Problems running MARK in clustered Linux environment

[BTO_IY]

Hi,
I'm hoping someone can offer some help advise in regard to running MARK (and RMark) on a clustered 64bit Linux environment.

We use Condor (http://research.cs.wisc.edu/htcondor/) on a cluster of servers for running R jobs and we are seeing problems when multiple R jobs which use RMark to call MARK are run on the same server at once.

For example we have a user trying to run multiple jobs on one server at the same time which leads to 1 job succeeding and the others failing. As each process should be separate this leads me to believe that the problem lies with some kind of file lock which MARK (or RMark) creates while it is running on a server (possibly a temp file which doesn't have a unique name?).

Any help/advice appreciated.

Thanks in advance.

[jlaake]

Unless you are using an old version of RMark, all files are uniquely named so that mark,wrapper,parallel will work. Did you see Evan's note about not using the Linux MARK version from the other day? What version of RMark are you using?

--jeff

[BTO_IY]

Unless you are using an old version of RMark, all files are uniquely named so that mark,wrapper,parallel will work. Did you see Evan's note about not using the Linux MARK version from the other day? What version of RMark are you using?

--jeff

Hi Jeff,
We're using RMark version 2.1.0

Do you mean this post about the Linux version being "quite out of date"? viewtopic.php?f=21&t=2422&p=7615#p7615

If we aren't supposed to be using the Linux version of then can anyone suggest an alternative? Do you know what (if any) the plans are for updating the Linux version of MARK?

Cheers.

[cooch]

Unless you are using an old version of RMark, all files are uniquely named so that mark,wrapper,parallel will work. Did you see Evan's note about not using the Linux MARK version from the other day? What version of RMark are you using?

--jeff

Hi Jeff,
We're using RMark version 2.1.0

Do you mean this post about the Linux version being "quite out of date"? viewtopic.php?f=21&t=2422&p=7615#p7615

If we aren't supposed to be using the Linux version of then can anyone suggest an alternative? Do you know what (if any) the plans are for updating the Linux version of MARK?

Cheers.

The online version isn't 'buggy', just out-of-date. It is no longer maintained (in fact, I'm just going to take the page down entirely, within the next few minutes). There is no immediate alternative.

Sometime this summer I'll compile the latest and greatest for Linux and (perhaps) Mac. Not until then.

[jlaake]

Based on my notes, 2.1.0 should not have the problem with conflicting filenames. But on the off chance that I made a fix and forgot to document, please update to 2.1.4 and try. Sorry I didn't mean to imply Linux mark.exe was buggy. Just that Evan recommended not using it but as long as you look at version dates and changes you may be just fine. Or you can wait until this summer as Evan noted. But in the meantime, see if you can get it to work with RMark 2.1.4 and let me know the outcome.

Evan, maybe move this discussion to the RMark sub-forum.

--jeff

[cooch]

Evan, maybe move this discussion to the RMark sub-forum.

--jeff

Done.