Problem with Miriad on Redhat EL5 OS

[bgaensler]

Hi all,

I maintain the Miriad installations at The University of Sydney. We have two sets of linux binaries -- Redhat EL5 OS and Redhat EL6 OS -- both hosted on the same filesystem. In the past, mirsync puts the relevant binaries into $MIR/linux/bin and $MIR/linux64/bin, respectively. To update Miriad, I log into an EL5 machine and run mirsync, and then log into an EL6 machine and run mirsync again.

Last week I ran 'mirsync' twice as usual, and everything updated normally. However, the EL5 OS version of Miriad is now no longer working, because 'uname -m' on an EL5 machine outputs 'x86_64'. This sets $MIRBIN to $MIR/linux64/bin, which in turn points to the EL6 binaries, which won't run on EL5. An example:

tycho: > ./invert
./invert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by ./invert)

If I manually change $MIRBIN to $MIR/linux/bin, it works fine.

(I am not sure what has changed, since this was all working fine until last week.)

How do I simultaneously maintain two sets of binaries and libraries, for EL5 and EL6, on the one file system?

regards
Bryan

[Mark.Wieringa]

Hi Bryan,

at the moment there are two binary miriad distributions available , 64 bit linux and 64 bit darwin/OSX. We used to have a 32 bit linux version ($MIR/linux/bin), but it was last updated (recompiled) two years ago, we also had a Solaris installation until recently, but it has now stopped as well, since ATNF no longer has any machines left that can build 32 bit linux or Solaris. If you still need installations on other architectures, you can install from source and build them yourself following the instruction on http://www.atnf.csiro.au/computing/soft ... tml#source.

As far as I know nothing has changed in the Miriad distribution setup in the last two weeks, maybe you were using a 32 bit machine to do the mirsync on EL5 before? You would have been getting an out of date version of miriad, but it might have worked with the old libc version on 32 bit machines. We've never supported EL5/EL6 specifically, just 32 bit and 64 bit linux, both with whatever debian version of linux atnf was running at the time.

Cheers,

Mark

[bgaensler]

Thanks Mark.

So is there a way to simultaneously support EL5 and EL6 versions within the same Miriad installation, in the same way that, say, linux64 and darwin_x86_64 binaries and libraries can both simultaneously sit within the same $MIR directory tree?

cheers
Bryan

[ste616]

Hi Bryan,

It sounds like you are running 64 bit installations of Redhat for both EL5 and EL6, but EL5 doesn't have the prerequisite version of GLIBC. As Mark said you won't have the latest version of Miriad, but to make it work like you're used to, I would recommend switching your test case from "uname -m" to "uname -r". There should be a difference between EL5 and EL6 from the output of this command (according to the web, EL5 should return 2.6.18-something and EL6 should return 2.6.32-something) and using that to set the $MIRBIN directory.

To do this easily, I would alter the $MIR/scripts/mirarch script. Currently, starting at line 12 it looks like:

Code: Select all

  case "$MIRARCH" in
  Linux)
    case `uname -m` in
    *86)
      MIRARCH=linux
      ;;
    *86_64)
      MIRARCH=linux64
      ;;
    esac
    ;;

You could change this to:

Code: Select all

  case "$MIRARCH" in
  Linux)
    case `uname -r` in
    2.6.18*)
      MIRARCH=linux
      ;;
    2.6.32*)
      MIRARCH=linux64
      ;;
    esac
    ;;

I think this would solve your immediate issue.

[bgaensler]

Thanks Jamie. But based on what Mark said, is it right that this would then mean EL5 would be using a set of binaries that are ~2 years old?

If I build binaries for EL5 and EL6 manually, does that mean I won't be able to use mirsync to update them, and I will need to re-install and re-build everything from scratch every time I want an update?

Is there any chance that CSIRO can add an extra build on EL5 so that mirsync will update automatically for both EL5 and EL6?

cheers
Bryan

[Mark.Wieringa]

Hi Bryan,

it's not quite that bad, once you've set it up to build it successfully once, you can just use a daily cronjob to do a mirsync -c for the new source code and rebuild. These days miriad doesn't change that often, so most days nothing will need to be done. We don't have EL5 (or 6) at ATNF, all our linux boxes run versions of debian more recent than EL5, so we can't really built it for you.

Cheers,

Mark

[ste616]

Hi Bryan,

As Mark said, you can use "mirsync -c" (or even "mirimport") to get source code changes, and then rerun "make" which will only remake the changed code.

But I don't think this will entirely solve your problem, which is that you're running two different distributions, both 64 bit, but with different underlying libraries. I think your best best is to use the older distribution to do the building, since its likely that the libraries in EL6 are backwards-compatible with EL5. I would start by testing this theory: download the latest Miriad source, compile it on an EL5 box, and test that it runs on both EL5 and EL6.