ri.eu/accounting-report-tool/). PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)](http://www.prace-ri.eu/accounting-report-tool/).
......
docs.it4i/salomon/shell-and-data-access.md
+ 6
− 21
View file @ 9538bfea
...@@ -20,7 +20,6 @@ The authentication is by the [private key](../get-started-with-it4innovations/ac ...@@ -20,7 +20,6 @@ The authentication is by the [private key](../get-started-with-it4innovations/ac
!!! Note "Note" !!! Note "Note"
Please verify SSH fingerprints during the first logon. They are identical on all login nodes: Please verify SSH fingerprints during the first logon. They are identical on all login nodes:
f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA) f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA)
70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA) 70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)
...@@ -38,23 +37,17 @@ If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to ...@@ -38,23 +37,17 @@ If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to
local $ chmod 600 /path/to/id_rsa local $ chmod 600 /path/to/id_rsa
``` ```
On **Windows**, use [PuTTY ssh client](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty/). On **Windows**, use [PuTTY ssh client](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md).
After logging in, you will see the command prompt: After logging in, you will see the command prompt:
<tty-player controls src=/src/salomon/login_salomon.ttyrec></tty-player>
!!! Note "Note" !!! Note "Note"
The environment is **not** shared between login nodes, except for [shared filesystems](storage/storage/). The environment is **not** shared between login nodes, except for [shared filesystems](storage/).
Data Transfer Data Transfer
------------- -------------
Data in and out of the system may be transferred by the [scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp protocols. Data in and out of the system may be transferred by the [scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp protocols.
In case large volumes of data are transferred, use dedicated data mover nodes cedge[1-3].salomon.it4i.cz for increased performance.
HTML commented section #1 (removed cedge servers from the table)
|Address|Port|Protocol| |Address|Port|Protocol|
|---|---| |---|---|
|salomon.it4i.cz|22|scp, sftp| |salomon.it4i.cz|22|scp, sftp|
...@@ -65,17 +58,12 @@ HTML commented section #1 (removed cedge servers from the table) ...@@ -65,17 +58,12 @@ HTML commented section #1 (removed cedge servers from the table)
The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/) The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
HTML commented section #2 (ssh transfer performance data need to be verified)
On linux or Mac, use scp or sftp client to transfer the data to Salomon: On linux or Mac, use scp or sftp client to transfer the data to Salomon:
```bash ```bash
local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.cz:directory/file local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.cz:directory/file
``` ```
For example how to using scp command:
<tty-player controls src=/src/salomon/transfer_scp_salomon.ttyrec></tty-player>
```bash ```bash
local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory
``` ```
...@@ -86,9 +74,6 @@ or ...@@ -86,9 +74,6 @@ or
local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz
``` ```
For example how to using sftp command:
<tty-player controls src=/src/salomon/transfer_sftp_salomon.ttyrec></tty-player>
Very convenient way to transfer files in and out of the Salomon computer is via the fuse filesystem [sshfs](http://linux.die.net/man/1/sshfs) Very convenient way to transfer files in and out of the Salomon computer is via the fuse filesystem [sshfs](http://linux.die.net/man/1/sshfs)
```bash ```bash
...@@ -107,7 +92,7 @@ $ man sshfs ...@@ -107,7 +92,7 @@ $ man sshfs
On Windows, use [WinSCP client](http://winscp.net/eng/download.php) to transfer the data. The [win-sshfs client](http://code.google.com/p/win-sshfs/) provides a way to mount the Salomon filesystems directly as an external disc. On Windows, use [WinSCP client](http://winscp.net/eng/download.php) to transfer the data. The [win-sshfs client](http://code.google.com/p/win-sshfs/) provides a way to mount the Salomon filesystems directly as an external disc.
More information about the shared file systems is available [here](storage/storage/). More information about the shared file systems is available [here](storage/).
Connection restrictions Connection restrictions
----------------------- -----------------------
...@@ -157,7 +142,7 @@ Note: Port number 6000 is chosen as an example only. Pick any free port. ...@@ -157,7 +142,7 @@ Note: Port number 6000 is chosen as an example only. Pick any free port.
Remote port forwarding from compute nodes allows applications running on the compute nodes to access hosts outside Salomon Cluster. Remote port forwarding from compute nodes allows applications running on the compute nodes to access hosts outside Salomon Cluster.
First, establish the remote port forwarding form the login node, as [described above](outgoing-connections/#port-forwarding-from-login-nodes). First, establish the remote port forwarding form the login node, as [described above](#port-forwarding-from-login-nodes).
Second, invoke port forwarding from the compute node to the login node. Insert following line into your jobscript or interactive shell Second, invoke port forwarding from the compute node to the login node. Insert following line into your jobscript or interactive shell
...@@ -182,10 +167,10 @@ local $ ssh -D 1080 localhost ...@@ -182,10 +167,10 @@ local $ ssh -D 1080 localhost
On Windows, install and run the free, open source [Sock Puppet](http://sockspuppet.com/) server. On Windows, install and run the free, open source [Sock Puppet](http://sockspuppet.com/) server.
Once the proxy server is running, establish ssh port forwarding from Salomon to the proxy server, port 1080, exactly as [described above](outgoing-connections/#port-forwarding-from-login-nodes). Once the proxy server is running, establish ssh port forwarding from Salomon to the proxy server, port 1080, exactly as [described above](#port-forwarding-from-login-nodes).
```bash ```bash
local $ ssh -R 6000:localhost:1080 salomon.it4i.cz local $ ssh -R 6000:localhost:1080 salomon.it4i.cz
``` ```
Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding to access the [proxy server from compute nodes](outgoing-connections/#port-forwarding-from-compute-nodes) as well . Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding to access the [proxy server from compute nodes](#port-forwarding-from-compute-nodes) as well .
docs.it4i/salomon/storage/storage.md → docs.it4i/salomon/storage.md
+ 109
− 8
View file @ 9538bfea
...@@ -3,7 +3,7 @@ Storage ...@@ -3,7 +3,7 @@ Storage
Introduction Introduction
------------ ------------
There are two main shared file systems on Salomon cluster, the [HOME](storage/storage/#home)and [SCRATCH](storage/#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 filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.
...@@ -11,26 +11,26 @@ Policy (in a nutshell) ...@@ -11,26 +11,26 @@ Policy (in a nutshell)
---------------------- ----------------------
!!! Note "Note" !!! Note "Note"
Use [ for your most valuable data and programs. Use [ for your most valuable data and programs.
Use [WORK](storage/#work) for your large project files. Use [WORK](#work) for your large project files.
Use [TEMP](storage/#temp) for large scratch data. Use [TEMP](#temp) for large scratch data.
Do not use for [archiving](storage/#archiving)! Do not use for [archiving](#archiving)!
Archiving 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](../../anselm-cluster-documentation/storage/cesnet-data-storage/), which is available via SSHFS. 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.
Shared Filesystems Shared Filesystems
---------------------- ----------------------
Salomon computer provides two main shared filesystems, the [ HOME filesystem](storage/#home-filesystem) and the [SCRATCH filesystem](storage/#scratch-filesystem). The SCRATCH filesystem is partitioned to [WORK and TEMP workspaces](storage/#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 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.
###HOME filesystem ###HOME filesystem
The HOME filesystem is realized as a Tiered filesystem, exported via NFS. The first tier has capacity 100TB, second tier has capacity 400TB. The filesystem is available on all login and computational nodes. The Home filesystem hosts the [HOME workspace](storage/#home). The HOME filesystem is realized as a Tiered filesystem, exported via NFS. The first tier has capacity 100TB, second tier has capacity 400TB. The filesystem is available on all login and computational nodes. The Home filesystem hosts the [HOME workspace](#home).
###SCRATCH filesystem ###SCRATCH filesystem
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](storage/#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 filesystem hosts the [WORK and TEMP workspaces](#shared-workspaces).
Configuration of the SCRATCH Lustre storage Configuration of the SCRATCH Lustre storage
...@@ -321,3 +321,104 @@ Summary ...@@ -321,3 +321,104 @@ Summary
|/scratch/work|large project files|Lustre|1.69 PB|30 GB/s|Quota|Compute and login nodes|none| |/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 100TB|Compute and login nodes|files older 90 days removed| |/scratch/temp|job temporary data|Lustre|1.69 PB|30 GB/s|Quota 100TB|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| |/ramdisk|job temporary data, node local|local|120GB|90 GB/s|none|Compute nodes|purged after job ends|
CESNET Data Storage
------------
Do not use shared filesystems 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/).
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 at <https://du.cesnet.cz/wiki/doku.php/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"))
CESNET storage access
---------------------
### Understanding Cesnet storage
!!! Note "Note"
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
!!! Note "Note"
SSHFS: The storage will be mounted like a local hard drive
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 harddrive. Files can be than copied in and out in a usual fashion.
First, create the mountpoint
```bash
$ mkdir cesnet
```
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 !)**:
```bash
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
```
For easy future access from Anselm, install your public key
```bash
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
```
Mount tier1_cache_tape for the Storage VO:
```bash
$ sshfs username@ssh.du1.cesnet.cz:/cache_tape/VO_storage/home/username cesnet/
```
View the archive, copy the files and directories in and out
```bash
$ ls cesnet/
$ cp -a mydir cesnet/.
$ cp cesnet/myfile .
```
Once done, please remember to unmount the storage
```bash
$ fusermount -u cesnet
```
### Rsync access
!!! Note "Note"
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 <https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele>
Transfer large files to/from Cesnet storage, assuming membership in the Storage VO
```bash
$ 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
```bash
$ 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 .
```
Transfer rates of about 28MB/s can be expected.
docs.it4i/salomon/storage/cesnet-data-storage.md deleted 100644 → 0
+ 0
− 103
View file @ 2ac17e4b
CESNET Data Storage
===================
Introduction
------------
Do not use shared filesystems 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/).
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 at <https://du.cesnet.cz/wiki/doku.php/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"))
CESNET storage access
---------------------
### Understanding Cesnet storage
!!! Note "Note"
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
!!! Note "Note"
SSHFS: The storage will be mounted like a local hard drive
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 harddrive. Files can be than copied in and out in a usual fashion.
First, create the mountpoint
```bash
$ mkdir cesnet
```
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 !)**:
```bash
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
```
For easy future access from Anselm, install your public key
```bash
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
```
Mount tier1_cache_tape for the Storage VO:
```bash
$ sshfs username@ssh.du1.cesnet.cz:/cache_tape/VO_storage/home/username cesnet/
```
View the archive, copy the files and directories in and out
```bash
$ ls cesnet/
$ cp -a mydir cesnet/.
$ cp cesnet/myfile .
```
Once done, please remember to unmount the storage
```bash
$ fusermount -u cesnet
```
### Rsync access
!!! Note "Note"
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 <https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele>
Transfer large files to/from Cesnet storage, assuming membership in the Storage VO
```bash
$ 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
```bash
$ 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 .
```
Transfer rates of about 28MB/s can be expected.
get_modules.sh
+ 1
− 0
View file @ 9538bfea
#!/bin/bash #!/bin/bash
curl -s https://code.it4i.cz/hrb33/modules-anselm/raw/master/anselm.md -o docs.it4i/modules-anselm.md curl -s https://code.it4i.cz/hrb33/modules-anselm/raw/master/anselm.md -o docs.it4i/modules-anselm.md
curl -s https://code.it4i.cz/hrb33/modules-salomon/raw/master/salomon.md -o docs.it4i/modules-salomon.md curl -s https://code.it4i.cz/hrb33/modules-salomon/raw/master/salomon.md -o docs.it4i/modules-salomon.md
curl -s https://code.it4i.cz/hrb33/modules-salomon/raw/master/salomon-uv.md -o docs.it4i/modules-salomon-uv.md
mkdocs.yml
+ 19
− 27
View file @ 9538bfea
...@@ -15,14 +15,12 @@ pages: ...@@ -15,14 +15,12 @@ pages:
- Accessing the Clusters: get-started-with-it4innovations/accessing-the-clusters/introduction.md - Accessing the Clusters: get-started-with-it4innovations/accessing-the-clusters/introduction.md
# - VPN-Connection-Fail-in-Win-8.1: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md # - VPN-Connection-Fail-in-Win-8.1: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
- SSH keys: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md - SSH keys: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
- Pageant SSH agent: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
- PuTTY key generator: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
- PuTTY: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md - PuTTY: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
- GUI Access: - PuTTY Pageant SSH agent: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
- Introduction: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md - PuTTY key generator: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
- X Window System: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md - X Window System: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
- X Window System using Cygwin: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
- VNC: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md - VNC: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
- Cygwin and x11 Forwarding: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
- Anselm Cluster: - Anselm Cluster:
- Introduction: anselm-cluster-documentation/introduction.md - Introduction: anselm-cluster-documentation/introduction.md
- Hardware Overview: anselm-cluster-documentation/hardware-overview.md - Hardware Overview: anselm-cluster-documentation/hardware-overview.md
...@@ -33,15 +31,12 @@ pages: ...@@ -33,15 +31,12 @@ pages:
- Remote visualization: anselm-cluster-documentation/remote-visualization.md - Remote visualization: anselm-cluster-documentation/remote-visualization.md
- Network: anselm-cluster-documentation/network.md - Network: anselm-cluster-documentation/network.md
- PRACE User Support: anselm-cluster-documentation/prace.md - PRACE User Support: anselm-cluster-documentation/prace.md
- Anselm Cluster Resource Allocation and Job Execution: - Resource Allocation and Job Execution : anselm-cluster-documentation/resource-allocation-and-job-execution.md
- Introduction: anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md - Resource allocation policy: anselm-cluster-documentation/resources-allocation-policy.md
- Job Priority: anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md - Job Priority: anselm-cluster-documentation/job-priority.md
- Job Submission and Execution: anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md - Job Submission and Execution: anselm-cluster-documentation/job-submission-and-execution.md
- Capacity computing: anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md - Capacity computing: anselm-cluster-documentation/capacity-computing.md
- Resource allocation policy: anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md - Storage: anselm-cluster-documentation/storage.md
- Anselm Cluster Storage:
- Cesnet Data Storage: anselm-cluster-documentation/storage/cesnet-data-storage.md
- Storage: anselm-cluster-documentation/storage/storage.md
- Anselm Cluster Software: anselm-cluster-documentation/software/index.md - Anselm Cluster Software: anselm-cluster-documentation/software/index.md
- '&nbsp;Anselm Cluster Software': - '&nbsp;Anselm Cluster Software':
- Modules: modules-anselm.md - Modules: modules-anselm.md
...@@ -118,22 +113,19 @@ pages: ...@@ -118,22 +113,19 @@ pages:
- VPN Access: salomon/vpn-access.md - VPN Access: salomon/vpn-access.md
- Compute Nodes: salomon/compute-nodes.md - Compute Nodes: salomon/compute-nodes.md
- List of modules: salomon/list_of_modules.md - List of modules: salomon/list_of_modules.md
- Salomon Cluster Network: - Salomon Cluster Network: salomon/network.md
- Introduction: salomon/network/network.md - IB single-plane topology: salomon/ib-single-plane-topology.md
- IB single-plane topology: salomon/network/ib-single-plane-topology.md - 7D Enhanced Hypercube: salomon/7d-enhanced-hypercube.md
- 7D Enhanced Hypercube: salomon/network/7d-enhanced-hypercube.md - Resource Allocation and Job Execution : salomon/resource-allocation-and-job-execution.md
- Salomon Cluster Resource Allocation and Job Execution: - Resources Allocation Policy: salomon/resources-allocation-policy.md
- Introduction: salomon/resource-allocation-and-job-execution/introduction.md - Job scheduling: salomon/job-priority.md
- Job scheduling: salomon/resource-allocation-and-job-execution/job-priority.md - Job submission and execution: salomon/job-submission-and-execution.md
- Job submission and execution: salomon/resource-allocation-and-job-execution/job-submission-and-execution.md - Capacity computing: salomon/capacity-computing.md
- Capacity computing: salomon/resource-allocation-and-job-execution/capacity-computing.md - Storage: salomon/storage.md
- Resources Allocation Policy: salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
- Salomon Cluster Storage:
- CESNET Data Storage: salomon/storage/cesnet-data-storage.md
- Storage: salomon/storage/storage.md
- Salomon Cluster Software: salomon/software/index.md - Salomon Cluster Software: salomon/software/index.md
- '&nbsp;Salomon Cluster Software': - '&nbsp;Salomon Cluster Software':
- Modules: modules-salomon.md - Modules: modules-salomon.md
- UV Modules: modules-salomon-uv.md
- Compilers: salomon/software/compilers.md - Compilers: salomon/software/compilers.md
- Intel Xeon Phi: salomon/software/intel-xeon-phi.md - Intel Xeon Phi: salomon/software/intel-xeon-phi.md
- Java: salomon/software/java.md - Java: salomon/software/java.md
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment