v1.37, 14 June 2022

Table of Contents

General information about the HSM system

What does HSM mean?

Hierarchical Storage Management. It means the DKRZ tape archive.

What type of HSM system is used at DKRZ?

The software is called StrongLink and it is developed and supplied by StrongBox Data Solutions (https://www.strongboxdata.com/stronglink).

Why did DKRZ get a new system?

The contract for the previous HSM system HPSS ends in 2021 and it was also not laid out to cope with the data volumes expected to be produced by DKRZ’s upcoming HPC system Levante. Therefore DKRZ ran a tender to purchase a new HSM system. The company Cristie Data was chosen to deliver the new HSM system called StrongLink. The new system allows for a higher data throughput to and from tape and is able to cope with larger volumes of data expected to be produced on Levante.

What are the main differences compared to the old system?

From a users’ perspecitve, a different command line tool to transfer data in and out of the tape archive has to be used. The new tool provides powerful metadata features. For details have a look at “Which new features does the HSM System provide?”. Technically, the new HSM system StrongLink allows for higher data throughput, is more scalable and is more resilient towards hardware failures compared to the current/old HPSS system.

Is the new HSM system accessbile via pftp?

No. pftp was replaced by a new command line tool slk. Additionally, a command line tool slk_helpers is provided which has some features that slk is lacking. slk is developed and maintained by StrongBox Data Solutions, whereas slk_helpers are developed and maintained at DKRZ.

Would it be possible/desirable to use only one command for slk and slk_helpers main classes?

Basically: yes. We decided otherwise because the development for slk is still ongoing and we do not want to clash with the development by StrongBox: features that we implement now, might later be implemented with slight functional changes by StrongBox.

Data Migration

When did the new HSM system go online?

The new HSM system went online on 1 November 2021 at 2 PM.

Are my archived data available on the new system?

All data were migrated automatically from HPSS to StrongLink. An exception are files which originate from the DXUL (Disc EXtended Unix Linux) system and were located on HPSS in the directory /dxul and below. These files will not be migrated.

How do I find out whether I have data from DXUL that have to be copied manually?

If you own or use legacy data created on HLRE-1 (Hurrikan) and earlier (before 2010), please check if there are data in /dxul and below. If you are working with data produced on HLRE-2 (Blizzard), HLRE-3 (Mistral) and HLRE-4 (Levante) then you are probably not affected. However, there might be config or forcing files of more recent simulations still located in /dxul.

How do I access DXUL data after the HPSS is shut down?

It is no longer possible to access the DXUL data via the new HSM system.

How to proceed if I still have DXUL data that need to be kept?

Please contact beratung@dkrz.de if you still need data from DXUL.

Training, Questions and Adaption of Workflows

Has there been an introduction session to the new HSM system and will there be such sessions in future?

Yes, a DKRZ Tech Talk took place on 6 July 2021. The new HSM system and the new command line tool slk were presented there. A recording of the Tech Talk available on YouTube: https://www.youtube.com/watch?v=JtmelPQ3ypw. We offered a HSM Q&A session each Thursday 11:30 - 12:30 AM from 30 Sept to end of December 2021. We plan a second TechTalk when the system is fully functional.

Where can I find written documentation about the new HSM system?

The user documentation is available at https://docs.dkrz.de.

Why is no exact time schedule for training and migration published yet?

A TechTalk which gave a broad overview over the StrongLink system and over slk took place on 6 July 2021 (https://youtu.be/JtmelPQ3ypw). The HPSS was taken offline on 15 Oct (user access deactivated at 8 AM). StrongLink went online on 1 November 2 PM. We offered a HSM Q&A session each Thursday 11:30 - 12:30 AM from 30 Sept to end of December 2021. We plan a second TechTalk when the system is fully functional.

Who do I contact when I have questions or issues regarding the new HSM system and its usage?

Please contact us via support@dkrz.de.

Archiving and Retrieval

How do I interact with the new system?

The official command line tool for tape access is called slk. Some features are deactivated for now. Additionally, the slk is missing a few small but very useful features. Therefore, a tool called slk_helpers was written at DKRZ to add these features. Details on these two tools are provided in the HSM Documentation at https://docs.dkrz.de . Additionally, a Python wrapper pyslk exists and packems was adapted to slk.

Where can I use slk and slk_helpers?

slk/slk_helpers are be installed as module slk on all Lenvate nodes. There are no limitations for the usage of slk commands except for retrieve, archive and search. slk retrieve is deactivated on all Levante login nodes. slk search is deactivated everywhere. Please use slk_helpers search_limited for the time being. On the login nodes, please use slk archive only for a few small files. If you wish to use slk archive or slk retrieve interactively, please use the interactive partition for this purpose (via salloc, see: Data Processing on Levante). For non-interactive archival and retrieval tasks, we recommend using the compute and shared partitions. We strongly recommend allocating 6 GB of memory (--mem=6GB, details: slk memory footprint).

Can I still use pftp to interact with the new HSM system?

No. A new command line tool is provided (please see “How do I interact with the new system?”).

How do I login to the HSM system?

Login is done via the command line tool slk login using your DKRZ credentials (LDAP; like used for luv). The command line tool stores a login token in ~/.slk/config.json for a specific time period (currently 30 days) so that you do not even need to go through the process of logging in for that period.

Does Kerberos authentication work on the new HSM system?

No, Kerberos does not work anymore. You only need to provide your login data to the command line tool in certain time intervals (currently 30 days).

Do I have to provide my login credentials each time I use the command line tool?

No, a login token is generated at first login. This token is valid for a fixed period of time (currently 30 days) and will then have to be renewed by performing a login operation. You do not need to wait for 30 days. But, the login token can be renewed at any time you wish. It is stored in ~/.slk/config.json.

Can I use the command line tool non-interactively?

Yes, it can be used non-interactively when a login token exists. From time to time an interactive session of the command line tool is necessary in order to renew the login token. The command line tool returns proper exit codes so that the success or failure of a program call can automatically be evaluated.

Can I access archived data from outside the DKRZ?

Currently, data in tape archive can only be accessed via Levante. New interfaces for access from outside of the DKRZ infrastructure are planned.

Do I have write access to the archive from outside the DKRZ?

No. slk is not made for data transfer via the internet. An exception are institutions who have direct network connection to DKRZ and currently have access to the HPSS via pftp. Users from these institutions will be able to use slk.

Will the new system be available as a Globus endpoint for external transfers?

No, not at the moment and not in the near future.

Does the tape quota (/arch, /doku), which was assigned to my computing time project, remain unchanged?

Yes, your tape quota remains the same.

How do I create directories in the HSM?

A slk mkdir does not exist but the slk_helpers provide it. Use slk_helpers mkdir /ex/am/ple/dir if /ex/am/ple already exists and you only want to create dir. If you want to create several nested folders (like mkdir -p does) please use slk_helpers mkdir -R /ex/am/ple/dir. If you do not want to use the slk_helpers and only slk, please do as follows: create empty directories locally, fill them with non-empty dummy files and archive them via slk archive -R. An example for this process is given in the Use Case section of the HSM documentation

Do I manually need to check the integrity of archived and retrieved files?

Is there an option to continue archiving if it was interrupted?

If the archival of several files was interrupted, please run the same call of slk archive a second time. The slk archive will only transfer those files, which (a) have not already been archived, (b) have only been partly archived or (c) have been modified since the first archival. The files, which are partly archived, are those files, which were currently transferred when slk archive was killed. Please be aware that these incomplete files are listed by slk list and may even have a checksum (of the incomplete file). These files can only be identified by comparing the checksum of the original file with the checksum calculated by StrongLink (slk_helpers checksum ...). If StrongLink does not hold a checksum of a file after a day, then the file should be assumed to be incomplete. The non-existence of a checksum in StrongLink is a sufficient and no necessary condition.

Details: Validate archivals

Does any command exist for deleting files immediately from /work in case of successful archival?

No, such a tool does not exist. We currently do not plan to provide such a tool.

Is it possible to archive into my existing folder structure created on HPSS?

Yes, the folder structure and write permissions remained untouched. Except the root folder /hpss was dropped.

Is there a “double” storage feature as for HPSS?

Yes, there is a “double” storage feature. Please see the chapter “Storage options and quota” in the new HSM documentation for details.

What does “namespace”, “global namespace” or “gns” mean?

StrongLink uses the term “namespace” or “global namespace” (=”gns”). A “(global) namespace” is comparable to a “directory” or “path” on a common file system.

How do I automatically/non-interactively check whether I own a valid slk login token?

slk does not provide a command that returns the status of the login tokes as true/false, valid/invalid or similar does not exist yet. But, you can check the validity of your login token via slk_helpers session. If you do not want to use the slk_helpers but check the status of the login token anyway, please use one of the following two commands:
# command 1:
$ slk list /dummy_input < /dev/null > /dev/null 2>&1

# command 2:
$ test `jq .expireDate ~/.slk/config.json` -gt `date +%s`

$? will be 0 if login token is valid and 1 if not. Thanks to Karl-Hermann Wieners for the first command.

You need to have the program jq available for the second command. jq is installed in /sw/rhel6-x64/devtools/jq-1.6-gcc48/bin/jq. You might add /sw/rhel6-x64/devtools/jq-1.6-gcc48/bin/ to your PATH or set an alias.

Is my slk login token still valid?

How to I check for how long my login token is still valid?

slk_helpers session will print the expiration date. Alternatively, the date/time until when the login token is stored in the slk config file (~/.slk/config.json). The key is expirationDate. You might open the config file with a text editor or print its content with tools like cat, less or jq.
jq .expireDate ~/.slk/config.json

You need to have the program jq available. jq is installed on Levante and available without loading any package.

Can I provide a file list to “slk archive” such as “-T” for “tar”?

Currently, this is not possible.

Can a user run multiple archival and retrieval requests at a time?

Yes, that is possible. However, we strongly recommend running only one slk call per 6 GB of allocated memory (see slk memory footprint). The transfer rate of slk archive and slk retrieve might be hardware-limited on shared nodes when other users copy data as well (see slk data transfer rate). Hence, splitting archival/retrieval requests up into multiple ones does not necessarily increase the transfer speed. We recommend aggregating file retrievals.

Where on Levante should I run slk?

Please see Where can I use “slk” and “slk_helpers”?

How does slk archive the files: does it tar them itself (similar to packems) or should we tar the files before hand?

slk does not packs/tar files. Metadata from netCDF files is automatically imported into the StrongLink database to simplify search and retrieval later on. Direct archiveal of nc-files is preferable with respect to the metadata import feature. However, many small files are bad for tape performance and might cost additional storage space (see Storage options and quota. Therefore, the usage of packems is reasonable in the case of large amount of very small files.

Are there requirements on the file size for the tape archival?

Preferred file size: 10 GB to 100 GB. Each file smaller than 1 GB will be charged 1 GB. Lower size limit: small files are not optimal for tape storage. Therefore, we encourage users to pack small files if there is no need to use the netCDF metadata features of StrongLink (see File Search and Metadata). Upper size limit: file sizes of a few TB are possible and have been successfully tested, but we recommend the same sizes as for HPSS: max. 500 GB.

I am member of a project but cannot access this projects data?

Please login again via slk login. For details please see group memberships of user updated on login.

Why do I get “Exception …: lateinit property websocket has not been initialized”?

When running slk archive with the argument --streams N please do only use values between 1 and 4` for N. For details please see slk archive: Exception …: lateinit property websocket has not been initialized.

My slk archive seems to hang. What should I do?

Please check whether /home is hanging. If /home is hanging, slk cannot access its login token and cannot write into its log. Therefore, slk hangs when /home is hanging.

Please check whether you are archiving a file of 0 Byte size. Details on the Known Issues page.

Additional features

Which new features does the HSM System provide?

Extended metadata is harvested from netCDF files which (a) have been archived into StrongLink and (b) were archived into HPSS but have been retrieved recently. It is possible to search files based on these extended metadata using slk_helpers search_limited. In future, slk search can be used for this purpose. Details on the search feature: File Search and Metadata

From which file types are extended metadata harvested?

Harvesting from netCDF files is implemented in StrongLink. Additionally, metadata is harvested from common picture, video, audio and document file formats (details in Reference: metadata schemata). Further formats are being investigated and could be introduced later after functional issues of slk are fixed. We don’t expect that this will happen soon.

Which metadata fields are harvested from netCDF files?

Most global attributes and variable names of netCDF files are stored in a metadata database. It is possible to search for each of these global attributes. Hence, properly self-described and standardized files are easier to find later on. These metadata are read-only. Metadata from a standardized subset of global attributes are be copied into an indexed metadata database. These can be modified and searched more efficiently. Please see the DKRZ documentation page on metadata schemata for details.

Is there a python interface available?

Yes, we offer a python wrapper package called pyslk. It is installed in python3/2022.01-gcc-11.2.0 on Levante. The slk module as to be loaded when pyslk is used. See for details please see https://hsm-tools.gitlab-pages.dkrz.de/pyslk .

Is it possible to use slk chmod and slk group (=chgrp) commands recursively by the user?

Yes, it is possible. Please provide -R to apply these commands recursively.

Are the search IDs user specific?

No, the search IDs are assigned globally. E.g. the search ID 423 exists only once. Each search ID can be used by every user. Thus, you can share your search IDs with your colleagues. However, the output of slk list SEARCH_ID or retrieval of slk retrieve SEARCH_ID ... depends on the read permissions of the executing user.

How long are the search IDs stored?

This is not decided yet. This is configurable by the administrators. We will monitor whether (or when) a performance degradation takes place and act accordingly.

Is a search ID automatically updated when new files are archived which match the original search query?

No, the IDs of files matching the search query are stored once when the search is performed. This list of file IDs will not be updated afterwards – except if files on the list are deleted. However, file specific metadata, such as file size or permission, are retrieved at the time when the search ID is used. slk list SEARCH_ID will show todays sizes of files covered by the search ID SEARCH_ID. Files that first matched the a search query are still listed by slk list even if they no longer match the original search query. This might happen if a file is renamed.

Can I share my search’s search ID with other DKRZ users?

Yes, you can. Please see “Are the search IDs user specific?” for details.

What does “RQL” mean?

RQL abbreviates “resource query language” and is another name for the “StrongLink Query Language”.

Is there any possibility to move around in the file system with something like the cd command?

No, this is not possible. The slk does not start its own shell like pftp or pure ftp do. It rather works like scp or rsync.

When slk list shows a file with “-” (not “t”) which means it exists at the cache: Does that mean it is not yet on the tape?

Right now it means that the file is in the cache. It can be on the tape – but not necessarily. If the t is shown, it means the file is only on tape - we are trying to show the duality at some point.

For a better overview of the archived files, Is there a possibility to list only folders, not all files?

When you use slk list with a specific namespace path, it shows all the files and namespaces in that specific namespace. It does not provide an argument like -d as ls does. You might use slk list GNS_PATH | grep -E "^d" to print only folders.

Alternatively, slk_helpers list_search -d SEARCH_ID can be used to print all namespaces that have been found by the search SEARCH_ID. Details on searches: File Search and Metadata

Is it possible to remove files from the archive?

Yes you can use slk delete for removing files and slk delete -R for removing namespaces and their content.

How to print the version of slk?

Please run slk version to print the version of slk. A --version flag or similar does not exist.

How to search non-recursively in a namespace?

slk search cannot search non-recursively in a namespace provided via path. As workaround, please get the object id of the particular namespace via slk_helpers exists and, then in your search query, use it as value for the search field resources.parent_id (see slk Usage Examples)

Is it possible to move files within the archive?

Yes you can use slk move for move a file or namespace from one namespace to another. Absolute paths have to be used: slk move /old_path/file.nc /new_path. Renaming cannot be done with slk move. I.e. this does not work: slk move /old_path/file.nc /new_path/new_file_name.nc. Please use slk rename for renaming operations.

Is it possible to rename files within the archive?

Yes you can use slk rename to rename a file or namespace. slk rename cannot be applied on multiple files/namespaces

How do I tag a folder with metadata?

Tagging folders with metadata is not possible in the moment.

How do I tag an individual file with metadata?

slk tag does not accept individual files as input. Instead, a search for the file has to be performed and the corresponding search id has to be used as input for slk tag. Details: Set metadata.

slk search does not find any resources although resources exist that seem to match the query

Example command:

$ slk search '{"resources.posix_uid": "25301"}'
Search continuing. .....
Search ID: 216


The query parser does not recognize when a wrong variable type is used. resources.posix_uid is of type integer and not string. Providing the wrong data types leads to 0 found results.


Write 25301 (integer) instead of "25301" (string) in the search query.

slk search '{"resources.posix_uid": 25301}'
Search continuing. ..... Search continuing. .....

Search ID: 217

Error: slk search yields RQL parse error

Example command and error:

$ slk search "{\"resources.size\":{\"$gt\": 1048576}}"
ERROR: Search failed. Reason: RQL parse error: No period found in collection field name ().


The $ in front of the gt was not escaped. Therefore, $gt is interpreted as environment variable by the shell before the query is handed to the slk. In most situations, no environment variable gt is defined leading to an empty string. If the query were surrounded by ' as delimiter and not by " then the $gt would not have been interpreted.

The above call of slk search as interpreted by the shell looks like

$ slk search "{\"resources.size\":{\"\": 1048576}}"


Either: use ' as delimiter of your search query instead of " to prevent operators starting with $ to be evaluated by your shell

Or: escape $’s in front of query operators by \ when you use " as delimiters of the query string.

'{"resources.size":{"$gt": 1048576}}'
"{\"resources.size\":{\"\$gt\": 1048576}}"


In some situations it might be very useful to use " as delimiter for your queries – e.g. if environment variables are part of your query.

$ export file_size=1048576
$ slk search "{\"resources.size\":{\"\$gt\": $file_size}}"

Advanced Technical Aspects

Can a user influence if data is written into the HSM cache or onto tape?

No. Fresh data (meant for archival) is first copied into the disc cache and then slowly written onto tape. When data is retrieved from tape, it is first copied into the disc cache and from there to the user-defined target file system. Small files of a few MB in size or smaller will remain in the HSM cache forever. Larger files that are stored on tape are regularly removed from the HSM cache.

How much time does a file stay on the cache?

We cannot give any numbers. The residence time in cache depends on the size of the files and the usage of the cache. We run clean up jobs regularly and monitor how fast the cache is filled.

How fast can be read from the HSM?

The target transfer rate between single nodes on Levante and the HSM cache is 1 GB/s. It might be higher in some situations and be reduced when the traffic is high. The retrieval rate from tape considerably depends on how many other read and write operations of other users are performed in parallel. If all tape drives are in us, slk retrieve will be idle until a tape drive is free.

How do I determine the id (uid) of a DKRZ user?

Please use one of the following commands:
# get your user id
$ id -u

# get the id of any user
$ id USER_NAME -u

# get the id of any user
$ getent passwd USER_NAME
#  OR
$ getent passwd USER_NAME | awk -F: '{ print $3 }'

How do I determine the id (gid) of a DKRZ group?

Please use one of the following commands:
# get group ID and group members
$ getent group GROUP_NAME
#  OR
$ getent group GROUP_NAME | awk -F: '{ print $3 }'

# get groups and their ids of all groups of which member you are
$ id

How do I determine the username of a DKRZ user when I have her/his id (uid)?

Please use the following command:
# get the name of a user with uid USER_ID
$ getent passwd USER_ID
#  OR
$ getent passwd USER_ID | awk -F: '{ print $1 }'

How do I determine the group name of a DKRZ group when I have its id (gid)?

Please use one of the following commands:
# get group name of a groupd with gid GROUP_ID
$ getent group GROUP_ID
#  OR
$ getent group GROUP_ID | awk -F: '{ print $1 }'

How do I determine the MIME type of a file?

You could use file --mime-type FILE or file -b --mime-type FILE to determine the MIME type on the Linux shell. Please be aware that different tools determine the MIME type differently (i.e. by file header or by file extension) and MIME type databases might differ. It might be better not to search for a specific MIME type but for a particular file extension – e.g. via {"resources.name": {"$regex": ".*nc$"}}. StrongLink allocates the MIME type application/x-netcdf to netCDF files.

Can the search ID of slk search be captured by a shell variable?

slk search (currently deactivated; please use slk_helpers search_limited) does not provide this feature out of the box. Currently (might change in future versions), the search ID is printed in columns >= 12 of the second row of the text output of slk search. We can use tail and sed to get the second line and extract a number or use tail and cut to get the second line and drop the first 11 characters. Example:
# normal call of slk search
$ slk search '{"resources.posix_uid": 23501}'
Search continuing. .....
Search ID: 466

# get ID using sed:
$ search_id=`slk search '{"resources.posix_uid": 23501}' | tail -n 1 | sed 's/[^0-9]*//g'`
$ echo $search_id

# get ID by dropping first 11 characters of the second line
$ search_id=`slk search '{"resources.posix_uid": 23501}' | tail -n 1 | cut -c12-20`
$ echo $search_id

# use awk pattern matching to get the correct line and correct column
$ search_id=`slk search '{"resources.posix_uid": 25301}' | awk '/Search ID/ {print($3)}'`
$ echo $search_id


This is an example for bash. When using csh, you need to prepend set `` in front of the assignments of the shell variables: ``set search_id=....

Is the metadata of files within zip/tar files evaluated/ingested?

No, the metadata of packed files is not ingested.

Does the packems package work with the new HSM system?

Yes, packems has been adapted to the new HSM system in coorperation with the MPI-M. unpackems needs slk retrieve to work and, hence, does not run on the login nodes. For packems we recommend having slk retrieve available. Additionally, packing and archiving files causes a high CPU and memory load. Therefore, we strongly recommend not using packems on the login nodes, Instead, please use the interactive, shared or compute partitions. Please have a look into the packems manual for details and usage of packems: https://code.mpimet.mpg.de/projects/esmenv/wiki/Packems.

Is it possible to use listems to list files that were archived with packems on the HPSS?

Yes, that’s possible.

Is it possible to use unpackems to retrieve files that were archived with packems on the HPSS?

Yes, that’s possible. However, unpackems does not run on the login nodes. Please see Does the packems package work with the new HSM system? for details.

Can you work directly with files in the archive (e.g. with Python)?

No, you have to download files to change them and archive them again.

Terminal cursor disapears after stopping a slk command. How to get it back?

If a slk command with a progress bar is canceled by the user, the shell cursor might disappear. One can make it re-appear by (a) running reset or (b) starting vim and leaving it directly (:q!).

Is a file stored in the HSM cache or exclusively on tape?

Solution a: In the output of slk list, please check the 11th character of the first column (permissions string). If this character is t then the file is exclusively stored on tape. If it is a - then the file is available from the HSM cache.

Solution b: Use slk_helpers iscached RESOURCE_PATH to check whether a file available from the HSM cache (exit code is 0) or not (exit code is 1).

What is an exit code?

While exiting, each program returns an integer number, which indicates whether the program finished successfully or not. Exit codes are not printed to the stdout or stderr streams but need to be explicitely captured by the user. An exit code of 0 indicates that everything went well. Exit codes >0 indicate that something went wrong. Non-zero exit codes do not necessarily mean that an error occurred. If grep or find do not match/find anything and not error occurs, they return 1 as exit code. These commands return 2 if an error occurs.

How do I capture exit codes?

The shell variable $? contains the exit code of the preceeding command. Examples:

# successful program call
$ slk version
SCLI Version 3.3.21
$ echo $?

# failed program call
$ slk retrieve abc def
ERROR: No resource exists with the following path: abc
echo $?

When commands are combined, the exit code of the command which exits last is available. Examples:

# we capture the exit code of slk list
$ slk list quatsch
ERROR: The list command requires a search ID, or a full namespace path starting with a forward slash (/).
$ echo $?

# we capture the exit code of cat (which exits successfully)
$ slk list quatsch | cat
ERROR: The list command requires a search ID, or a full namespace path starting with a forward slash (/).
$ echo $?

In some situations it might be valuable to store the exit code in a variable. This example is from a script:

slk retrieve real_data.nc /arch/bm0146/k204221/test_data
if [ $exit_code -ne 0 ]; then
    >&2 echo "an error of $exit_code occurred at `date` in slk retrieve call. Proceeding with next retrieval"
    echo "retrieval successful"

If time is used with another command, the other command’s exit code is always returned also time finalizes last.

Which exit codes does slk return?

Please see here

Which exit codes do the slk_helpers return?

Please see here

Common issues

Please see the extra page Known Issues


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