Paul, On 28 June 2009 at 14:40, Paul Johnson wrote: | I'm asking here, rather than R-devel, because it seems to be a Linux | specific question and because I'm using Ubuntu-9.04.
Quite right! | I'm trying to profile an package, and got errors, so I decided to | follow BDR's (http://tolstoy.newcastle.edu.au/R/devel/06/02/4254.html) | example exactly, and got same problem. | | Can anyone replicate? | | $ sudo mkdir -p /var/tmp//usr/lib/R/library/stats/libs | | $ chown -R pauljohn.pauljohn /var/tmp/usr/lib/R | | $ export LD_PROFILE=/usr/lib/R/library/stats/libs/stats.so | | $ R | | ### in R session, type | >example(smooth.spline) | > q() | | Observe that does create the profile file: | | $ ls -la /var/tmp/usr/lib/R/library/stats/libs | total 20 | drwxr-xr-x 2 pauljohn pauljohn 4096 2009-06-28 14:26 . | drwxr-xr-x 3 pauljohn pauljohn 4096 2009-06-28 14:25 .. | -rw-r--r-- 1 pauljohn pauljohn 1356800 2009-06-28 14:26 stats.so.profile | | $ sprof /usr/lib/R/library/stats/libs/stats.so | /var/tmp/usr/lib/R/library/stats/libs/stats.so.profile | Inconsistency detected by ld.so: dl-open.c: 652: _dl_open: Assertion | `_dl_debug_initialize (0, args.nsid)->r_state == RT_CONSISTENT' | failed! | paulj...@pols124:Siena-Profiling$ sudo sprof /usr/lib/R/library/stats/ | libs/stats.so /var/tmp/usr/lib/R/library/stats/libs/stats.so.profile | Inconsistency detected by ld.so: dl-open.c: 652: _dl_open: Assertion | `_dl_debug_initialize (0, args.nsid)->r_state == RT_CONSISTENT' | failed! | | I Google to find one discussion that there's a bug in glibc that was | unearthed in 2008 and there was debate on whether "sprof" is now | deprecated. I don't understand the details completely. | (http://sources.redhat.com/ml/libc-alpha/2008-08/msg00013.html) | | Nobody on Ubuntu has tried it lately? | | Instead of sprof, I'll try oprofile, I guess. No, sorry. While I mention both sprof and oprofile in my tutorial notes on 'an introduction to high-performance computing with R', I actually stress Google's profiling tool with a worked example. On Debian and Ubuntu, this tool is in package libgoogle-perftools0 with frontend /usr/bin/google-pprof. The last release version of the tutorial notes is http://dirk.eddelbuettel.com/papers/bocDec2008introHPCwithR.pdf and there is likely to be an updated version following UseR 2009 and the tutorial session there. | I already tried to do this with gprof applied to the specific package, | but no profile is produced. I believe that means I need to re-build | all of R with the -pg flag, and I'm a bit reluctant to break | everything by doing that. Yes, rebuilding only the parts you want to profile using google-perftools is easier. Hope this helps, Dirk -- Three out of two people have difficulties with fractions. _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian