[Openmd-users] clock skew

Dan Gezelter gezelter at nd.edu
Mon Jul 26 20:56:59 EDT 2010


Vamsee,

  The atom2md executable is only built if configure finds openbabel on your system.  Likewise the openmd_MPI executable is only built if the MPI includes and libraries are found.  Can you email us the configure line you entered and give us some more details about the system (OS/distribution, version, architecture, compilers) you are using?

You should also verify that your system has the prerequisites for OpenMD installed:  http://openmd.net/?p=56

And also that you are specifying the correct locations for the external libraries and compilers you want to use:  http://openmd.net/?p=83

Clock skew problems usually arise when the build directory resides on a file server that has a different clock setting than the machine doing the build.  As the files are written, they get a different time stamp than the build machine was expecting, and this can lead to some strange behavior by the make system.   If you can synchronize the clock on the build machine to the server (i.e. with "sudo rdate -s your.server.edu" or by using ntpd ) that will usually clear up clock skew issues in builds.

http://www.oreillynet.com/linux/cmd/r/rdate.html
http://www.brennan.id.au/09-Network_Time_Protocol.html

Best regards,

 --Dan Gezelter

On Jul 26, 2010, at 7:45 PM, Vamsee Voora wrote:

> Hi, 
> 
> I'm unable to make completely I believe. Since I always find an error: clock skew detected. Also, could you please tell me how to use atom2md. I don't find the executable in the after make install, may be because of the incomplete configure. 
> 
> At the end of the make install, I could run openMD, but not parallely. Do I have to use make -j instad of make . If you need I could send the log file. 
> 
> Thank you
> 
> Vamsee Voora
> Eberly 332
> Ken Jordan's Group: http://www.pitt.edu/~jordan/
> Department of Chemistry
> University of Pittsburgh
> PA 15260
> 
> _______________________________________________
> Openmd-users mailing list
> Openmd-users at maul.chem.nd.edu
> http://maul.chem.nd.edu/mailman/listinfo/openmd-users

***********************************************
  J. Daniel Gezelter
  Associate Professor and
  Director of Graduate Admissions
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
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