I tried building the ssh CLI interface and it builds but fails with: ead is QThread(0x2aa3ca0) avogadro: symbol lookup error: /home/ucfbcoh/lib/avogadro/1_1/contrib/xtalopt.so: undefined symbol: _ZN9OpenBabel12OBConversion11SetInFormatEPNS_8OBFormatE
By the way, all the Qt errors make it very hard to find the real errors --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 [email protected] office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Thu, Aug 20, 2015 at 7:57 AM, Cohen, Ronald <[email protected]> wrote: > I can't get a job to work for more than a few hours when it fails with: > > SSHConnectionLibSSH::isConnected(): server timeout. > > SSH error: Failed to resolve hostname legion.rc.ucl.ac.uk (Name or > service not known) > > "Cannot connect to ssh server [email protected]:22" > > Warning: "Cannot connect to ssh server" > > SSHConnectionLibSSH::isConnected(): server timeout. > > SSH error: Failed to resolve hostname legion.rc.ucl.ac.uk (Name or > service not known) > > "Cannot connect to ssh server [email protected]:22" > > Warning: "Cannot connect to ssh server" > > Meanwhile we had ping running in another window and it showed no > errors and loss of network or nameservice. > > I think the host just didn't respond to the ssh call immediately and > the call timed out and xtalopt then dies. > I know how to fix this but have to find time. > > Ron > > --- > Ronald Cohen > Geophysical Laboratory > Carnegie Institution > 5251 Broad Branch Rd., N.W. > Washington, D.C. 20015 > [email protected] > office: 202-478-8937 > skype: ronaldcohen > https://twitter.com/recohen3 > https://www.linkedin.com/profile/view?id=163327727 > > > On Sun, Aug 16, 2015 at 4:35 PM, Patrick Avery <[email protected]> wrote: >> Hey Ron, >> >> So, we have been making several updates for a new release that is coming out >> soon. We MIGHT have already fixed this issue (although I don't recall >> explicitly fixing it). But I ran a test today to see what would happen. Let >> me know if you think this test adequately mimics your glitch that you found: >> >> I submitted a couple of jobs with XtalOpt, then disconnected my wifi for >> about 20 seconds (so the connection to the remote cluster would fail). Then, >> I reconnected it, and it read the output from the runs and updated >> successfully - no job restarts. >> >> I tried it again for a longer period of time (I disconnected the wifi for >> about 3 minutes). After several server timeouts (and it mentioned "Warning: >> "Cannot connect to ssh server"" three times in that time period), I >> reconnected the wifi. Unfortunately, the run did not continue - it appeared >> to be frozen (something we may want to fix). But after exiting out and >> resuming the run, it took it a while, but it updated the structures >> successfully from the output - no job restarts. >> >> Thanks, >> Patrick >> >> On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald <[email protected]> >> wrote: >>> >>> I had fixed this in an earlier version but don't remember how. >>> Sometimes the connection to the server or nameserver goes down (about >>> once a day) and I see an error like: >>> >>> SSHConnectionLibSSH::isConnected(): server timeout. >>> SSH error: Failed to resolve hostname legion.rc.ucl.ac.uk (Name or >>> service not known) >>> "Cannot connect to ssh server [email protected]:22" >>> Warning: "Cannot connect to ssh server" >>> >>> However, jobs are still running on the server and it comes back, but >>> in the meantime xtalopt hangs and never recovers without a restart, >>> and loss of the running jobs. It should just wait until the server >>> connection comes back. >>> >>> Ron >>> >>> --- >>> Ronald Cohen >>> Geophysical Laboratory >>> Carnegie Institution >>> 5251 Broad Branch Rd., N.W. >>> Washington, D.C. 20015 >>> [email protected] >>> office: 202-478-8937 >>> skype: ronaldcohen >>> https://twitter.com/recohen3 >>> https://www.linkedin.com/profile/view?id=163327727 >> >> ------------------------------------------------------------------------------ _______________________________________________ Avogadro-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-devel
