diff --git a/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md b/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md index 46ff6483a19cb37e73f6403fc5d300bb6fb9fc95..924d98077b2489ba5f2516f3e21fe49004747ad2 100644 --- a/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md +++ b/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md @@ -44,7 +44,7 @@ beegfs The default filesystem is `scratch`. If you prefer another filesystem (cf. section [List Available Filesystems](#list-available-filesystems)), you have to explictly - provide the option `--filesystem=<fs>` to the workspace commands. + provide the option `--filesystem=<filesystem>` to the workspace commands. ### List Current Workspaces @@ -171,10 +171,10 @@ Options: !!! example "Workspace allocation on specific filesystem" In order to allocate a workspace on a non-default filesystem, the option - `--filesystem <filesystem>` is required. + `--filesystem=<filesystem>` is required. ```console - marie@login$ ws_allocate --filesystem scratch_fast test-workspace 3 + marie@login$ ws_allocate --filesystem=scratch_fast test-workspace 3 Info: creating workspace. /lustre/ssd/ws/marie-test-workspace remaining extensions : 2 @@ -188,7 +188,7 @@ Options: day starting 7 days prior to expiration. We strongly recommend setting this e-mail reminder. ```console - marie@login$ ws_allocate --reminder 7 --mailaddress marie.testuser@tu-dresden.de test-workspace 90 + marie@login$ ws_allocate --reminder=7 --mailaddress=marie.testuser@tu-dresden.de test-workspace 90 Info: creating workspace. /scratch/ws/marie-test-workspace remaining extensions : 10 @@ -209,7 +209,7 @@ group workspaces. The lifetime of a workspace is finite and different filesystems (storage systems) have different maximum durations. A workspace can be extended multiple times, depending on the filesystem. -| Filesystem (use with parameter `--filesystem=<fs>`) | Duration, days | Extensions | [Filesystem Feature](../jobs_and_resources/slurm.md#filesystem-features) | Remarks | +| Filesystem (use with parameter `--filesystem=<filesystem>`) | Duration, days | Extensions | [Filesystem Feature](../jobs_and_resources/slurm.md#filesystem-features) | Remarks | |:-------------------------------------|---------------:|-----------:|:-------------------------------------------------------------------------|:--------| | `scratch` (default) | 100 | 10 | `fs_lustre_scratch2` | Scratch filesystem (`/lustre/scratch2`, symbolic link: `/scratch`) with high streaming bandwidth, based on spinning disks | | `ssd` | 30 | 2 | `fs_lustre_ssd` | High-IOPS filesystem (`/lustre/ssd`, symbolic link: `/ssd`) on SSDs. | @@ -433,7 +433,7 @@ the following example (which works [for the program g16](../software/nanoscale_s # Allocate workspace for this job. Adjust time span to time limit of the job (-d <N>). WSNAME=computation_$SLURM_JOB_ID - export WSDDIR=$(ws_allocate -F ssd -n ${WSNAME} -d 2) + export WSDDIR=$(ws_allocate --filesystem=ssd --name=${WSNAME} --duration=2) echo ${WSDIR} # Check allocation @@ -476,7 +476,7 @@ For a series of jobs or calculations that work on the same data, you should allo once, e.g., in `scratch` for 100 days: ```console -marie@login$ ws_allocate -F scratch my_scratchdata 100 +marie@login$ ws_allocate --filesystem=scratch my_scratchdata 100 Info: creating workspace. /scratch/ws/marie-my_scratchdata remaining extensions : 2 @@ -505,7 +505,7 @@ this is mounted read-only on the compute nodes, so you cannot use it as a work d jobs! ```console -marie@login$ ws_allocate -F warm_archive my_inputdata 365 +marie@login$ ws_allocate --filesystem=warm_archive my_inputdata 365 /warm_archive/ws/marie-my_inputdata remaining extensions : 2 remaining time in days: 365 @@ -551,7 +551,7 @@ to others (if in the same group) via `ws_list -g`. in the project `p_number_crunch`, she can allocate a so-called group workspace. ```console - marie@login$ ws_allocate --group --name numbercrunch --duration 30 + marie@login$ ws_allocate --group --name=numbercrunch --duration=30 Info: creating workspace. /scratch/ws/0/marie-numbercrunch remaining extensions : 10 @@ -610,6 +610,11 @@ wrong name. Use only the short name that is listed after `id:` when using `ws_li **Q**: I forgot to specify an e-mail alert when allocating my workspace. How can I add the e-mail alert functionality to an existing workspace? -**A**: You can add the e-mail alert by "overwriting" the workspace settings via `ws_allocate -x -m -<mail address> -r <days> -n <ws-name> -d <duration> -F <fs>`. (This will lower the remaining -extensions by one.) +**A**: You can add the e-mail alert by "overwriting" the workspace settings via + +```console +marie@login$ ws_allocate --extension --mailaddress=<mail address> --reminder=<days> \ + --name=<workspace-name> --duration=<duration> --filesystem=<filesystem> +``` + +This will lower the remaining extensions by one. diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/barnard_test.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/barnard_test.md index 59a33d2049e94f10a792a1155e30505c8a2442d6..1529565f8555712da22f15e16141d8be3ad7d301 100644 --- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/barnard_test.md +++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/barnard_test.md @@ -6,85 +6,45 @@ and workflows for production there. For general hints please refer to these site * [Details on architecture](/jobs_and_resources/architecture_2023), * [Description of the migration](migration_2023.md). -Please provide your feedback directly via our ticket system. For better processing, +We value your feedback. Please provide it directly via our ticket system. For better processing, please add "Barnard:" as a prefix to the subject of the [support ticket](../support/support). Here, you can find few hints which might help you with the first steps. ## Login to Barnard -* All users and projects from Taurus now can work on Barnard. -* They can use `login[1-4].barnard.hpc.tu-dresden.de` to access the system +All users and projects from Taurus now can work on Barnard. + +They can use `login[2-4].barnard.hpc.tu-dresden.de` to access the system from campus (or VPN). [Fingerprints](/access/key_fingerprints/#barnard) -* All users have *new* home file systems, this means: +All users have **new empty HOME** file systems, this means you have first have to... + +??? "... install your public ssh key on the system" + - Please create a new SSH keypair with ed25519 encryption, secured with - a passphrase. Please refer to this - [page for instructions](../../access/ssh_login#before-your-first-connection). + a passphrase. Please refer to this + [page for instructions](../../access/ssh_login#before-your-first-connection). - After login, add the public key to your `.ssh/authorized_keys` file - on Barnard. + on Barnard. ## Data Management * The `/project` filesystem is the same on Taurus and Barnard (mounted read-only on the compute nodes). -* The **new work filesystem** is `/data/horse`. The slower `/data/walrus` can be used -to store e.g. results. Both can be accesed via workspaces. Please refer to the -[workspace page](../../data_lifecycle/workspaces/), if you are not familiar with workspaces. To list -all available workspace filessystem, invoke the command `ws_list -l`. - -!!! Note - - **To work with your data from Taurus you might have to move/copy them to the new storages.** +* The new work filesystem is `/data/horse`. +* The slower `/data/walrus` can be considered as a substitute for the old + `/warm_archive`- mounted **read-only** on the compute nodes. + It can be used to store e.g. results. -For this, we have four new [datamover nodes](/data_transfer/datamover) that have mounted all storages -of the old and new system. (Do not use the datamovers from Taurus!) - -Please use the command `dtinfo` to get the current mount points: - -``` -marie@login1> dtinfo -PARTITION AVAIL TIMELIMIT NODES STATE NODELIST -datamover* up infinite 1 down* service5 -datamover* up infinite 3 idle service[1-4] --------------------------------------------------------------------------------- -directory on datamover mounting clusters directory on cluster - -/data/old/home Taurus /home -/data/old/lustre/scratch2 Taurus /scratch -/data/old/lustre/ssd Taurus /lustre/ssd -/data/old/beegfs Taurus /beegfs -/data/old/warm_archive Taurus /warm_archive -/data/horse Barnard /data/horse -/data/walrus Barnard /data/walrus --------------------------------------------------------------------------------- -``` - -* In May (!) we have copied all workspaces from `/scratch/ws` data to -` /data/horse/lustre/scratch2/ws`. This replication took a **few weeks**. Ideally you -can now just *move* their *content* to a newly created workspace. - Of course, -everything newer than May is not there. -* Please manually copy your needed data from your `beegfs` or `ssd` workspaces. These -old storages will be purged, probably by the end of November. - -The process of syncing data from `/warm_archive` to `/data/walrus` is still ongoing. - -### Transfer Data to New Home Directory - -Your personal (old) home directory at Taurus will not be automatically transferred to the new Barnard -system. **You are responsible for this task.** Please do not copy your entire home, but consider -this opportunity for cleaning up you data. E.g., it might make sense to delete outdated scripts, old -log files, etc., and move other files to an archive filesystem. Thus, please transfer only selected -directories and files that you need on the new system. - -The well-known [datamover tools](../../data_transfer/datamover/) are available to run such transfer -jobs under Slurm. The steps are as follows: - -1. Login to Barnard: `ssh login[1-4].barnard.tu-dresden.de` -1. The command `dtinfo` will provide you the mountpoints +These `/data/horse` and `/data/walrus` can be accesed via workspaces. Please refer to the +[workspace page](../../data_lifecycle/workspaces/), if you are not familiar with workspaces. - ```console - marie@barnard$ dtinfo +??? "Tips on workspaces" + * To list all available workspace filessystem, invoke the command `ws_list -l`." + * Please use the command `dtinfo` to get the current mount points: + ``` + marie@login1> dtinfo [...] directory on datamover mounting clusters directory on cluster @@ -94,32 +54,110 @@ jobs under Slurm. The steps are as follows: [...] ``` -1. Use the `dtls` command to list your files on the old home directory: `marie@barnard$ dtls - /data/old/home/marie` -1. Use `dtcp` command to invoke a transfer job, e.g., +!!! Warning - ```console - marie@barnard$ dtcp --recursive /data/old/home/marie/<useful data> /home/marie/ - ``` + All old filesystems fill be shutdown by the end of 2023. - **Note**, please adopt the source and target paths to your needs. All available options can be - queried via `dtinfo --help`. + To work with your data from Taurus you might have to move/copy them to the new storages. -!!! warning +For this, we have four new [datamover nodes](/data_transfer/datamover) that have mounted all storages +of the old and new system. (Do not use the datamovers from Taurus!) + +??? "Migration from Home Directory" + + Your personal (old) home directory at Taurus will not be automatically transferred to the new Barnard + system. **You are responsible for this task.** Please do not copy your entire home, but consider + this opportunity for cleaning up you data. E.g., it might make sense to delete outdated scripts, old + log files, etc., and move other files to an archive filesystem. Thus, please transfer only selected + directories and files that you need on the new system. + + The well-known [datamover tools](../../data_transfer/datamover/) are available to run such transfer + jobs under Slurm. The steps are as follows: - Please be aware that there is **no synchronisation process** between your home directories at - Taurus and Barnard. Thus, with the very first transfer, they will become divergent. + 1. Login to Barnard: `ssh login[1-4].barnard.tu-dresden.de` + 1. The command `dtinfo` will provide you the mountpoints - We recommand to **take some minutes for planing the transfer process**. Do not act with - precipitation. + ```console + marie@barnard$ dtinfo + [...] + directory on datamover mounting clusters directory on cluster + + /data/old/home Taurus /home + /data/old/lustre/scratch2 Taurus /scratch + /data/old/lustre/ssd Taurus /lustre/ssd + [...] + ``` + + 1. Use the `dtls` command to list your files on the old home directory: `marie@barnard$ dtls + /data/old/home/marie` + 1. Use `dtcp` command to invoke a transfer job, e.g., + + ```console + marie@barnard$ dtcp --recursive /data/old/home/marie/<useful data> /home/marie/ + ``` + + **Note**, please adopt the source and target paths to your needs. All available options can be + queried via `dtinfo --help`. + + !!! warning + + Please be aware that there is **no synchronisation process** between your home directories at + Taurus and Barnard. Thus, after the very first transfer, they will become divergent. + + We recommand to **take some minutes for planing the transfer process**. Do not act with + precipitation. + +??? "Migration from `/lustre/ssd` or `/beegfs`" + + **You** are entirely responsible for the transfer of these data to the new location. + Start the dtrsync process as soon as possible. (And maybe repeat it at a later time.) + +??? "Migration from `/lustre/scratch2` aka `/scratch`" + + We are synchronizing this (**last: October 18**) to `/data/horse/lustre/scratch2/`. + + Please do **NOT** copy those data yourself. Instead check if it is already sychronized + to `/data/walrus/warm_archive/ws`. + + In case you need to update this (Gigabytes, not Terabytes!) please run `dtrsync` like in + `dtrsync -a /data/old/lustre/scratch2/ws/0/my-workspace/newest/ /data/horse/lustre/scratch2/ws/0/my-workspace/newest/` + +??? "Migration from `/warm_archive`" + + We are preparing another sync from `/warm_archive` to `The process of syncing data from `/warm_archive` to `/data/walrus/warm_archive` is still ongoing. + + Please do **NOT** copy those data yourself. Instead check if it is already sychronized + to `/data/walrus/warm_archive/ws`. + + In case you need to update this (Gigabytes, not Terabytes!) please run `dtrsync` like in + `dtrsync -a /data/old/warm_archive/ws/my-workspace/newest/ /data/walrus/warm_archive/ws/my-workspace/newest/` + +When the last compute system will have been migrated the old file systems will be +set write-protected and we start a final synchronization (sratch+walrus). +The target directories for synchronization `/data/horse/lustre/scratch2/ws` and +`/data/walrus/warm_archive/ws/` will not be deleted automatically in the mean time. ## Software -Please use `module spider` to identify the software modules you need to load. Like +Please use `module spider` to identify the software modules you need to load.Like on Taurus. + The default release version is 23.10. + ## Slurm * We are running the most recent Slurm version. * You must not use the old partition names. * Not all things are tested. + +## Updates after your feedback (state: October 19) + +* A **second synchronization** from `/scratch` has started on **October, 18**, and is + now nearly done. +* A first, and incomplete synchronization from `/warm_archive` has been done (see above). + With support from NEC we are transferring the rest in the next weeks. +* The **data transfer tools** now work fine. +* After fixing too tight security restrictions, **all users can login** now. +* **ANSYS** now starts: please check if your specific use case works. +* **login1** is under construction, do not use it at the moment. Workspace creation does + not work there.