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Scientific Volume Imaging B.V.

Scientific Volume Imaging

Deconvolution - Visualization - Analysis


Running SCP in batch mode

SCP (Secure CoPy) and SSH in general can be used in batch mode without asking for passwords. That is very convenient for scripts.

Instructions to do so are a little ambiguous in different places . (See some references below). This worked in my case, using OpenSSH both in the server and the client.

Procedure

1. In these instructions, the user name is the same in both machines. Instructions for different user names could differ from these (but see note below!!!)

2. The user keys will be stored in ~/.ssh in both machines.

3. At the client, run:
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ssh-keygen -t dsa
to generate a key pair. Accept default options by pressing return. Specially, do not enter any passphrase. (Option -d seems to be an alias of -t dsa in some platforms).

4. Change the permissions of the generated .pub file to 600 by commanding chmod 600 id_dsa.pub

5. Copy the public key to the server with
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scp id_dsa.pub user@server:~/.ssh/authorized_keys
. (Caution: if that destination file already exists on the server, copy first to a different file foo and then append the contents with cat foo >> authorized_keys executed on the server).

6. Done!!! Verify that now you can connect directly from the client with ssh user@server without being prompted for a password or username.

7. If it doesn't work, verify that in the server your home directory, the ~/.ssh subdirectory, and the authorized_keys file do not have writing permissions to others. If they do, they won't be considered to grant access. You can correct this with something like:

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chmod 755 ~ 0
chmod 700 ~/.ssh
chmod 600 ~/.ssh/authorized_keys

8. If it still doesn't work, try changing the authorized_keys file name to authorized_keys2, or ask your system administrator what file name is ssh actually using.

9. If it worked, you can now run SCP in batch mode with the -B option, as in
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scp -B foofile user@server:~/foodir/
.

Notes

The name of the server must have been registered in the known_hosts. This can be done with a regular (with password) ssh connection, and accepting the host as known. Then, the host name should be the same as the one accepted!!! If you used user@server first, do not use user@server.domain.tk later on!!!

SSH protocol 2 is assumed in this procedure (it uses dsa keys). If your ssh configuration files (at /etc/ssh/) do not establish this as a default, you may have to force it with the -2 option of the ssh and scp. Moreover, if the default public key is not configured to be "id_dsa.pub" you can specify what key to use for identification with the -i option.

The same procedure worked fine when the username was different in both machines. I simply copied userA's public key at the end of userB's authorized_keys file, then I could login from my client as userA with ssh userB@server.

References

This article is part of the SVI-wiki on 3D microscopy and image restoration. Scientific Volume Imaging is the maker of the Huygens Software.