Difference between revisions of "Accessing Swestore with the ARC client"

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(FAQ)
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[[Category:Swestore user guide]]
 
[[Category:Swestore user guide]]
  
[[Swestore|< Swestore]]
+
[[Swestore-dCache|< Swestore-dCache]]
  
 
This guide describes how to use the [http://www.nordugrid.org 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.
 
This guide describes how to use the [http://www.nordugrid.org 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.
  
 
= Requirements =
 
= Requirements =
To access Swestore using the ARC client you need to [[Grid_certificates|have a grid certificate]] and a [[Swestore|storage project]].
+
To access Swestore using the ARC client you need to have done the [[Certificate Setup for Swestore]] and a be a member of a Swestore storage project, see [[Swestore#Getting access to Swestore]].
 +
 
 +
You also need to have the certificate installed on the resource where you want to run the ARC commands. For SNIC resources this process includes [[Exporting_a_client_certificate|exporting the certificate from your browser]], transfering it to the intended SNIC resource and [[Preparing_a_client_certificate|prepare it for use with grid tools]].
  
 
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 [[ARC_client_installation|here]], or see the official Nordugrid [http://www.nordugrid.org/documents/arc-client-install.html ARC installation] page for more information.
 
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 [[ARC_client_installation|here]], or see the official Nordugrid [http://www.nordugrid.org/documents/arc-client-install.html ARC installation] page for more information.
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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>.
 +
 +
= Unlock your certificate =
 +
 +
Your certificate needs to be unlocked before you can do anything. Think of the process as logging in. When successful, a ''proxy certificate'' is the result.
 +
 +
arcproxy
 +
 +
To see the lifetime of your session, use:
 +
 +
arcproxy -I
  
 
= Copying files =  
 
= Copying files =  
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normal '''cp''' command as shown in the following example:
 
normal '''cp''' command as shown in the following example:
  
  $ arccp archive.tar.gz gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/
+
  arccp archive.tar.gz gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/
  
 
Please note the trailing / which marks the destination as a directory.
 
Please note the trailing / which marks the destination as a directory.
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Example:
 
Example:
  
  $ arccp --recursive=999 foobar/ gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/
+
  arccp --recursive=999 foobar/ gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/
  
 
'''NOTE:''' The above example will copy all files in the directory <code>foobar</code> into  
 
'''NOTE:''' The above example will copy all files in the directory <code>foobar</code> into  
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to be part of the destination path you have to explicitly supply it as shown in the example below:
 
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/
+
  arccp --recursive=999 foobar/ gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/foobar/
  
 
== Long-running operations ==
 
== Long-running operations ==
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following example:
 
following example:
  
  $ arcls gsiftp://gsiftp.swestore.se/snic/bils/db/uniprot/2012_05
+
  arcls gsiftp://gsiftp.swestore.se/snic/bils/db/uniprot/2012_05
 +
 
 +
Example output:
 
  reldate.txt
 
  reldate.txt
 
  speclist.txt
 
  speclist.txt
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Additional information can be listed by adding the '''--long''' option:
 
Additional information can be listed by adding the '''--long''' option:
  
  $ arcls --long gsiftp://gsiftp.swestore.se/snic/bils/db/uniprot/2012_05
+
  arcls --long gsiftp://gsiftp.swestore.se/snic/bils/db/uniprot/2012_05
 +
 
 +
Example output:
 
  <Name> <Type> <Size> <Creation> <Validity> <CheckSum> <Latency>
 
  <Name> <Type> <Size> <Creation> <Validity> <CheckSum> <Latency>
 
  reldate.txt file 151 2012-05-23 03:00:19 (n/a) adler32:f3f52f1d (n/a)
 
  reldate.txt file 151 2012-05-23 03:00:19 (n/a) adler32:f3f52f1d (n/a)
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Examples:
 
Examples:
  
  $ arcls --metadata gsiftp://gsiftp.swestore.se/ops/nikke/smallfile
+
  arcls --metadata gsiftp://gsiftp.swestore.se/ops/nikke/smallfile
 +
 
 +
Example output:
 
  /ops/nikke/smallfile
 
  /ops/nikke/smallfile
 
  checksum:adler32:762606eb
 
  checksum:adler32:762606eb
Line 109: Line 127:
 
  type:file
 
  type:file
  
  $ arcls --metadata srm://srm.swegrid.se/ops/nikke/smallfile
+
  arcls --metadata srm://srm.swegrid.se/ops/nikke/smallfile
 +
 
 +
Example output:
 
  /ops/nikke/smallfile
 
  /ops/nikke/smallfile
 
  accessperm:rw-r-----
 
  accessperm:rw-r-----
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= Creating directories =  
 
= Creating directories =  
 +
Directories are generally created on demand. If you copy a file with the destination /snic/YOUR_PROJECT_NAME/newdir/dummyfile the newdir directory will be created if missing. But you can explicitly create directories using the arcmkdir command.
  
  $ arcmkdir gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir
+
  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 =
  
= 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/dummyfile
+
  arcrm gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir/
$ arcrm gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir/
 
  
 
To remove directories they have to be empty.
 
To remove directories they have to be empty.
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= FAQ =
 
= FAQ =
  
* I get this message when I try to list files:
+
1) I get this message when I try to list files:
 
   $ arcls gsiftp://gsiftp.swestore.se/snic/
 
   $ arcls gsiftp://gsiftp.swestore.se/snic/
 
   ERROR: Unsupported URL given
 
   ERROR: Unsupported URL given
The nordugrid-arc-plugins-globus package is missing. Without it ARC is not able to use the gsiftp protocol.
+
* The nordugrid-arc-plugins-globus package is missing. Without it ARC is not able to use the gsiftp protocol.
 +
 
 +
2) <code>arcproxy</code> gives WARNING or ERROR messages.
 +
* The most common reason is a missing certificate file. See [[#Requirements]]
 +
 
 +
3) I get this warning when using the gsiftp:// protocol:
 +
  WARNING: Can not find voms service configuration file (vomses) in default locations: ~/.arc/vomses, ~/.voms/vomses, $ARC_LOCATION/etc/vomses, $ARC_LOCATION/etc/grid-security/vomses, $PWD/vomses, /etc/vomses, /etc/grid-security/vomses
 +
* This warning is benign and due to a bug in the ARC client.
 +
* A workaround to silence the warning is to create an empty vomses file, for example: <code>mkdir -p ~/.arc ; touch ~/.arc/vomses</code>

Revision as of 07:45, 10 March 2022


< Swestore-dCache

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.

Requirements

To access Swestore using the ARC client you need to have done the Certificate Setup for Swestore and a be a member of a Swestore storage project, see Swestore#Getting access to Swestore.

You also need to have the certificate installed on the resource where you want to run the ARC commands. For SNIC resources this process includes exporting the certificate from your browser, transfering it to the intended SNIC resource and prepare it for use with grid tools.

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 to ls. Example arcls gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME
arcmkdir - for creating directories. Works similarly to mkdir. Example arcmkdir gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir
arccp - for copying files. Works similarly to cp. Example arccp myfile.txt gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/myfile.txt
arcrm - for deleting files. Works similarly to rm. Example arcrm 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/....

Unlock your certificate

Your certificate needs to be unlocked before you can do anything. Think of the process as logging in. When successful, a proxy certificate is the result.

arcproxy

To see the lifetime of your session, use:

arcproxy -I

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 might fail if you're not aware of the following:

  • Your login session created with the arcproxy command has a limited lifetime. Use arcproxy -I to show the remaining time. Use arcproxy -c validityPeriod=xxH to initiate a session with longer lifetime.
  • The command will abort if you lose your network connection with the computer where you are running arccp. A utility such as screen or tmux 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

Example output:

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

Example output:

<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

Example output:

/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

Example output:

/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

Directories are generally created on demand. If you copy a file with the destination /snic/YOUR_PROJECT_NAME/newdir/dummyfile the newdir directory will be created if missing. But you can explicitly create directories using the arcmkdir command.

arcmkdir gsiftp://gsiftp.swestore.se/snic/YOUR_PROJECT_NAME/newdir

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.

FAQ

1) I get this message when I try to list files:

 $ arcls gsiftp://gsiftp.swestore.se/snic/
 ERROR: Unsupported URL given
  • The nordugrid-arc-plugins-globus package is missing. Without it ARC is not able to use the gsiftp protocol.

2) arcproxy gives WARNING or ERROR messages.

  • The most common reason is a missing certificate file. See #Requirements

3) I get this warning when using the gsiftp:// protocol:

 WARNING: Can not find voms service configuration file (vomses) in default locations: ~/.arc/vomses, ~/.voms/vomses, $ARC_LOCATION/etc/vomses, $ARC_LOCATION/etc/grid-security/vomses, $PWD/vomses, /etc/vomses, /etc/grid-security/vomses
  • This warning is benign and due to a bug in the ARC client.
  • A workaround to silence the warning is to create an empty vomses file, for example: mkdir -p ~/.arc ; touch ~/.arc/vomses