library(rmpi) crashing upon init

[Steffen Neumann]

Binary package hint: r-cran-rmpi

Hi,

this bug is related to #210273, but this time I can confirm this
with all-ubuntu packages using a current hardy -386 system,
whereas #210273 describes the same symptoms using
upstream versions R-2.7 and rmpi-0.5.6 directly.

I can provide whatever bug debugging information would help.

Yours,
Steffen

Subject: r-cran-rmpi: library(rmpi) crashing upon init
Package: r-cran-rmpi
Version: 0.5-5-1
Severity: grave
Justification: renders package unusable

-- System Information:
Debian Release: lenny/sid
  APT prefers hardy-updates
  APT policy: (500, 'hardy-updates'), (500, 'hardy-security'), (500, 'hardy-proposed'), (500, 'hardy-backports'), (500,
Architecture: i386 (i686)

Kernel: Linux 2.6.24-12-generic (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages r-cran-rmpi depends on:
ii libc6 2.7-9ubuntu2 GNU C Library: Shared libraries
ii libopenmpi1 1.2.5-1ubuntu1 high performance message passing l
ii openmpi-bin 1.2.5-1ubuntu1 high performance message passing l
ii r-base-core 2.6.2-2 GNU R core of statistical computin

R

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> library(Rmpi)
[samson:31510] *** Process received signal ***
[samson:31510] Signal: Segmentation fault (11)
[samson:31510] Signal code: Address not mapped (1)
[samson:31510] Failing at address: 0x8c93004
[samson:31510] [ 0] [0xb7f74440]
[samson:31510] [ 1] /usr/lib/libopen-pal.so.0(free+0xc4) [0xb7472ae4]
[samson:31510] [ 2] /usr/lib/libopen-pal.so.0 [0xb7458d3e]
[samson:31510] [ 3] /usr/lib/libopen-pal.so.0 [0xb74588ea]
[samson:31510] [ 4] /usr/lib/libopen-pal.so.0(lt_dlforeachfile+0x3d) [0xb74589dd]
[samson:31510] [ 5] /usr/lib/libopen-pal.so.0(mca_base_component_find+0x327) [0xb74611d7]
[samson:31510] [ 6] /usr/lib/libopen-pal.so.0(mca_base_components_open+0x18a) [0xb7461bca]
[samson:31510] [ 7] /usr/lib/libopen-rte.so.0(orte_gpr_base_open+0x7ed) [0xb74be70d]
[samson:31510] [ 8] /usr/lib/libopen-rte.so.0(orte_init_stage1+0x23c) [0xb74af98c]
[samson:31510] [ 9] /usr/lib/libmpi.so.0(ompi_mpi_init+0xd3) [0xb753d373]
[samson:31510] [10] /usr/lib/libmpi.so.0(MPI_Init+0x18f) [0xb756062f]
[samson:31510] [11] /usr/lib/R/site-library/Rmpi/libs/Rmpi.so(mpi_initialize+0x54) [0xb7752154]
[samson:31510] [12] /usr/lib/R/lib/libR.so [0xb7d28c1d]
[samson:31510] [13] /usr/lib/R/lib/libR.so(Rf_eval+0x714) [0xb7d4fd64]
[samson:31510] [14] /usr/lib/R/lib/libR.so [0xb7d508af]
[samson:31510] [15] /usr/lib/R/lib/libR.so(Rf_eval+0x542) [0xb7d4fb92]
[samson:31510] [16] /usr/lib/R/lib/libR.so [0xb7d51acf]
[samson:31510] [17] /usr/lib/R/lib/libR.so(Rf_eval+0x451) [0xb7d4faa1]
[samson:31510] [18] /usr/lib/R/lib/libR.so [0xb7d510b0]
[samson:31510] [19] /usr/lib/R/lib/libR.so(Rf_eval+0x451) [0xb7d4faa1]
[samson:31510] [20] /usr/lib/R/lib/libR.so(Rf_applyClosure+0x2ac) [0xb7d530fc]
[samson:31510] [21] /usr/lib/R/lib/libR.so(Rf_eval+0x349) [0xb7d4f999]
[samson:31510] [22] /usr/lib/R/lib/libR.so [0xb7d51b52]
[samson:31510] [23] /usr/lib/R/lib/libR.so(Rf_eval+0x451) [0xb7d4faa1]
[samson:31510] [24] /usr/lib/R/lib/libR.so [0xb7d510b0]
[samson:31510] [25] /usr/lib/R/lib/libR.so(Rf_eval+0x451) [0xb7d4faa1]
[samson:31510] [26] /usr/lib/R/lib/libR.so [0xb7d51b52]
[samson:31510] [27] /usr/lib/R/lib/libR.so(Rf_eval+0x451) [0xb7d4faa1]
[samson:31510] [28] /usr/lib/R/lib/libR.so [0xb7d510b0]
[samson:31510] [29] /usr/lib/R/lib/libR.so(Rf_eval+0x451) [0xb7d4faa1]
[samson:31510] *** End of error message ***
Segmentation fault

ProblemType: Bug
Architecture: i386
Date: Tue Apr 1 20:09:12 2008
DistroRelease: Ubuntu 8.04
ExecutablePath: /usr/bin/yelp
NonfreeKernelModules: fglrx
Package: yelp 2.22.0-0ubuntu3
PackageArchitecture: i386
ProcEnviron:
 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
 LANG=en_US.UTF-8
 SHELL=/bin/bash
SourcePackage: yelp
Uname: Linux 2.6.24-12-generic i686

[Steffen Neumann (sneumann)]

I just uploaded the apport crash report as bug #210409

Yours,
Steffen

[Christopher D. Long (galizur)]

I can confirm that the package r-cran-rmpi crashes on init on hardy-amd64 and also on hardy-386.

Further information:

1) compiling the rmpi source package using libmpich results in the exact same crash
2) compiling the rmpi source package using openmpi results in an rmpi library which doesn't crash upon loading, but which is non-functional

-Chris