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scp
,sftp
,rsync
- these are automatically installed on Mac and Linuxpscp
,psftp
- Windows-only. These can be installed with the PuTTY ssh program.ftp
- available on O2 for downloading from external sites which only accept FTP logins. But, O2 does not accept incoming FTP logins.aspera - a data transport and streaming technology, now owned by IBM.
awscli - Amazon AWS command line interface
basemount - an Illumina tool to mount BaseSpace Sequence Hub data.
bbcp - a point-to-point network file copy application from NERSC
lftp - can transfer files via FTP, FTPS, HTTP, HTTPS, FISH, SFTP, BitTorrent, and FTP over HTTP proxy.
gcloud - Google Cloud command line interface, including the gsutil command
NBIA Data Retriever - a tool for downloading data from the TCIA Data Portal , installed under
/opt/NBIADataRetriever
rclone - rsync for cloud storage
Globus - If the other side support Globus
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For graphical tools, see the documentation that came with the program. Also, see our instructions on how to use these tools with two-factor auth. Many tools will by default copy somewhere in your /home
directory, which has a small 100GB 100GiB storage quota. Make sure to explicitly specify whether you want to copy there or to a different location like: /n/scratch3/users/m/mfk8/
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The O2 login nodes and most compute nodes do not currently mount /n/files
. There are 2 ways to access this filesystem from O2:
Use O2's dedicated file transfer servers:
SSH login to the hostname: transfer.rc.hms.harvard.edu . You will be connected to a system which has access to
/n/files
.Once logged in, just run your commands (e.g.
rsync
,scp
,cp
) normally without using sbatch.Transfer servers can not submit jobs to the cluster, and research applications (modules) are not available from those systems.
If you have a batch job workflow that must use /n/files , you can request access to be able to use the "transfer" job partition. This partition has access to a few lower performance compute nodes which mount /n/files . They are only recommended when using the transfer servers is not an option, as these nodes are slower and generally less available.
Using the transfer job partition
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