[Rd] 00LOCK and nfs
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Jun 10 13:54:03 CEST 2010
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 >
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.
> 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
>> (patches to files in the utils package) and both
>> R-devel (R version 2.12.0 Under development (unstable) (2010-05-17 r52025))
>> 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
>> 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.
> R-devel at r-project.org mailing list
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
More information about the R-devel