Difference between revisions of "Accessing Swestore with the ARC client"
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== Paths == | == Paths == | ||
− | The ARC commands supports multiple storage protocols, we recommend using GridFTP with paths on the form <code><nowiki>gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/...</nowiki></code> | + | The ARC commands supports multiple storage protocols, we recommend using GridFTP with paths on the form <code><nowiki>gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/...</nowiki></code>. |
= Copying files = | = Copying files = |
Revision as of 13:18, 14 July 2016
< Getting started with SweGrid
< Swestore
This guide describes how to use the Nordugrid ARC client for storing and retrieving files from Swestore. The ARC client is usually used for sending grid jobs to grid clusters, but it also contains commands for data management. A complete user guide for the ARC client can be found in http://www.nordugrid.org/documents/arc-ui.pdf.
Contents
Requirements
To access Swestore using the ARC client you need to get a grid certificate and a storage project.
All SNIC HPC systems should have the ARC client installed. If yours doesn't, please contact support at your centre so they can fix this as soon as possible. To install the ARC client on your own computer, please follow instructions here, or see the official Nordugrid ARC installation page for more information.
Quickstart
Basic commands
arcproxy
- unlock your certificate so you can use it. See Proxy certificates for details.arcls
- for listing files. Works similarly tols
. Examplearcls gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME
arcmkdir
- for creating directories. Works similarly tomkdir
. Examplearcmkdir gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir
arccp
- for copying files. Works similarly tocp
. Examplearccp myfile.txt gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/myfile.txt
arcrm
- for deleting files. Works similarly torm
. Examplearcrm gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/whoops.txt
Use man
and --help
to get more info on each command. Examples: man arcrm
or arcls --help
Paths
The ARC commands supports multiple storage protocols, we recommend using GridFTP with paths on the form gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/...
.
Copying files
Copying files to and from resources is accomplished using the arccp command.
Copying single files
Copying single files is accomplished in the same way as using the normal cp command as shown in the following example:
$ arccp archive.tar.gz gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/
Please note the trailing / which marks the destination as a directory. Without a / the destination will be a file, which may or may not be what you wanted. All required directories are created when needed so the destination may be a nonexisting directory.
Recursive copying
Recursive copying is accomplished using the --recursive option
to arccp. The argument to the option determines the depth of the
recursive copy, just supply a really big number like 999
if
you want the entire source directory tree.
Example:
$ arccp --recursive=999 foobar/ gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/
NOTE: The above example will copy all files in the directory foobar
into
the destination directory YOUR_PROJECT_NAME
. If you want the directory foobar
to be part of the destination path you have to explicitly supply it as shown in the example below:
$ arccp --recursive=999 foobar/ gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/foobar/
Long-running operations
Note that copying large directory trees can take quite some time, and will fail if you're not aware of the following:
- Your login session created with the
arcproxy
command has a limited lifetime. Usearcproxy -I
to show the remaining time. Usearcproxy -c validityPeriod=xxH
to initiate a session with longer lifetime. - If you loose connectivity with the resource you're running arccp on the command will abort. A utility such as
screen
ortmux
can be used to create a terminal session you can reattach to. - Transfer rates are largely dependent on the average file size, if you have a lot of small files the transfer will be slower than if you have large files.
- We recommend to limit your transfer sessions (ie. the directory tree copied with each arccp command) to 1TB if you have mostly large (100+MB) files and to 100GB if you have smaller files.
Listing files
Listing files on a resources is done using the arcls command. In the simplest form the command just takes a URL as input and displays names and directories without any extra information as shown in the following example:
$ arcls gsiftp://gsiftp.swestore.se/snic/bils/db/uniprot/2012_05 reldate.txt speclist.txt uniprot_sprot.dat.gz uniprot_sprot.fasta.gz uniprot_trembl.dat.gz uniprot_trembl.fasta.gz
Additional information can be listed by adding the --long option:
$ arcls --long gsiftp://gsiftp.swestore.se/snic/bils/db/uniprot/2012_05 <Name> <Type> <Size> <Creation> <Validity> <CheckSum> <Latency> reldate.txt file 151 2012-05-23 03:00:19 (n/a) adler32:f3f52f1d (n/a) speclist.txt file 1715169 2012-05-23 03:00:17 (n/a) adler32:91e59dae (n/a) uniprot_sprot.dat.gz file 462895141 2012-05-23 02:57:18 (n/a) adler32:0f131bb2 (n/a) uniprot_sprot.fasta.gz file 79935897 2012-05-23 03:00:20 (n/a) adler32:89844c57 (n/a) uniprot_trembl.dat.gz file 9162678278 2012-05-23 02:52:01 (n/a) adler32:b2d7cfd5 (n/a) uniprot_trembl.fasta.gz file 4456514443 2012-05-23 02:57:34 (n/a) adler32:2b73b2a1 (n/a)
Metadata
Metadatainformation on a specific file can be listed by specifying the -m or --metadata option. Worth noting is that the amount of metadata available differs depending on which protocol is used.
Examples:
$ arcls --metadata gsiftp://gsiftp.swestore.se/ops/nikke/smallfile /ops/nikke/smallfile checksum:adler32:762606eb mtime:2013-04-12 11:06:56 path:/ops/nikke/smallfile size:30 type:file
$ arcls --metadata srm://srm.swegrid.se/ops/nikke/smallfile /ops/nikke/smallfile accessperm:rw-r----- checksum:adler32:762606eb ctime:2013-04-12 11:06:56 filestoragetype:PERMANENT group:25001 latency:ONLINE lifetimeassigned:PT1S lifetimeleft:PT1S mtime:2013-04-12 11:06:56 owner:25001 path:/ops/nikke/smallfile size:30 spacetokens: type:file
Creating directories
$ arcmkdir gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir
If the arcmkdir command is missing the ARC utilities need to be upgraded. You can work around this by copying a dummy file to the path you want and then deleting the dummy file.
Removing files or directories
$ arcrm gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir/dummyfile $ arcrm gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir/
To remove directories they have to be empty.