Bug#690766: rheolef_6.1-2 is wrongly packaged in sid & wheezy ; a fix, as rheolef_6.1-3, is now available
saramito
Pierre.Saramito at imag.fr
Wed Oct 17 14:20:09 UTC 2012
Dear all,
Please find enclosed a detailled bug description.
The 6.1-2 rheolef library (sid & wheezy) is not usable as is
and a new version is required:
a fixed version of the rheolef debianization is available as 6.1-3 in svn.
Yours sincerely,
Pierre
--
Pierre.Saramito at imag.fr
Directeur de Recherche CNRS
Laboratoire Jean Kuntzmann, Grenoble, France
http://www-ljk.imag.fr/membres/Pierre.Saramito
---------------------------------------------------------------------------
detailled bug description and why a new version is required
---------------------------------------------------------------------------
lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description: Debian GNU/Linux testing (wheezy)
Release: testing
Codename: wheezy
sudo apt-get install rheolef librheolef1 librheolef-dev rheolef-doc
apt-cache policy rheolef
rheolef:
Installé : 6.1-2
Candidat : 6.1-2
Table de version :
*** 6.1-2 0
500 http://ftp.debian.org/debian/ testing/main amd64 Packages
100 /var/lib/dpkg/status
cp -a /usr/share/doc/rheolef-doc/examples .
cd examples
make dirichlet
mkgeo_grid -t 10 > square.geo
./dirichlet square.geo P1 > square.field
! load "./square.geo"
*** glibc detected *** ./dirichlet: free(): invalid pointer: 0x0000000000bc1b18 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x75b76)[0x7f7174b36b76]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f7174b3b8ac]
./dirichlet(_ZNSt10_List_baseISt4pairImN5boost3mpi7requestEESaIN7rheolef16geo_element_hackEEE8_M_clearEv+0x2b)[0x42a4cb]
/usr/lib/librheolef.so.1(_ZN7rheolef18hack_array_mpi_repINS_16geo_element_hackESaIS1_EE6resizeERKNS_11distributorERKNS_11geo_element14parameter_typeE+0x80)[0x7f7179cb11d0]
/usr/lib/librheolef.so.1(_ZN7rheolef7geo_repId11distributedE3getERNS_11idiststreamE+0x296c)[0x7f7179cbac6c]
/usr/lib/librheolef.so.1(_ZN7rheolef7geo_repId11distributedE4loadESsRKN5boost3mpi12communicatorE+0x271)[0x7f7179cbb5b1]
./dirichlet(_ZN7rheolef9geo_basicId11distributedEC2ESsRKN5boost3mpi12communicatorE+0x6f)[0x42e7ff]
./dirichlet[0x4220c3]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)[0x7f7174adfead]
./dirichlet[0x4227e5]
======= Memory map: ========
00400000-00444000 r-xp 00000000 08:06 34906153 /home/saramito/dvt/rheolef-examples-6.1/dirichlet
00644000-00645000 rw-p 00044000 08:06 34906153 /home/saramito/dvt/rheolef-examples-6.1/dirichlet
00645000-00647000 rw-p 00000000 00:00 0
007fc000-00c33000 rw-p 00000000 00:00 0 [heap]
7f7168000000-7f7168021000 rw-p 00000000 00:00 0
7f7168021000-7f716c000000 ---p 00000000 00:00 0
7f716dcee000-7f716dcfb000 r-xp 00000000 08:01 564010 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
7f716dcfb000-7f716defb000 ---p 0000d000 08:01 564010 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
7f716defb000-7f716defc000 rw-p 0000d000 08:01 564010 /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so
7f716defc000-7f716df06000 r-xp 00000000 08:01 564009 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
7f716df06000-7f716e105000 ---p 0000a000 08:01 564009 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
7f716e105000-7f716e107000 rw-p 00009000 08:01 564009 /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so
7f716e107000-7f716e120000 r-xp 00000000 08:01 563983 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
7f716e120000-7f716e320000 ---p 00019000 08:01 563983 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
7f716e320000-7f716e321000 rw-p 00019000 08:01 563983 /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so
7f716e321000-7f716e324000 r-xp 00000000 08:01 563982 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
7f716e324000-7f716e523000 ---p 00003000 08:01 563982 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
7f716e523000-7f716e524000 rw-p 00002000 08:01 563982 /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so
7f716e729000-7f716e72b000 r-xp 00000000 08:01 563980 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
7f716e72b000-7f716e92a000 ---p 00002000 08:01 563980 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
7f716e92a000-7f716e92b000 rw-p 00001000 08:01 563980 /usr/lib/openmpi/lib/openmpi/mca_coll_self.so
7f716e92b000-7f716e92e000 r-xp 00000000 08:01 563979 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
7f716e92e000-7f716eb2d000 ---p 00003000 08:01 563979 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
7f716eb2d000-7f716eb2e000 rw-p 00002000 08:01 563979 /usr/lib/openmpi/lib/openmpi/mca_coll_inter.so
7f716eb2e000-7f716eb32000 r-xp 00000000 08:01 563978 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
7f716eb32000-7f716ed32000 ---p 00004000 08:01 563978 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
7f716ed32000-7f716ed33000 rw-p 00004000 08:01 563978 /usr/lib/openmpi/lib/openmpi/mca_coll_hierarch.so
7f716ed33000-7f716ed3b000 r-xp 00000000 08:01 563977 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
7f716ed3b000-7f716ef3a000 ---p 00008000 08:01 563977 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
7f716ef3a000-7f716ef3b000 rw-p 00007000 08:01 563977 /usr/lib/openmpi/lib/openmpi/mca_coll_basic.so
7f716ef3b000-7f716ef46000 r-xp 00000000 08:01 563974 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
7f716ef46000-7f716f145000 ---p 0000b000 08:01 563974 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
7f716f145000-7f716f147000 rw-p 0000a000 08:01 563974 /usr/lib/openmpi/lib/openmpi/mca_btl_tcp.so
7f716f147000-7f716f1c7000 rw-p 00000000 00:00 0
7f716f1c7000-7f716f1cc000 r-xp 00000000 08:01 563973 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
7f716f1cc000-7f716f3cc000 ---p 00005000 08:01 563973 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
7f716f3cc000-7f716f3cd000 rw-p 00005000 08:01 563973 /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so
7f716f3cd000-7f716f3d0000 r-xp 00000000 08:01 563972 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
7f716f3d0000-7f716f5cf000 ---p 00003000 08:01 563972 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
7f716f5cf000-7f716f5d0000 rw-p 00002000 08:01 563972 /usr/lib/openmpi/lib/openmpi/mca_btl_self.so
7f716fc09000-7f716fc0d000 r-xp 00000000 08:01 563969 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
7f716fc0d000-7f716fe0c000 ---p 00004000 08:01 563969 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
7f716fe0c000-7f716fe0d000 rw-p 00003000 08:01 563969 /usr/lib/openmpi/lib/openmpi/mca_bml_r2.so
7f7170011000-7f7170026000 r-xp 00000000 08:01 564018 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
7f7170026000-7f7170225000 ---p 00015000 08:01 564018 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
7f7170225000-7f7170227000 rw-p 00014000 08:01 564018 /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so
7f7170446000-7f717044b000 r-xp 00000000 08:01 563987 /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so
7f717044b000-7f717064a000 ---p 00005000 08:01 563987 /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so
7f717064a000-7f717064b000 rw-p 00004000 08:01 563987 /usr/lib/openmpi/lib/openmpi/mca_dpm_orte.so
7f717064b000-7f717064e000 r-xp 00000000 08:01 564020 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
7f717064e000-7f717084d000 ---p 00003000 08:01 564020 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
7f717084d000-7f717084e000 rw-p 00002000 08:01 564020 /usr/lib/openmpi/lib/openmpi/mca_pubsub_orte.so
7f717084e000-7f7170850000 r-xp 00000000 08:01 563964 /usr/lib/openmpi/lib/libmca_common_sm.so.1.0.2
7f7170850000-7f7170a50000 ---p 00002000 08:01 563964 /usr/lib/openmpi/lib/libmca_common_sm.so.1.0.2
7f7170a50000-7f7170a51000 rw-p 00002000 08:01 563964 /usr/lib/openmpi/lib/libmca_common_sm.so.1.0.2
7f7170a51000-7f7170a53000 r-xp 00000000 08:01 564005 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
7f7170a53000-7f7170c52000 ---p 00002000 08:01 564005 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
7f7170c52000-7f7170c53000 rw-p 00001000 08:01 564005 /usr/lib/openmpi/lib/openmpi/mca_mpool_sm.so
7f7170c53000-7f7170c56000 r-xp 00000000 08:01 564004 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
7f7170c56000-7f7170e55000 ---p 00003000 08:01 564004 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
7f7170e55000-7f7170e56000 rw-p 00002000 08:01 564004 /usr/lib/openmpi/lib/openmpi/mca_mpool_rdma.so
7f7170e56000-7f7170e57000 r-xp 00000000 08:01 564003 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
7f7170e57000-7f7171056000 ---p 00001000 08:01 564003 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
7f7171056000-7f7171057000 rw-p 00000000 08:01 564003 /usr/lib/openmpi/lib/openmpi/mca_mpool_fake.so
7f7171057000-7f717105a000 r-xp 00000000 08:01 564023 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
7f717105a000-7f7171259000 ---p 00003000 08:01 564023 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
7f7171259000-7f717125a000 rw-p 00002000 08:01 564023 /usr/lib/openmpi/lib/openmpi/mca_rcache_vma.so
7f717125a000-7f717125c000 r-xp 00000000 08:01 563967 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
7f717125c000-7f717145b000 ---p 00002000 08:01 563967 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
7f717145b000-7f717145c000 rw-p 00001000 08:01 563967 /usr/lib/openmpi/lib/openmpi/mca_allocator_basic.so
7f717145c000-7f7171467000 r-xp 00000000 08:01 394004 /lib/x86_64-linux-gnu/libnss_files-2.13.so
7f7171467000-7f7171666000 ---p 0000b000 08:01 394004 /lib/x86_64-linux-gnu/libnss_files-2.13.so
7f7171666000-7f7171667000 r--p 0000a000 08:01 394004 /lib/x86_64-linux-gnu/libnss_files-2.13.so
7f7171667000-7f7171668000 rw-p 0000b000 08:01 394004 /lib/x86_64-linux-gnu/libnss_files-2.13.so
7f7171668000-7f7171672000 r-xp 00000000 08:01 394000 /lib/x86_64-linux-gnu/libnss_nis-2.13.so
7f7171672000-7f7171871000 ---p 0000a000 08:01 394000 /lib/x86_64-linux-gnu/libnss_nis-2.13.so
7f7171871000-7f7171872000 r--p 00009000 08:01 394000 /lib/x86_64-linux-gnu/libnss_nis-2.13.so
7f7171872000-7f7171873000 rw-p 0000a000 08:01 394000 /lib/x86_64-linux-gnu/libnss_nis-2.13.so
7f7171873000-7f717187a000 r-xp 00000000 08:01 393993 /lib/x86_64-linux-gnu/libnss_compat-2.13.so
7f717187a000-7f7171a79000 ---p 00007000 08:01 393993 /lib/x86_64-linux-gnu/libnss_compat-2.13.so
7f7171a79000-7f7171a7a000 r--p 00006000 08:01 393993 /lib/x86_64-linux-gnu/libnss_compat-2.13.so
7f7171a7a000-7f7171a7b000 rw-p 00007000 08:01 393993 /lib/x86_64-linux-gnu/libnss_compat-2.13.so
7f7171a7b000-7f7171a7e000 r-xp 00000000 08:01 563995 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
7f7171a7e000-7f7171c7d000 ---p 00003000 08:01 563995 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
7f7171c7d000-7f7171c7e000 rw-p 00002000 08:01 563995 /usr/lib/openmpi/lib/openmpi/mca_grpcomm_bad.so
7f7171c7e000-7f7171c8c000 r-xp 00000000 08:01 564008 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
7f7171c8c000-7f7171e8c000 ---p 0000e000 08:01 564008 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
7f7171e8c000-7f7171e8e000 rw-p 0000e000 08:01 564008 /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so
7f7171e8e000-7f7171e93000 r-xp 00000000 08:01 564029 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
7f7171e93000-7f7172093000 ---p 00005000 08:01 564029 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
7f7172093000-7f7172094000 rw-p 00005000 08:01 564029 /usr/lib/openmpi/lib/openmpi/mca_rml_oob.so
7f7172094000-7f7172097000 r-xp 00000000 08:01 563991 /usr/lib/openmpi/lib/openmpi/mca_ess_singleton.so
7f7172097000-7f7172297000 ---p 00003000 08:01 563991 /usr/lib/openmpi/lib/openmpi/mca_ess_singleton.so
7f7172297000-7f7172298000 rw-p 00003000 08:01 563991 /usr/lib/openmpi/lib/openmpi/mca_ess_singleton.so
7f7172299000-7f717229b000 r-xp 00000000 08:01 563968 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
7f717229b000-7f717249a000 ---p 00002000 08:01 563968 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
7f717249a000-7f717249b000 rw-p 00001000 08:01 563968 /usr/lib/openmpi/lib/openmpi/mca_allocator_bucket.so
7f717249b000-7f717249f000 r-xp 00000000 08:01 564030 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
7f717249f000-7f717269f000 ---p 00004000 08:01 564030 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
7f717269f000-7f71726a0000 rw-p 00004000 08:01 564030 /usr/lib/openmpi/lib/openmpi/mca_routed_binomial.so
7f71726a0000-7f71726a2000 r-xp 00000000 08:01 563985 /usr/lib/openmpi/lib/openmpi/mca_crs_none.so
7f71726a2000-7f71728a1000 ---p 00002000 08:01 563985 /usr/lib/openmpi/lib/openmpi/mca_crs_none.so
7f71728a1000-7f71728a2000 rw-p 00001000 08:01 563985 /usr/lib/openmpi/lib/openmpi/mca_crs_none.so
7f71728a2000-7f71728a3000 r-xp 00000000 08:01 563975 /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect.so
7f71728a3000-7f7172aa3000 ---p 00001000 08:01 563975 /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect.so
7f7172aa3000-7f7172aa4000 rw-p 00001000 08:01 563975 /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect.so
7f7172aa4000-7f7172aa9000 r-xp 00000000 08:01 564011 /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so
7f7172aa9000-7f7172ca8000 ---p 00005000 08:01 564011 /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so
7f7172ca8000-7f7172ca9000 rw-p 00004000 08:01 564011 /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so
7f7172ca9000-7f7172cb8000 r-xp 00000000 08:01 394012 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f7172cb8000-7f7172eb7000 ---p 0000f000 08:01 394012 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f7172eb7000-7f7172eb8000 r--p 0000e000 08:01 394012 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f7172eb8000-7f7172eb9000 rw-p 0000f000 08:01 394012 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f7172eb9000-7f7172eba000 r-xp 00000000 08:01 570818 /usr/lib/libscotcherr-5.1.so
7f7172eba000-7f71730b9000 ---p 00001000 08:01 570818 /usr/lib/libscotcherr-5.1.so
7f71730b9000-7f71730ba000 rw-p 00000000 08:01 570818 /usr/lib/libscotcherr-5.1.so
7f71730ba000-7f71730d0000 r-xp 00000000 08:01 394075 /lib/x86_64-linux-gnu/libz.so.1.2.7
7f71730d0000-7f71732cf000 ---p 00016000 08:01 394075 /lib/x86_64-linux-gnu/libz.so.1.2.7
7f71732cf000-7f71732d0000 r--p 00015000 08:01 394075 /lib/x86_64-linux-gnu/libz.so.1.2.7
7f71732d0000-7f71732d1000 rw-p 00016000 08:01 394075 /lib/x86_64-linux-gnu/libz.so.1.2.7
7f71732d1000-7f71732d2000 r-xp 00000000 08:01 570823 /usr/lib/libptscotcherr-5.1.so
7f71732d2000-7f71734d2000 ---p 00001000 08:01 570823 /usr/lib/libptscotcherr-5.1.so
7f71734d2000-7f71734d3000 rw-p 00001000 08:01 570823 /usr/lib/libptscotcherr-5.1.so
7f71734d3000-7f71734d5000 r-xp 00000000 08:01 394009 /lib/x86_64-linux-gnu/libutil-2.13.so
7f71734d5000-7f71736d4000 ---p 00002000 08:01 394009 /lib/x86_64-linux-gnu/libutil-2.13.so[mobydick:02250] *** Process received signal ***
[mobydick:02250] Signal: Aborted (6)
[mobydick:02250] Signal code: (-6)
[mobydick:02250] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xf030) [0x7f7174e57030]
[mobydick:02250] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x7f7174af3475]
[mobydick:02250] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x180) [0x7f7174af66f0]
[mobydick:02250] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x6c32b) [0x7f7174b2d32b]
[mobydick:02250] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x75b76) [0x7f7174b36b76]
[mobydick:02250] [ 5] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c) [0x7f7174b3b8ac]
[mobydick:02250] [ 6] ./dirichlet(_ZNSt10_List_baseISt4pairImN5boost3mpi7requestEESaIN7rheolef16geo_element_hackEEE8_M_clearEv+0x2b) [0x42a4cb]
[mobydick:02250] [ 7] /usr/lib/librheolef.so.1(_ZN7rheolef18hack_array_mpi_repINS_16geo_element_hackESaIS1_EE6resizeERKNS_11distributorERKNS_11geo_element14parameter_typeE+0x80) [0x7f7179cb11d0]
[mobydick:02250] [ 8] /usr/lib/librheolef.so.1(_ZN7rheolef7geo_repId11distributedE3getERNS_11idiststreamE+0x296c) [0x7f7179cbac6c]
[mobydick:02250] [ 9] /usr/lib/librheolef.so.1(_ZN7rheolef7geo_repId11distributedE4loadESsRKN5boost3mpi12communicatorE+0x271) [0x7f7179cbb5b1]
[mobydick:02250] [10] ./dirichlet(_ZN7rheolef9geo_basicId11distributedEC2ESsRKN5boost3mpi12communicatorE+0x6f) [0x42e7ff]
[mobydick:02250] [11] ./dirichlet() [0x4220c3]
[mobydick:02250] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f7174adfead]
[mobydick:02250] [13] ./dirichlet() [0x4227e5]
[mobydick:02250] *** End of error message ***
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