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| abstract:caviness:transfer [2020-11-10 10:42] – [Transferring files to/from Caviness] anita | abstract:caviness:transfer [2024-04-08 17:00] (current) – anita |
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| //The following sections use the wiki's [[:#documentation-conventions|documentation conventions]].// | //The following sections use the wiki's [[:#documentation-conventions|documentation conventions]].// |
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| <note important>Be careful about modifications you make to your startup files (e.g. ''.bash*''). Commands that produce output such as VALET commands may cause your file transfer command or application to not work. Log into the cluster with ''ssh'' to check what happens during login, and modify your startup files accordingly to remove any commands which are producing output and try again. See computing environment [[abstract:caviness:app_dev:compute_env#startup-and-logout-scripts|startup and logout scripts]] for help.</note> | <note important>Be careful about modifications you make to your startup files (e.g. ''.bash*''). Commands that produce output such as VALET or workgroup commands may cause your file transfer command or application to fail. Log into the cluster with ''ssh'' to check what happens during login, and modify your startup files accordingly to remove any commands which are producing output and try again. See computing environment [[abstract:caviness:app_dev:compute_env#startup-and-logout-scripts|startup and logout scripts]] for help.</note> |
| ===== Common clients for file transfer ===== | ===== Common clients for file transfer ===== |
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| | **hpn-scp**| Recommended for batch script use with at least 1Gbps network connection, and high speed disk drives at both source and destination. ((**hpn-** command-line variants are based on [[http://www.psc.edu/index.php/hpn-ssh|High Performance SSH/SCP - HPN-SSH]], OpenSSH 6.1 with hpn13v14 patch.)) | | | **hpn-scp**| Recommended for batch script use with at least 1Gbps network connection, and high speed disk drives at both source and destination. ((**hpn-** command-line variants are based on [[http://www.psc.edu/index.php/hpn-ssh|High Performance SSH/SCP - HPN-SSH]], OpenSSH 6.1 with hpn13v14 patch.)) | |
| | **rsync**| Most appropriate for synchronizing the file directories of two systems when only a small fraction \\ of the files have been changed since the last synchronization. | | | **rsync**| Most appropriate for synchronizing the file directories of two systems when only a small fraction \\ of the files have been changed since the last synchronization. | |
| | **Rclone**| [[https://rclone.org/|Rclone]] is a command line program to sync files and directories to and from popular cloud storage services. | | | **Globus**| [[https://www.globusonline.org/|Globus]] is web browser based and recommended for 'fire and forget' high-performance data transfers between systems within and across organizations.\\ See [[software:globus:globus|Globus]] for more details.| |
| | | **Rclone**| [[https://rclone.org/|Rclone]] is a command line program to sync files and directories to and from popular cloud storage services. \\ See [[abstract:caviness:transfer:rclone|Rclone on Caviness]] for setting up a remote configuration for Google Drive.| |
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| | [[http://filezilla-project.org/download.php?type=client|filezilla]] | Windows, Mac OS X, UNIX, Linux | | | [[http://filezilla-project.org/download.php?type=client|filezilla]] | Windows, Mac OS X, UNIX, Linux | |
| | [[http://cyberduck.ch/|cyberduck]] | Windows, Mac OS X (command line version for Linux) | | | [[http://cyberduck.ch/|cyberduck]] | Windows, Mac OS X (command line version for Linux) | |
| | | [[https://www.globusonline.org/|Globus]] | Web browser. See [[software:globus:globus|Globus]] for more details.| |
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| <note tip> | <note tip> |
| </note> | </note> |
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| <note warning>For **Windows** clients editing files on Windows desktops and then transferring them back to the cluster, you may find that your file becomes "corrupt" during file transfer process. The symptoms are very subtle because the file appears to be okay, but in fact contains ''CRLF'' line terminators. This causes problems when reading the file on a Unix cluster and generates very strange errors. Some examples might be a file used for submitting a batch job such as ''submit.qs'' and one you have used before and know is correct, will no longer work. Or an input file used for ABAQUS like ''tissue.inp'' which has worked many times before produces an error like ''Abaqus Error: Command line option "input" must have a value.''. | <note warning>For **Windows** clients editing files on Windows desktops and then transferring them back to the cluster, you may find that your file becomes "corrupt" during file transfer process. The symptoms are very subtle because the file appears to be okay, but in fact contains ''CRLF'' line terminators. This causes problems when reading the file on a Linux cluster and generates very strange errors. Some examples might be a file used for submitting a batch job such as ''submit.qs'' and one you have used before and know is correct, will no longer work. Or an input file used for ABAQUS like ''tissue.inp'' which has worked many times before produces an error like ''Abaqus Error: Command line option "input" must have a value.''. |
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| Use the utility ''file'' to check for ''CRLF'' line terminators and ''dos2unix'' to fix it, like this below | Use the utility ''file'' to check for ''CRLF'' line terminators and ''dos2unix'' to fix it, like this below |
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| <code bash> | <code bash> |
| scp -c arcfour -r fuelcell traine@caviness.hpc.udel.edu:/home/work/it_css/projects | scp -c arcfour -r fuelcell traine@caviness.hpc.udel.edu:/work/it_css/projects |
| </code> | </code> |
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| copies the ''fuelcell'' directory in your local current working directory into the ''/home/work/it_css/projects'' directory on the Caviness cluster. The ''/home/work/it_css/projects'' directory on the Caviness cluster must exist, and ''traine'' must have write access to it. | copies the ''fuelcell'' directory in your local current working directory into the ''/work/it_css/projects'' directory on the Caviness cluster. The ''/work/it_css/projects'' directory on the Caviness cluster must exist, and ''traine'' must have write access to it. |
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| ===== Copying files from the cluster ===== | ===== Copying files from the cluster ===== |
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| <code bash> | <code bash> |
| scp -c arcfour -r traine@caviness.hpc.udel.edu:/home/work/it_css/project/fuelcell . | scp -c arcfour -r traine@caviness.hpc.udel.edu:/work/it_css/project/fuelcell . |
| </code> | </code> |
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| ssh -A traine@farber.hpc.udel.edu | ssh -A traine@farber.hpc.udel.edu |
| cd archive/it_css/project | cd archive/it_css/project |
| scp -c arcfour -r fuelcell traine@caviness.hpc.udel.edu:/home/work/it_css/project/fuelcell | scp -c arcfour -r fuelcell traine@caviness.hpc.udel.edu:/work/it_css/project/fuelcell |
| </code> | </code> |
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| will copy the directory ''fuelcell'' from Farber to a new ''fuelcell'' directory on Caviness. | will copy the directory ''fuelcell'' from Farber to a new ''fuelcell'' directory on Caviness. |
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