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| abstract:farber:transfer [2018-05-23 11:41] – anita | abstract:farber:transfer [2021-12-01 11:10] (current) – anita |
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| ====== Transfer Files to/from Farber ====== | ====== Transferring files to/from Farber ====== |
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| | //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.</note> | <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.</note> |
| </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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| copies the ''fuelcell'' directory in your local current working directory into the ''/home/work/it_css/projects'' directory on the Farber cluster. The ''/home/work/it_css/projects'' directory on the Farber cluster must exist, and ''traine'' must have write access to it. | copies the ''fuelcell'' directory in your local current working directory into the ''/home/work/it_css/projects'' directory on the Farber cluster. The ''/home/work/it_css/projects'' directory on the Farber cluster must exist, and ''traine'' must have write access to it. |
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| //This section uses the wiki's [[:#documentation-conventions|documentation conventions]].// | |
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| ===== Copying files from the cluster ===== | ===== Copying files from the cluster ===== |
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| will copy the directory ''fuelcell'' on the Farber cluster into a new ''fuelcell'' directory in your local system's current working directory. (Note the final period in the command.) | will copy the directory ''fuelcell'' on the Farber cluster into a new ''fuelcell'' directory in your local system's current working directory. (Note the final period in the command.) |
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| //This section uses the wiki's [[:#documentation-conventions|documentation conventions]].// | |
| ===== Copying files between clusters ===== | ===== Copying files between clusters ===== |
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| will copy the directory ''fuelcell'' from Mills to a new ''fuelcell'' directory on Farber. | will copy the directory ''fuelcell'' from Mills to a new ''fuelcell'' directory on Farber. |
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| //This section uses the wiki's [[:#documentation-conventions|documentation conventions]].// | |