Hi Alan and everybody and thanks for your reply, I subscribed to the list but am not getting the messages (no it's not set to digest), so I've pasted your replies below. Please cc me in replies.
2011-05-13 12:37, Daniel Lundin wrote: > Hi, > > I have just started looking at Taverna (2.2.0 on Linux/Java 6 (I've > tried both openjdk and sun)). The first things I'd like to get running > are invocation of jobs via ssh, but I've failed so far. > > I've managed to get a call to a test script on my local machine to work, > but not on a remote machine via ssh. I've looked in the docs and > searched the mailing list archives but to no avail. I have a set of > questions and observations: > > 1. I can do a test connect from "Configure UseCase invocation/Configure > ssh invocation/Add a new..." dialog. > A: Did you do "Save and close" in that dialog? Yes, and the entry "localhost" appears in the "Ssh worker nodes" list. It's still there after I close and reopen the configure dialog. > 2. Running a workflow with the ssh worker from 1 doesn't work, though it > appears that the ssh connection works (at least I get no error dialog > nor error message in the log). I click run and then it runs (at least > for an hour) until I cancel the job. The connection is not recorded in > the taverna-2.2.0.log. See attached log file. > A: Can you check what is in the files usecase-method.conf and usecase-ssh.conf in Taverna's home directory? The home directory is probably .taverna-2.2.0 in your own home directory. The usecase-method.conf contains only "ssh", while the usecase-ssh.conf looks like this: localhost 22 user pass keyfile /tmp/ A: Have you looked on the remote machine to see if the working directory for the tool invocation was created and what it contains? /tmp exists of course, and when I change that to /tmp/taverna the connection test fails with a dialog saying: "2: No such file". No new files appear in the /tmp directory after I run the workflow. Sometimes a new dialog appears after I click run, prompting me to store the username and password in the credential manager. I saw part of a thread someplace which seemed to indicate that the usecase plugin doesn't use the credential manager(?). Storing seems to fail however, judging by the log message: Refused to register component as enter-username-and-password - not in map I'm a bit confused here. > 3a. Public key authentication doesn't work. I type in the passphrase to > the private key and immediately get a new dialog box prompting me for > the passphrase. > A: When exactly are you seeing these dialogs? Right after clicking the "Test" button. > 3b. The dialog box prompting me for the passphrase to the private key > shows what I'm typing in clear text, which doesn't seem right to me. I > also found that passwords are stored and viewable as clear text in the > credentials manager. > A: They are viewable in plain text inside Taverna but they are stored encrypted on the file system. The passwords are only viewable once you have entered the master password to the credential manager. Still a pity I think, since these passwords can be to systems with high security demands and it's easy to glean a password looking over the shoulder of someone. > What's the best way of debugging my connections? > A: At the moment there is no monitoring exposed. Do you think it should be? At debug level I'd like to see messages such as "successfully connected" or, in case connection failed, ideally an ssh traceback. Perhaps a call to pwd and env once logged in could be piped back to the client? (Requires a unix server of course.) BTW, when I switched to the Sun java implementation, I couldn't log in to the credentials manager. I even tried moving away the old .taverna-2.2.0 directory to force a reinitialisation. Setting the password seemed OK, but I still can't login. > /Daniel > /Daniel -- Daniel Lundin, Postdoc SciLifeLab, School of biotechnology, KTH Royal institute of technology, Stockholm, Sweden Postal address: Box 1031 171 21 Solna Sweden Visiting address: Tomtebodavägen 23 A Mobile: +46 (0)708 123 922 Email: [email protected] ------------------------------------------------------------------------------ Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/
