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rdms:access:windows:cyberduck [2025/01/27 15:24] – burcurdms:access:windows:cyberduck [2026/07/09 06:50] (current) – burcu
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 {{ :rdms:access:cyberducklogo.png?direct&100|}} {{ :rdms:access:cyberducklogo.png?direct&100|}}
  
-Cyberduck is a solution to transfer files to and from the RDMS. To manage data, metadata, users, and projects on the RDMS, you need to connect to the [[rdms:webapp|RDMS WebApp]].+Cyberduck is a solution for transferring files to and from the RDMS. To manage data, metadata, users, and projects on the RDMS, you need to connect to the [[rdms:webapp|RDMS WebApp]].
  
-To access the Default zone, Cyberduck can connect to the RDMS using both the **WebDAV** and the **native iRODS** protocol. For the [[https://wiki.hpc.rug.nl/rdms/solution/multizone|Sensitive Data (SD) zone]], you should use the **RDMS SD Cyberduck Profile**. Instructions om how to configure Cyberduck for each case are provided below.+To access the Default zone, Cyberduck can connect to the RDMS using both the **WebDAV** and the **native iRODS** protocol. For the [[https://wiki.hpc.rug.nl/rdms/solution/multizone|Sensitive Data (SD) zone]], you should use the **RDMS SD Cyberduck Profile**. Instructions on how to configure Cyberduck for each case are provided below.
  
 **Notes:**  **Notes:** 
-  * In case you want to transfer folders with many files (of the order of thousand or more), it is recommended to compress/bundle these folders (ZIP/TAR) in order to have more stable transfers, or transfer such folders one-by-one instead of selecting all of them at once.+  * In case you want to transfer folders with many files (of the order of thousands or more), it is recommended to compress/bundle these folders (ZIP/TAR) in order to have more stable transfers, or transfer such folders one-by-one instead of selecting all of them at once.
   * If you receive a ''Hierarchy error'' message while transferring data to RDMS, first select the ''Continue'' option. Then, if known, delete the file(s) that caused the error in your RDMS environment and restart the transfer. If you cannot delete a file, move it to another location and contact RDMS support.   * If you receive a ''Hierarchy error'' message while transferring data to RDMS, first select the ''Continue'' option. Then, if known, delete the file(s) that caused the error in your RDMS environment and restart the transfer. If you cannot delete a file, move it to another location and contact RDMS support.
-  * For tips regarding optimum transfer settings, please also take a look at the [[https://wiki.hpc.rug.nl/rdms/access/windows/cyberduck#transfer_preferences|Cyberduck transfer preferences]] section which includes recommended Cyberduck settings which could resolve your issues.   +  * For tips regarding optimum transfer settings, please also take a look at the [[https://wiki.hpc.rug.nl/rdms/access/windows/cyberduck#transfer_preferences|Cyberduck transfer preferences]] section, which includes recommended Cyberduck settings that could resolve your issues.   
  
 ===== Configuration of Cyberduck using the WebDAV Protocol ===== ===== Configuration of Cyberduck using the WebDAV Protocol =====
Line 29: Line 29:
  
 ===== Configuration of Cyberduck using the native iRODS Protocol ===== ===== Configuration of Cyberduck using the native iRODS Protocol =====
 +**Note: As of July 2026, there is a new iRODS native template for the Cyberduck profile. If you are using the old profile, Cyberduck will fail to connect and will ask for your credentials again. The profile in the Wiki is updated.**
  
-If you would like to use the native iRODS protocol for connecting Cyberduck to the RDMS, you can download the iRODS (RUG) Cyberduck profile directly by clicking on the link below or by copying the content to a text editor of your choice and then save as a ''*.cyberduckprofile'' file. Afterwards, double click the downloaded/created ''*.cyberduckprofile'' file to install add it to Cyberduck.+ 
 +If you would like to use the native iRODS protocol for connecting Cyberduck to the RDMS, you can download the iRODS (RUG) Cyberduck profile directly by clicking on the link below or by copying the content to a text editor of your choice and then saving it as a ''*.cyberduckprofile'' file. Afterwards, double-click the downloaded/created ''*.cyberduckprofile'' file to install and add it to Cyberduck.
  
 **iRODS Cyberduck profile**:  **iRODS Cyberduck profile**: 
Line 36: Line 38:
 <file xml RDMS.cyberduckprofile> <file xml RDMS.cyberduckprofile>
 <?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
 +<!--
 +  ~ Copyright (c) 2002-2017 iterate GmbH. All rights reserved.
 +  ~ https://cyberduck.io/
 +  ~
 +  ~ This program is free software; you can redistribute it and/or modify
 +  ~ it under the terms of the GNU General Public License as published by
 +  ~ the Free Software Foundation; either version 2 of the License, or
 +  ~ (at your option) any later version.
 +  ~
 +  ~ This program is distributed in the hope that it will be useful,
 +  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
 +  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 +  ~ GNU General Public License for more details.
 +  -->
 +
 <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
 <plist version="1.0"> <plist version="1.0">
     <dict>     <dict>
 +        <!-- DO NOT CHANGE. This is the purpose of the profile-->
         <key>Protocol</key>         <key>Protocol</key>
         <string>irods</string>         <string>irods</string>
 +
 +        <!-- Undocumented for CLI, the URI prefix, e.g., rug:// -->
         <key>Vendor</key>         <key>Vendor</key>
         <string>rug</string>         <string>rug</string>
 +
 +        <!-- Name of the profile -->
         <key>Description</key>         <key>Description</key>
-        <string>RDMS (rug)</string>+        <string>RDMS (rug) 9.4.0+, iRODS 4.3.2+</string> 
 + 
 +        <!-- Default name of bookmark -->
         <key>Default Nickname</key>         <key>Default Nickname</key>
         <string>RDMS rug zone</string>         <string>RDMS rug zone</string>
 +
 +        <!-- iRODS hostname settings -->
 +        <key>Hostname Configurable</key>
 +        <false/>
         <key>Default Hostname</key>         <key>Default Hostname</key>
         <string>store.data.rug.nl</string>         <string>store.data.rug.nl</string>
-        <key>Hostname Configurable</key>+ 
 +        <!-- iRODS port settings --> 
 +        <key>Port Configurable</key>
         <false/>         <false/>
-        <key>Region</key> 
-        <string>rug:rootResc</string> 
         <key>Default Port</key>         <key>Default Port</key>
         <string>1247</string>         <string>1247</string>
-        <key>Port Configurable</key> + 
-        <false/> +        <!-- Default path to open -->
-        <key>Username Configurable</key> +
-        <true/>+
         <key>Default Path</key>         <key>Default Path</key>
         <string>/rug/home</string>         <string>/rug/home</string>
-        <key>Path Configurable</key> + 
-        <true/>+        <!-- The zone of the iRODS server to connect to.  For backward --> 
 +        <!-- compatibility, a root resource can be specified by appending --> 
 +        <!-- ":<resource>" to the zone.  The specified resource is only --> 
 +        <!-- used when uploading files.  Prefer setting "Destination --> 
 +        <!-- Resource" under the "Properties" section. --> 
 +        <key>Region</key> 
 +        <string>rug</string> 
 + 
 +        <!-- The authentication scheme used to establish a connection to --> 
 +        <!-- an iRODS server.  Must be set to "native" or "pam_password". --> 
 +        <!-- "standard" is an alias for "native". -->
         <key>Authorization</key>         <key>Authorization</key>
-        <string>PAM</string>+        <string>pam_password</string> 
 + 
 +        <!-- Advanced properties --> 
 +        <key>Properties</key> 
 +        <dict> 
 +            <!-- The root resource to target when uploading files. --> 
 +            <!-- DO NOT define this option unless needed. --> 
 +            <!-- This option supersedes any resource defined by "Region". --> 
 +            <key>Destination Resource</key> 
 +            <string>rootResc</string> 
 + 
 +            <!-- Controls whether deletion of an object permanently --> 
 +            <!-- removes or moves it into the trash collection. --> 
 +            <key>Delete Objects Permanently</key> 
 +            <string>no</string> 
 + 
 +            <!-- The size (in bytes) of a file that must be exceeded before --> 
 +            <!-- using parallel transfer. --> 
 +            <!-- The value must satisfy the range [1, 2^31-1]. --> 
 +            <key>Parallel Transfer Threshold</key> 
 +            <string>33554432</string> 
 + 
 +            <!-- The number of iRODS connections used for parallel transfer --> 
 +            <!-- of a single file.  Each transfer will use the specified --> 
 +            <!-- number of iRODS connections. The value must satisfy the --> 
 +            <!-- range [2, 10]. --> 
 +            <key>Parallel Transfer Connections</key> 
 +            <string>3</string> 
 + 
 +            <!-- The buffer size (in bytes) used for parallel transfer of --> 
 +            <!-- a single file. Applies to uploads and downloads.  The --> 
 +            <!-- value must satisfy the range [1, 128MB]. --> 
 +            <key>Parallel Transfer Buffer Size</key> 
 +            <string>4194304</string> 
 + 
 +            <!-- Secure communication options must be one of "CS_NEG_REQUIRE", --> 
 +            <!-- "CS_NEG_DONT_CARE", or "CS_NEG_REFUSE". --> 
 +            <!-- - CS_NEG_REQUIRE:   Demand TLS be used. --> 
 +            <!-- - CS_NEG_DONT_CARE: Let the server decide if TLS is used. --> 
 +            <!-- - CS_NEG_REFUSE:    Do not use TLS. --> 
 +            <key>Client Server Negotiation</key> 
 +            <string>CS_NEG_REQUIRE</string> 
 + 
 +            <!-- TLS options, when enabled. --> 
 +            <key>Encryption Algorithm</key> 
 +            <string>AES-256-CBC</string> 
 +            <key>Encryption Key Size</key> 
 +            <string>32</string> 
 +            <key>Encryption Salt Size</key> 
 +            <string>8</string> 
 +            <key>Encryption Hash Rounds</key> 
 +            <string>16</string> 
 +        </dict>
     </dict>     </dict>
 </plist> </plist>
 +
 </file> </file>
  
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 If everything went right, you will see the login screen below.  It will connect you to the RDMS "rug" zone using the native iRODS protocol. Simply insert your UG email address (lowercase!) and associated password to connect to the system. It should have also created an editable bookmark for your connection. If everything went right, you will see the login screen below.  It will connect you to the RDMS "rug" zone using the native iRODS protocol. Simply insert your UG email address (lowercase!) and associated password to connect to the system. It should have also created an editable bookmark for your connection.
  
-{{ :rdms:access:windows:cyberduck_rug_connection.png?direct&500 |}}+{{ :rdms:access:windows:newcyberduckprofile_rug.png?direct&400 |}}
  
 ===== Configuration of Cyberduck to access the RDMS SD Zone ===== ===== Configuration of Cyberduck to access the RDMS SD Zone =====
 +**Note: As of July 2026, there is a new iRODS native template for the Cyberduck profile. If you are using the old profile, Cyberduck will fail to connect and will ask for your credentials again. The profile in the Wiki is updated.**
  
-In order to access the RDMS SD zone via Cyberduck, click **Open Connection**, select the RDMS SD Cyberduck Profile protocol, and configure the login credentials as follows:+In order to access the RDMS SD zone, you need to first download the RDMS Sensitive data zone Cyberduck profile directly by clicking on the link below or by copying the content to a text editor of your choice and then saving it as a ''*.cyberduckprofile'' file. Afterwards, double-click the downloaded/created ''*.cyberduckprofile'' file to install and add it to Cyberduck. Then, click **Open Connection**, select the RDMS SD Cyberduck Profile protocol, and configure the login credentials as follows:
  
 ++++ Cyberduck profile for the Sensitive Data Zone | ++++ Cyberduck profile for the Sensitive Data Zone |
 <file xml RDMSsd.cyberduckprofile> <file xml RDMSsd.cyberduckprofile>
 <?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
 +<!--
 +  ~ Copyright (c) 2002-2017 iterate GmbH. All rights reserved.
 +  ~ https://cyberduck.io/
 +  ~
 +  ~ This program is free software; you can redistribute it and/or modify
 +  ~ it under the terms of the GNU General Public License as published by
 +  ~ the Free Software Foundation; either version 2 of the License, or
 +  ~ (at your option) any later version.
 +  ~
 +  ~ This program is distributed in the hope that it will be useful,
 +  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
 +  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 +  ~ GNU General Public License for more details.
 +  -->
 +
 <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
 <plist version="1.0"> <plist version="1.0">
     <dict>     <dict>
 +        <!-- DO NOT CHANGE. This is the purpose of the profile-->
         <key>Protocol</key>         <key>Protocol</key>
         <string>irods</string>         <string>irods</string>
 +
 +        <!-- Undocumented for CLI, the URI prefix, e.g., rug:// -->
         <key>Vendor</key>         <key>Vendor</key>
         <string>sdrug</string>         <string>sdrug</string>
 +
 +        <!-- Name of the profile -->
         <key>Description</key>         <key>Description</key>
-        <string>RDMS (sdrugZone)</string>+        <string>RDMS (sdrugZone) 9.4.0+, iRODS 4.3.2+</string> 
 + 
 +        <!-- Default name of bookmark -->
         <key>Default Nickname</key>         <key>Default Nickname</key>
         <string>RDMS sdrugZone zone</string>         <string>RDMS sdrugZone zone</string>
 +
 +        <!-- iRODS hostname settings -->
 +        <key>Hostname Configurable</key>
 +        <false/>
         <key>Default Hostname</key>         <key>Default Hostname</key>
         <string>store-sd.data.rug.nl</string>         <string>store-sd.data.rug.nl</string>
-        <key>Hostname Configurable</key>+ 
 +        <!-- iRODS port settings --> 
 +        <key>Port Configurable</key>
         <false/>         <false/>
-        <key>Region</key> 
-        <string>sdrugZone:rootResc</string> 
         <key>Default Port</key>         <key>Default Port</key>
         <string>1247</string>         <string>1247</string>
-        <key>Port Configurable</key> + 
-        <false/> +        <!-- Default path to open -->
-        <key>Username Configurable</key> +
-        <true/>+
         <key>Default Path</key>         <key>Default Path</key>
         <string>/sdrugZone/home</string>         <string>/sdrugZone/home</string>
-        <key>Path Configurable</key> + 
-        <true/>+        <!-- The zone of the iRODS server to connect to.  For backward --> 
 +        <!-- compatibility, a root resource can be specified by appending --> 
 +        <!-- ":<resource>" to the zone.  The specified resource is only --> 
 +        <!-- used when uploading files.  Prefer setting "Destination --> 
 +        <!-- Resource" under the "Properties" section. --> 
 +        <key>Region</key> 
 +        <string>sdrugZone</string> 
 + 
 +        <!-- The authentication scheme used to establish a connection to --> 
 +        <!-- an iRODS server.  Must be set to "native" or "pam_password". --> 
 +        <!-- "standard" is an alias for "native". -->
         <key>Authorization</key>         <key>Authorization</key>
-        <string>PAM</string>+        <string>pam_password</string> 
 + 
 +        <!-- Advanced properties --> 
 +        <key>Properties</key> 
 +        <dict> 
 +            <!-- The root resource to target when uploading files. --> 
 +            <!-- DO NOT define this option unless needed. --> 
 +            <!-- This option supersedes any resource defined by "Region". --> 
 +            <key>Destination Resource</key> 
 +            <string>rootResc</string> 
 + 
 +            <!-- Controls whether deletion of an object permanently --> 
 +            <!-- removes or moves it into the trash collection. --> 
 +            <key>Delete Objects Permanently</key> 
 +            <string>no</string> 
 + 
 +            <!-- The size (in bytes) of a file that must be exceeded before --> 
 +            <!-- using parallel transfer. --> 
 +            <!-- The value must satisfy the range [1, 2^31-1]. --> 
 +            <key>Parallel Transfer Threshold</key> 
 +            <string>33554432</string> 
 + 
 +            <!-- The number of iRODS connections used for parallel transfer --> 
 +            <!-- of a single file.  Each transfer will use the specified --> 
 +            <!-- number of iRODS connections. The value must satisfy the --> 
 +            <!-- range [2, 10]. --> 
 +            <key>Parallel Transfer Connections</key> 
 +            <string>3</string> 
 + 
 +            <!-- The buffer size (in bytes) used for parallel transfer of --> 
 +            <!-- a single file. Applies to uploads and downloads.  The --> 
 +            <!-- value must satisfy the range [1, 128MB]. --> 
 +            <key>Parallel Transfer Buffer Size</key> 
 +            <string>4194304</string> 
 + 
 +            <!-- Secure communication options must be one of "CS_NEG_REQUIRE", --> 
 +            <!-- "CS_NEG_DONT_CARE", or "CS_NEG_REFUSE". --> 
 +            <!-- - CS_NEG_REQUIRE:   Demand TLS be used. --> 
 +            <!-- - CS_NEG_DONT_CARE: Let the server decide if TLS is used. --> 
 +            <!-- - CS_NEG_REFUSE:    Do not use TLS. --> 
 +            <key>Client Server Negotiation</key> 
 +            <string>CS_NEG_REQUIRE</string> 
 + 
 +            <!-- TLS options, when enabled. --> 
 +            <key>Encryption Algorithm</key> 
 +            <string>AES-256-CBC</string> 
 +            <key>Encryption Key Size</key> 
 +            <string>32</string> 
 +            <key>Encryption Salt Size</key> 
 +            <string>8</string> 
 +            <key>Encryption Hash Rounds</key> 
 +            <string>16</string> 
 +        </dict>
     </dict>     </dict>
 </plist> </plist>
Line 122: Line 298:
   * **Password:** Your UG password   * **Password:** Your UG password
  
-{{ :rdms:access:windows:cyberduck_sd1.png?direct&700 |}}+{{ :rdms:access:windows:cyberduck_sd1.png?direct&600 |}}
  
 **Note:** If you experience issues with this, please make sure that you specified your username in lowercase. The login to the RDMS is case sensitive! **Note:** If you experience issues with this, please make sure that you specified your username in lowercase. The login to the RDMS is case sensitive!
Line 128: Line 304:
 ===== Transferring Data to and from the RDMS via Cyberduck ===== ===== Transferring Data to and from the RDMS via Cyberduck =====
  
-The instructions below give details on how to use the transfer dialogs to upload, download, and synchronize your data.  Be aware that drag-and-drop from/to file explorer is also supported with the same results.+The instructions below give details on how to use the transfer dialogs to upload, download, and synchronize your data.  Be aware that drag-and-drop from/to the file explorer is also supported with the same results.
 ==== Upload ==== ==== Upload ====
  
Line 144: Line 320:
 {{ :rdms:access:windows:cyberduck_step_2.png?direct&600 |}} {{ :rdms:access:windows:cyberduck_step_2.png?direct&600 |}}
  
-The upload will now start and the window shown in the picture will appear.+The upload will now start, and the window shown in the picture will appear.
 {{ :rdms:access:windows:cyberduck_step_3.png?direct&600 |}} {{ :rdms:access:windows:cyberduck_step_3.png?direct&600 |}}
  
Line 174: Line 350:
 ==== Synchronization ==== ==== Synchronization ====
  
-Apart from up- or downloading files or entire folders manually in Cyberduck, you can also give the client the command to synchronize one of your local folders to a collection on the RDMS. The advantage of using synchronizing rather than up- or downloading the data, is that the synchronization will not transfer every file but only act on files that have been changed or that don't exist in the target directory. This will reduce the amount of data you will transfer at any one time.+Apart from uploading or downloading files or entire folders manually in Cyberduck, you can also give the client the command to synchronize one of your local folders to a collection on the RDMS. The advantage of using synchronization rather than uploading or downloading the data is that the synchronization will not transfer every file, but only act on files that have been changed or that don't exist in the target directory. This will reduce the amount of data you will transfer at any one time.
  
 ++++ Click to display section | ++++ Click to display section |
-To synchronize your folder, simply right-click the collection you wish to sync and the following menu will be displayed.+To synchronize your folder, simply right-click the collection you wish to sync, and the following menu will be displayed.
 {{ :rdms:access:windows:sync_1.png?direct&600 |}} {{ :rdms:access:windows:sync_1.png?direct&600 |}}
  
-Click on ''Synchronize...'' (red underlined) and the next window will open. There you can navigate to the folder on your local machine that you wish to sync to the RDMS collection. Once you have selected it and confirmed, the transfer window will open and after a few seconds, this window will appear.+Click on ''Synchronize...'' (red underlined), and the next window will open. There, you can navigate to the folder on your local machine that you wish to sync to the RDMS collection. Once you have selected it and confirmed, the transfer window will open, and after a few seconds, this window will appear.
 {{ :rdms:access:windows:sync_2.png?direct&600 |}} {{ :rdms:access:windows:sync_2.png?direct&600 |}}
  
Line 186: Line 362:
 {{ :rdms:access:windows:sync_3.png?direct&600 |}} {{ :rdms:access:windows:sync_3.png?direct&600 |}}
  
-Finally, if you click the red box shown above, you will be given three options of how Cyberduck is going to handle your sync. Your options are:+Finally, if you click the red box shown above, you will be given three options for how Cyberduck is going to handle your sync. Your options are:
   * **Download**: Changes to the RDMS collection will be reflected in your local folder. Changes to your local folder will not be reflected in the RDMS collection.   * **Download**: Changes to the RDMS collection will be reflected in your local folder. Changes to your local folder will not be reflected in the RDMS collection.
   * **Upload**: Changes to your local folder will be reflected in the RDMS collection. Changes to the RDMS collection will not be reflected in your local folder.   * **Upload**: Changes to your local folder will be reflected in the RDMS collection. Changes to the RDMS collection will not be reflected in your local folder.
   * **Mirror**: Any difference between the folders will be transferred, no matter if it was changed in your local folder or in the RDMS.    * **Mirror**: Any difference between the folders will be transferred, no matter if it was changed in your local folder or in the RDMS. 
  
-We suggest that you either use "Upload" or "Download" when using the Sync option, as you have a better handle of what is going to be changed. Please also keep in mind that Cyberduck's synchronization feature is a one-time action. If you wish to sync your folder again, it will not happen automatically, but you will need to repeat the steps above.+We suggest that you either use "Upload" or "Download" when using the Sync option, as you have a better handle on what is going to be changed. Please also keep in mind that Cyberduck's synchronization feature is a one-time action. If you wish to sync your folder again, it will not happen automatically, but you will need to repeat the steps above.
 ++++ ++++
 ==== Transfer Preferences ==== ==== Transfer Preferences ====
  
-Cyberduck lets you edit the way your transfers happen through choosing certain preferences. Below we list the main preferences you might want to adjust before starting your first transfer.+Cyberduck lets you edit the way your transfers happen by choosing certain preferences. Below we list the main preferences you might want to adjust before starting your first transfer.
  
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 {{ :rdms:access:windows:pref_2.png?direct&600 |}} {{ :rdms:access:windows:pref_2.png?direct&600 |}}
  
-This is not a necessary change, but if you are running into connection timeout issues with Cyberduck, navigate the the "General" tab in the "Transfers" window. Changing the option under "Transfer Files" from "Open Multiple Connections" to "Open Single Connection" can help solve that problem.+This is not a necessary change, but if you are running into connection timeout issues with Cyberduck, navigate to the "General" tab in the "Transfers" window. Changing the option under "Transfer Files" from "Open Multiple Connections" to "Open Single Connection" can help solve that problem.
  
 Furthermore, be sure that you **disable the option for segmented downloads** as this can introduce issues with your downloads.  Furthermore, be sure that you **disable the option for segmented downloads** as this can introduce issues with your downloads.