SSH From Matlab (updated) + SFTP/SCP

Hi, I'm enjoying playing around with this function but I can't get it to do what I want. I was wondering if maybe I should be using an alternative. I've developed a series of scripts to analyse some model outputs and the way the script works is by looking at which directory is the newest and then taking information from the filenames to determine automatically quite a lot of information about the runs I've done. However, I'm now doing some runs on a computer other than my own that I only have remote access to, and, which, doesn't have matlab.

So, is there anyway I can get matlab to see the directories on the remote machine as if it was a local directory so that I can use functions such as dir, textscan and cell2mat to extract the model information from the remote directories?

Any assistance would be greatly appreciated.

Nick

After SSHing into the remote computer, I am trying to run the byobu command so I can run the remote in root. I use the command below:
[conn, res] = sshfrommatlabissue(conn,'byobu') and the result returns ']0;roboard@a-laptop - byobuMust be connected to a terminal.'. I was hoping you could give me some insight as how to run byobu so I can run the remote in root.

Thanks,
Matt

Hi, great submission!
I use this package to run simple commands on a condor cluster. But there appear to be certain commands which when run using an external SSH tool, print commands to the prompt screen

In particular: condor submitters -username

When I try to run that command from SSH_MATLAB, obviously, it will not give me any feedback, or command response.

Is there a setting somewhere I can adjust, that would allow for me to see the same feedback at my MATLAB Command Window, that I see when I run condor submitters from the SSH GUI?

Hi Roel,

It is difficult, but I don't think impossible to connect through two machines.

If you're able to run Matlab on the first machine, you should be able to use this package to ssh into the second machine.

Otherwise, you can use public key authentication on the first machine and a script to automatically connect and execute your function.

This hacks are needed because the SSH package for matlab can only execute commands and cannot run interactively.

This files look great! However, when I try to use sshfrommatlab, I get,

Error using ch.ethz.ssh2.Connection/authenticateWithPassword
Java exception occurred:
java.io.IOException: Password authentication failed.
at ch.ethz.ssh2.auth.AuthenticationManager.authenticatePassword(AuthenticationManager.java:328)
at ch.ethz.ssh2.Connection.authenticateWithPassword(Connection.java:311)
Caused by: java.io.IOException: Authentication method password not supported by the server at this stage.
at ch.ethz.ssh2.auth.AuthenticationManager.authenticatePassword(AuthenticationManager.java:298)
... 1 more

Error in sshfrommatlab (line 53)
isAuthenticated = channel.authenticateWithPassword(userName,password);

And I am sure that my username, server and password are ok... :(

When I try to execute the scptomatlab function, I get an error message associated with this portion of code:

import ch.ethz.ssh2.SCPClient;
import ch.ethz.ssh2.SCPClient;
import ch.ethz.ssh2.Session;

which says

??? Error: File: scptomatlab.m Line: 23 Column: 8
Arguments to IMPORT must either end with ".*"
or else specify a fully qualified class name: "ch.ethz.ssh2.SCPClient" fails
this test.

If I add .* to the end of each one and then execute, this error appears:

??? Error using ==> scptomatlab at 45
Error: SCPTOMATLAB could not connect to the remote machine

followed by the host name I’m trying to connect to. Do you know what is going wrong? This code has worked for my coworker, so I know that the hostname must be correct.

Rebecca

Thank you very much David. This helped me out a bunch!

Hi David. If this helps, the user is trying to connect to a BeagleBoard xM. I am ssh in as root so we should have root privelages. Through other methods of ssh (like putty), I have been able to connect to the remot host and send these commands as well so that should be verified.

Initially, when connected, I sent these commands (which worked correctly):

[conn,res] = sshfrommatlabissue(conn,'pwd');disp(res);
[conn,res] = sshfrommatlabissue(conn,'cd ..; ls');disp(res);

and then I tried to run a program, but I was given a null return and send back to root's home directory. When I first started to run a command, besides trying to shutdown/restart, I tried to run a program with this following command:

[conn,res] = sshfrommatlabissue(conn,'./Program');disp(res);

Once again, I was given a null return. Then I tried to restart with the "shutdown -r now" which I have always done to restart, and a "shutdown -h now" to shutdown. After multiple tries, I was unable to restart the computer. I really appreciate this help!

Hi Trennt, Are you sure the user is authorized to shutdown the computer? Have you verified this command "shutdown -r now" works from the same computer using an ssh2 client? Also, please make sure you have a made a connection object correctly. Have you tried running "hostname" to if you have made a good connection? I expect if you can verify this, you should be able to restart the machine.

I always thought the command was shutdown -r 0

Hi Sébastien, you should check out the v2 of this file SSH/SFTP/SCP For Matlab (v2)at the top. It has public key support for sftp and scp functions.

I am trying to connect to an external server to call parallel simulations directly from a matlab GUI, and then fetch the results back to my computer. The sshfrommatlab package works well to make an ssh connexion to another personal computer, but I got the following error when trying to connect to the server:

Error using ch.ethz.ssh2.Connection/authenticateWithPassword
Java exception occurred:
java.io.IOException: Password authentication failed.
at ch.ethz.ssh2.auth.AuthenticationManager.authenticatePassword(AuthenticationManager.java:318)
at ch.ethz.ssh2.Connection.authenticateWithPassword(Connection.java:311)
Caused by: java.io.IOException: Authentication method password not supported by the server at this stage.
at ch.ethz.ssh2.auth.AuthenticationManager.authenticatePassword(AuthenticationManager.java:288)
... 1 more

Error in sshfrommatlab (line 53)
isAuthenticated = channel.authenticateWithPassword(userName,password);

I don't understand. I am sure I use the correct username, host name and password. I usually don't get this error when I try to connect via the computer's common line using the ssh command and a password. I am currently working on mac OS X and the server uses linux (SUSE).

Thank you for your help

on trying to use the sftp, i get:

sftpcl = SFTPv3Client(channel)
Java exception occurred:
java.io.IOException: Illegal sftp packet len: 757951599

at ch.ethz.ssh2.SFTPv3Client.receiveMessage(SFTPv3Client.java:245)

at ch.ethz.ssh2.SFTPv3Client.init(SFTPv3Client.java:861)

at ch.ethz.ssh2.SFTPv3Client.<init>(SFTPv3Client.java:108)

at ch.ethz.ssh2.SFTPv3Client.<init>(SFTPv3Client.java:119)

please help . . . .

Got it sorted, thanks! Works fine now.

Hi Sophie,

Have you tried running
sshfrommatlabinstall(1)
once
and then

sshfrommatlabinstall
every time you restart matlab, but before you run sshfrommatlab
?

Hi Dmoninic, I cannot tell what's wrong from your above statement. Have you verified that your connection works with a simple "ls"? Also, ssh2 does not open a bash or csh, meaning any parameters you expect (.bash_profile) must be setup interdependently. i.e. "source ~/.bash_profile; ./script-parameter"

I tried to execute script using sshfrommatlabissue(channel,''./script -parameter); but it doesn't work.
What's the problem here?

Thank you!

Is there a way to change the port?

Because of the nested try catch in sshfrommatlab.m, the error 'SSHFROMMATLAB could not find the SSH2 java package' is always thrown, even if the actual error is that the connection was unsuccessful. This could be fixed with something like:

%
% Build the connection using the JSch package
%
try
import ch.ethz.ssh2.*;
try
channel = Connection(hostName);
channel.connect();
catch
error('SSHFRMMATLAB:noconnection', ...
['Error: SSHFROMMATLAB could not connect to the remote machine %s ...'],...
hostName);
end
catch

LE = lasterror;

if isequal(LE.identifier, 'SSHFRMMATLAB:noconnection')
rethrow(LE);
else
error('Error: SSHFROMMATLAB could not find the SSH2 java package');
end

end

Hi David, I am having a problem using the
sftpfrommatlab. I used the following commands the I get the errors bellow:
>> h = sshfrommatlab('user','host','pswd');
>> sftpfrommatlab('user','host','pswd','C:\GPS_POS_1.dat','user@user-dir/dir/dir/')

??? Java exception occurred:
ch.ethz.ssh2.SFTPException: No such file (SSH_FX_NO_SUCH_FILE: A reference was made to a file which does not
exist.)

at ch.ethz.ssh2.SFTPv3Client.openFile(SFTPv3Client.java:1198)

at ch.ethz.ssh2.SFTPv3Client.createFile(SFTPv3Client.java:1071)

at ch.ethz.ssh2.SFTPv3Client.createFile(SFTPv3Client.java:1052)

Error in ==> sftpfrommatlab at 67
localf=sftpcl.createFile(remotefilename);

Do you have any idea whatcould be the source of such error?

Great tool thanks, it work with the beta 251 build which I accidentally downloaded too.

Hi Koenraad, unfortunately, the SCP library doesn't support wildcards. I would ...
nevermind, your workaround is what I would suggest. Nice work!

I was using scptomatlab to copy multiple files.

localFolder= c:\temp\
remotefilename = /tmp/*

where /tmp/ on the remote machine has multiple files (more than 100)

but only one file is copied to my c:\temp

Could it be that the tool does not support to copy multiple files?

oops, the file was not updated correctly, you should find it shortly. The file you're looking for is sshfrommatlabissue_dontwait.m

Thanks. I will wait for the new additions and then give you a 5 star rating. Your programs have been incredibly useful.

Hi David

I am launching a batch job on a unix machine. When I launch it from this program it hangs up because there are so many jobs I am sending. I would rather like to launch the job in the background and then check periodically whether it has finished. I tried all sorts of syntax, but it just doesn't seem to work. I will keep on trying.

Hi David

I managed to get the commands to work, but woudl like to be able to launch a batch command from SSH. I noticed that you can use a -f option in ssh. Is this functionality available in your routines. I have tried the nohup option and the & operator at the end of the command, to no avail.

Hi David

The tool is working very well, but now I am trying to run a Korn shell script to no avail. I noticed the comments above about exporting the environment variables etc. Can you please explain how you do this?

Thanks

Etienne

Jonathan, to use sshfrommatlab.m with a private/public key you can try this one:

remove/comment the following lines:
% isAuthenticated = channel.authenticateWithPassword(userName,password);
% if(~isAuthenticated)
% error...
% (['Error: SSHFROMMATLAB could not authenticate the',...
% ' SSH connection...']);
% end

and write instead:

id_dsa = sprintf('<your_dsa_or_rsa_key>')
isAuthenticated = channel.authenticateWithDSA(userName,id_dsa, password)

For me it works.
Erika

First Thomas, I have no idea what's causing the problem. You should verify that you can ssh to this local machine.

There is no private/public key support at the moment, but that is a limitation of the matlab code, not the SSH library.

Finally, Clark, this is an SSH/SFTP tool and it appears to me that you're trying to SSH to the host. There is not FTP support in this version. This is either built into Matlab, or passive mode support is provided by another matlab central upload.

Hi,

I am able to use SFTP functionality with password authentication, but not with public key authentication. Can some one confirm for me that this is indeed a limitation of the code, and not an error on my part? If so, are there plans to add this functionality?

Thanks for the great tool!
Yoni

Hi, I have some trouble with using sshfrommatlab.m. I am not able to make the connection with remote host in my local network. When I enter "channel = Connection(hostName)" result is "channel = ch.ethz.ssh2.Connection@b243d7" - I think this is OK. But executing of next command "channel.connect()" gives error:

??? Java exception occurred:
java.io.IOException: There was a problem while connecting to PETER-NTB:22

at ch.ethz.ssh2.Connection.connect(Connection.java:753)

at ch.ethz.ssh2.Connection.connect(Connection.java:543)

Caused by: java.net.ConnectException: Connection timed out: connect

at java.net.PlainSocketImpl.socketConnect(Native Method)

at java.net.PlainSocketImpl.doConnect(Unknown Source)

at java.net.PlainSocketImpl.connectToAddress(Unknown Source)

at java.net.PlainSocketImpl.connect(Unknown Source)

at java.net.SocksSocketImpl.connect(Unknown Source)

at java.net.Socket.connect(Unknown Source)

at ch.ethz.ssh2.transport.TransportManager.establishConnection(TransportManager.java:342)

at ch.ethz.ssh2.transport.TransportManager.initialize(TransportManager.java:450)

at ch.ethz.ssh2.Connection.connect(Connection.java:697)

... 1 more

I am sorry, it is so long log... but after two-day thinking and trying I still cannot find how to make connection. I am sure that hostname, username and password are right. I tried use IP address (private 192.168.1.4) instead of hostname but result was the same. Is here anyone who could help me?

Hi: I am having some trouble. I am able to get the connection and issue an 'ls' command with the result being a listing of the contents of my home directory, however, when trying to 'cd' to any other directory I get an empty result and when I issue a subsequent 'ls' command I still get home contents. For example:

[conn,res] = sshfrommatlabissue(conn, 'ls'); disp(res);
[conn,res] = sshfrommatlabissue(conn, 'cd ..'); disp(res);
[conn,res] = sshfrommatlabissue(conn, 'ls'); disp(res);

This results in the same listing before and after the cd command.

I am running off a Mac OSX Matlab 2009b version. Thanks.

Hi,
very nice tool. I need to specify a proxy server (socks 5) and a port number to connect to a ssh server because I'm inside a company network. Putty e.g. give you the possibility to specify a proxy.
Matlab itselfs only allows to configure proxys for Internet-connection, but not for ssh

Philip

Ronald, the issue stems from the fact you are not getting a bash (or tcsh) shell, and are therefore not getting any of the typical variables. This was a problem for me too, and I had to create a file that "exports" the variables, and after I log in, I include a "source" command before I issue any statements. It's kinda a pain, but that's the way it has to be. You may want to check the FAQ I'm posting in the next reply.

This works great for running defaul commands, but I noticed that I am missing all of my custom environment variables when creating an SSH session from MATLAB. Do you know why some of the environment variables are being dropped?

Note: I am able to use PuTTY on the same machine and get the full list of environment variables.

I really appreciate the version, and I did learn a lot about using the java package to control SSH. Again, thank you very much,

I have another question though. I've been trying to use this file to connect to a host, and then trying to ssh into another remote (only connected to the aforementioned host). The problem is that whenever the server's response is a question (e.g. RSA key question, or password), the sshfrommatlabissue does not grab the question (it's just an empty string), and there's no way to issue an answer.

So for example, if I connect to a server using "sshfrommatlab", and then use "sshfrommatlabissue(conn, 'ssh 155.226.32.136')"
, I only get back an empty string as result, and I can't answer the password challenge. Would there be any way to accomplish this?

(I've looked at the code, and it seems like "sshfrommatlabissue" always close session...maybe that's the reason? I would really appreciate any help! )

Hi, I removed the hidden MacOS files. Also to transfer files back locally, I added the SCP function. I use this to transfer files back locally.

Looks like this could be very useful, especially for initiating parallel processing jobs on a cluster of servers.

One quick suggestion, try to be careful to not include the MaxOS hidden files (__MACOSX, .DS_Store, etc) in the zip file. Kinda annoying to go thru and clean all of those out. Thanks!