Difference between revisions of "Icommands"
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Bioinformatics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|icommands}} | |{{#vardefine:app|icommands}} | ||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
| Line 18: | Line 18: | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | iCommands is a collection of commands for Unix and Windows that are used in | + | iCommands is a collection of commands for Unix and Windows that are used in the iRODS system to interact with the CyVerse Data Store. Many commands are very similar to Unix utilities. For example, to list files and directories, you use ls in Linux, but in iCommands you use ils. |
| − | the iRODS system to interact with the CyVerse Data Store. Many commands are | ||
| − | very similar to Unix utilities. For example, to list files and directories, | ||
| − | you use ls in Linux, but in iCommands you use ils. | ||
| − | While iCommands are great for all transfers and for automating tasks via | + | While iCommands are great for all transfers and for automating tasks via scripts, they are the best choice for large files (2-100 GB each) and for bulk file transfers (many small files). For a comparison of the different methods of uploading and downloading data items, see Downloading and Uploading Data. |
| − | scripts, they are the best choice for large files (2-100 GB each) and for | ||
| − | bulk file transfers (many small files). For a comparison of the different | ||
| − | methods of uploading and downloading data items, see Downloading and | ||
| − | Uploading Data. | ||
| − | Using iCommands with your CyVerse username and password allows you access to | + | Using iCommands with your CyVerse username and password allows you access to all files that have been shared by other users; however, you can download data sets that have been made public without a CyVerse account. |
| − | all files that have been shared by other users; however, you can download | ||
| − | data sets that have been made public without a CyVerse account | ||
| − | |||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Required Modules== |
| − | + | ===Serial=== | |
| + | * {{#var:app}} | ||
| + | <!-- | ||
| + | ===Parallel (OpenMP)=== | ||
| + | * intel | ||
| + | * {{#var:app}} | ||
| + | ===Parallel (MPI)=== | ||
| + | * intel | ||
| + | * openmpi | ||
| + | * {{#var:app}} | ||
| + | --> | ||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 46: | Line 46: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Since iCommands binaries are not compatible with our system iCommands binaries have to be launched with the 'launch_icommands' command. | |
| + | |||
| + | For example: | ||
| + | |||
| + | $ module load icommands | ||
| + | $ launch_icommands ienv -h | ||
|}} | |}} | ||
Revision as of 17:06, 27 May 2022
Description
iCommands is a collection of commands for Unix and Windows that are used in the iRODS system to interact with the CyVerse Data Store. Many commands are very similar to Unix utilities. For example, to list files and directories, you use ls in Linux, but in iCommands you use ils.
While iCommands are great for all transfers and for automating tasks via scripts, they are the best choice for large files (2-100 GB each) and for bulk file transfers (many small files). For a comparison of the different methods of uploading and downloading data items, see Downloading and Uploading Data.
Using iCommands with your CyVerse username and password allows you access to all files that have been shared by other users; however, you can download data sets that have been made public without a CyVerse account.
Required Modules
Serial
- icommands
System Variables
- HPC_ICOMMANDS_DIR - installation directory
Additional Information
Since iCommands binaries are not compatible with our system iCommands binaries have to be launched with the 'launch_icommands' command.
For example:
$ module load icommands $ launch_icommands ienv -h