SweStore/iRODS icommand
For accessing the Swestore national storage, we use (since Nov 2013 iRODS, and more specifically the iRODS client called "icommands", which is a set of commands similar to the unix commands "ls", "cd", "imkdir" etc, but with an "i" in front, plus two FTP-like commands: "iput" and "iget" (plus some more, but those are the ones you need most).
Note that data put on Swestore via iRODS is not accessible through other means.
Activate the iRODS icommands The iRODS icommands client is activated through the module system, as so many other things on SNIC clusters.
1. Log in to SNIC cluster 2. Execute:
module load irods iinit After activating the iRODS icommands, you will be placed in one of your projects. if you run "ils", you will then see a listing of files and folders in that project, something like this:
[samuel@kalkyl4 ~]$ ils
/ssUppnexZone/proj/b2011221: C- /ssUppnexZone/proj/b2011221/firstRun
Navigate around To enter one of the (or the only) folder(s), do:
icd [proj-id] ... in this case:
icd firstrun To switch to another project, use
icd .. to back up a level. After that, you can change to another project or folder using icd as previously
icd b2011222 Upload files To upload the above mentioned folder, do (-r is needed to recurse into directories):
iput -r [a local folder] For single files, the -r flag is not needed:
iput [a local file] To list the newly uploaded file/directory:
ils To create folders, do:
imkdir [folder-name] If you want to verify the upload outside of iRODS, there's a utility called ssverify.sh that will let you do that.
$ ssverify.sh test /ssUppnexZone/proj/p2061001/test Checking if test/a matches /ssUppnexZone/proj/p2061001/test/a... seems good! Checking if test/b matches /ssUppnexZone/proj/p2061001/test/b... seems good! Checking if test/c matches /ssUppnexZone/proj/p2061001/test/c... seems good! Checking if test/du matches /ssUppnexZone/proj/p2061001/test/du... seems good! Checking if test/foo matches /ssUppnexZone/proj/p2061001/test/foo... seems good! It seems test matches /ssUppnexZone/proj/p2061001/test on Swestore. $ echo femtiofyra > test/c $ ssverify.sh test /ssUppnexZone/proj/p2061001/test Checking if test/a matches /ssUppnexZone/proj/p2061001/test/a... seems good! Checking if test/b matches /ssUppnexZone/proj/p2061001/test/b... seems good! Checking if test/c matches /ssUppnexZone/proj/p2061001/test/c... NO! Something is wrong! Either the files don't match or something went wrong, please contact staff@uppmax.uu.se to investigate. Downloading files To download a file again, do:
iget [a file in iRODS] ... or, for folders, do it recursively:
iget -r [a folder in iRODS] File removal To remove a file, you'll like need to use -f to irm in order to bypass the use of a trash area, which is currently not supported at Uppmax.
More hints You can have iput show the progress with the -P flag If you want to be placed in a particular directory when you load the irods module, you can create a file called $HOME/.irods/.irodsEnv containing irodsHome '/ssUppnexZone/proj/myproj' irodsCwd '/ssUppnexZone/proj/myproj' where myproj is replaced by your project id. Read more info about the respective i-commands with "[command] -h"
