Archive for November, 2009

Problems continuing calculations on using Schrödinger checkpoint files.

Sunday, November 22nd, 2009

I recently helped identifying a problem with continuing calculations from a checkpoint file performed by desmond of the Schrödinger software portfolio. The error we got was

fail to extract simulation parameters from checkpoint file <filename>

It worked for a lot of people, but not for others. I searched high and low for differences:

  • Different unix environment settings.
  • Differnet MPI settings (intel mpi vs. gcc mpi vs. software mpi)
  • Different permission settings on home dirs
  • Differences in groupmembership between those who could continue calculations and those who couldn’t.
  • Performing the calculations on different nodes in the calculation clusters.

As it turned out it was neither of these points that was responsible for problems. Instead it was the use of non-english chars in the comment field in the /etc/password file for the users who could not continue the calculations from a checkpoint file. The fix for this is simple:

usermod -c "new name, only english chars" <userid>

Everything was fine after that.

passwd problem on nis master

Wednesday, November 4th, 2009

I was bitten lately by a problem of chaning passwords for users on a NIS master running RHEL 3. The actual error was

RPC: Can’t encode arguments
The password has not been changed on <nis master>.
passwd: Failed preliminary check by password service

I could not easily find anything on google about it. It took a while to figure out, so for reference I document my fix here. I merely removed the word ‘nis’ from /etc/pam.d/system-auth, and that seems to have solved the issue. It has worked previously with that word, so why it started to fail is beyond me, but who cares anyway.