Re: [Rd] 00LOCK and nfs

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Thu, 10 Jun 2010 12:54:03 +0100 (BST)

Note that this patch is incomplete: there are three separate branches in install.packages() where R CMD INSTALL is used, and one already uses --pkglock. (So a short-term solution for you is to set Ncpus > 1.)

However, I think this request has been subsumed by a more general need to be able to pass options to INSTALL, and R-devel now has an INSTALL_opts argument to install.packages(). So I believe you could just use install.packages( ... , INSTALL_opts = "--pkglock") .

On Tue, 1 Jun 2010, Kasper Daniel Hansen wrote:

> Further experimentation using this patch to install.packages shows
> that I sometimes have remaining 00LOCK-pkgname directories after doing
> a massive update on a multi-user system with R installed on NFS.
> However, I have never had install.packages/update.packages stop midway
> because of an unremovable 00LOCK directory. I therefore consider the
> patch to be big improvement for people like me, having a multi-user R
> installed on NFS. Private followups to my original email shows that I
> am not the only one with this problem.

But I should point out that others with well-tuned NFS do not have the problem -- my sysadmins say that it was common with NFSv3 but they've hardly seen it with NFSv4.

> I would very much like the patch (or some variant hereof) to be
> considered for inclusion in R-devel.
>
> Kasper
>
> On Tue, May 18, 2010 at 11:59 AM, Kasper Daniel Hansen
> <kasperdanielhansen_at_gmail.com> wrote:
>> This is a follow-up to an old thread with kind of solution to the
>> 00LOCK problem on NFS.
>>
>> I have made a patch to install.packages to accept a new argument
>>  locktype = c("lock", "no-lock", "pkglock")
>> which is passed to R CMD INSTALL.  This addition might have
>> independent interest aside from the NFS problem, as it exposes
>> functionality from R CMD INSTALL to install.packages and the very
>> convenient update.packages.  Patches are at
>>  http://www.biostat.jhsph.edu/~khansen/packages2.R-patch
>>  http://www.biostat.jhsph.edu/~khansen/install.packages.Rd-patch
>> (patches to files in the utils package) and both
>>  R-devel (R version 2.12.0 Under development (unstable) (2010-05-17 r52025))
>> and
>>  R-2.11 (R version 2.11.0 Patched (2010-05-17 r52025))
>> passed make check-all with these two patches applied.  I thought about
>> adding a note describing my findings below to the details section, but
>> decided against it.
>>
>> Regarding the 00LOCK problem.  In my testing, using the patches above
>> and setting locktype = "pkglock", makes it possible to deal with the
>> NFS problem.  Specifically, I have not been able to make
>> update.packages() fail midway, due to a un-removable 00LOCK file
>> (which is not too surprising, as I now have a per-package lock).
>>
>> However, sometimes (but far less frequently than before), a
>> 00LOCK-pkgname directory remains after update/install.packages.
>> Sometimes this 00LOCK-pkgname directory does not contain any .nfs*
>> files (!?) and sometimes it does. For this reason, I still precede any
>> install/update.packages with a check for the existence of a
>> 00LOCK-pkgname directory and an attempt to remove it.
>>
>> The difference between using locktype = "pkglock" and not is
>> specifically that without, it was possible for update.packages to fail
>> midway even though there were no 00LOCK* files at the start of the
>> update process.
>>
>> Originally I hypothesized that the presence of the .nfs* files in the
>> 00LOCK directory had to do with synchronization issues between the
>> file server and the compute node.  In order to approach this I tried
>> to insert a
>>  system("sleep 10")
>> at the beginning of
>>  do_cleanup
>> in
>>  tools/R/install.R
>> but that did not work.
>>
>> Since the pkglock approach described above seems to solve this issue
>> for me, I have not pursued the synchronization issue further.
>>
>> Kasper
>>
>
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>

-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


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