[R-sig-Debian] sprof works on your Debian/Ubuntu ?
Dirk Eddelbuettel
edd at debian.org
Sun Jun 28 22:04:58 CEST 2009
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!
| pauljohn at 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.
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