Re: [Avogadro-Discuss] XTALOPT hangs if server connection lost
Unfortunately the CLI is not correct! I get: Warning: Optimizer::Update: Error loading structure at /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/ and when I look at that directory I find on the client: ls /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/ 3x00051 job.sh structure.state xtal.in ucfbcoh@tomcat:~/src/xtalopt2/build$ ls /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/3x00051/ job.sh pwscf.save xtal.in xtal.out I had fixed this also long ago, but it is back again. It is storing one directory down. Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Fri, Aug 21, 2015 at 1:48 AM, Ronald Cohen rco...@carnegiescience.edu wrote: I switched to the CLI ssh and so far no problems! I guess it is a problem with sshlib. Ron Sent from my iPad On Aug 17, 2015, at 9:41 AM, David Lonie david.lo...@kitware.com wrote: On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu 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 ucfb...@legion.rc.ucl.ac.uk:22 Warning: Cannot connect to ssh server If you're having issues resolving hosts, there's not much that can be done about that from the XtalOpt side of things. Might be VPN related? Dave -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] XTALOPT hangs if server connection lost
Hi Ron, We did actually fix this issue for the new update that is coming soon. Let me know if you have any issues with your fix and I can give you the updated version of that file. Thanks, Patrick On Friday, August 21, 2015, Cohen, Ronald rco...@carnegiescience.edu wrote: I think the attached code I edited fixes this problem. Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu javascript:; office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Fri, Aug 21, 2015 at 12:08 PM, Cohen, Ronald rco...@carnegiescience.edu javascript:; wrote: Unfortunately the CLI is not correct! I get: Warning: Optimizer::Update: Error loading structure at /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/ and when I look at that directory I find on the client: ls /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/ 3x00051 job.sh structure.state xtal.in ucfbcoh@tomcat:~/src/xtalopt2/build$ ls /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/3x00051/ job.sh pwscf.save xtal.in xtal.out I had fixed this also long ago, but it is back again. It is storing one directory down. Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu javascript:; office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Fri, Aug 21, 2015 at 1:48 AM, Ronald Cohen rco...@carnegiescience.edu javascript:; wrote: I switched to the CLI ssh and so far no problems! I guess it is a problem with sshlib. Ron Sent from my iPad On Aug 17, 2015, at 9:41 AM, David Lonie david.lo...@kitware.com javascript:; wrote: On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu javascript:; 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 ucfb...@legion.rc.ucl.ac.uk:22 Warning: Cannot connect to ssh server If you're having issues resolving hosts, there's not much that can be done about that from the XtalOpt side of things. Might be VPN related? Dave -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net javascript:; https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] XTALOPT hangs if server connection lost
No, it is a xtalopt error. There is no problem for any other application or the command line. I suspect the call is timing out (in a very short amount of time) and not trying again. Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Mon, Aug 17, 2015 at 9:41 AM, David Lonie david.lo...@kitware.com wrote: On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu 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 ucfb...@legion.rc.ucl.ac.uk:22 Warning: Cannot connect to ssh server If you're having issues resolving hosts, there's not much that can be done about that from the XtalOpt side of things. Might be VPN related? Dave -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] XTALOPT hangs if server connection lost
On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu 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 ucfb...@legion.rc.ucl.ac.uk:22 Warning: Cannot connect to ssh server If you're having issues resolving hosts, there's not much that can be done about that from the XtalOpt side of things. Might be VPN related? Dave -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] XTALOPT hangs if server connection lost
I can do it myself againi guess my changes from some years ago didn't stick. What is needed is to loop with say 60 second sleeps after testing for success from ssh. Even if a server or network is down for hours then xtalopt won't skip a beat and jobs will complete and be tallied from the server as soon as the network comes back. Sincerely, Ron Sent from my iPad On Aug 17, 2015, at 9:41 AM, David Lonie david.lo...@kitware.com wrote: On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu 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 ucfb...@legion.rc.ucl.ac.uk:22 Warning: Cannot connect to ssh server If you're having issues resolving hosts, there's not much that can be done about that from the XtalOpt side of things. Might be VPN related? Dave -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
