Bug#888879: rheolef FTBFS on several architectures: test runs forever
Andreas Tille
andreas at an3as.eu
Tue Feb 6 10:59:19 UTC 2018
Hi Pierre,
as I mentioned on Debian Science maintainers list[1] this problem does
not come unexpected. Pierre, could you please confirm whether you keep
on maintaining this package and will check this issue?
>From my uneducated perspective the test failures always existed but the
test were simply not run before. Thus a first course of action might be
to ask ftpmaster for removal of those architectures where rheolef does
not build and reduce severity of the bug to say "important".
Please note that I do not have any time resources to work on this
package.
Kind regards
Andreas.
[1] https://lists.alioth.debian.org/pipermail/debian-science-maintainers/2018-January/057544.html
On Tue, Jan 30, 2018 at 10:24:18PM +0200, Adrian Bunk wrote:
> Source: rheolef
> Version: 6.7-5
> Severity: serious
>
> https://buildd.debian.org/status/package.php?p=rheolef&suite=sid
>
> ...
> mpirun -np 1 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 left >/dev/null 2>/dev/null
> mpirun -np 2 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 left >/dev/null 2>/dev/null
> mpirun -np 3 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 left >/dev/null 2>/dev/null
> mpirun -np 1 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 right >/dev/null 2>/dev/null
> mpirun -np 2 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 right >/dev/null 2>/dev/null
> E: Build killed with signal TERM after 150 minutes of inactivity
>
>
> I've reproduced this on i386, two processes are running
> forever (aborted after 6 hours on a fast CPU) with 100% CPU.
>
> Backtraces:
>
> Thread 3 (Thread 0xf50ffb40 (LWP 29032)):
> #0 0xf7ed6db9 in __kernel_vsyscall ()
> #1 0xf70fabd3 in __GI___poll (fds=0xf47005d0, nfds=2, timeout=3600000) at ../sysdeps/unix/sysv/linux/poll.c:29
> #2 0xf5caed4a in poll (__timeout=3600000, __nfds=2, __fds=0xf47005d0) at /usr/include/i386-linux-gnu/bits/poll2.h:46
> #3 poll_dispatch (base=0x578eb9c0, tv=0xf50f9bfc) at poll.c:165
> #4 0xf5ca59e9 in opal_libevent2022_event_base_loop (base=<optimized out>, flags=<optimized out>) at event.c:1630
> #5 0xf5c6b3bd in progress_engine (obj=0x578eb950) at runtime/opal_progress_threads.c:105
> #6 0xf5df6316 in start_thread (arg=0xf50ffb40) at pthread_create.c:465
> #7 0xf7105296 in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:108
>
> Thread 2 (Thread 0xf5ac5b40 (LWP 29031)):
> #0 0xf7ed6db9 in __kernel_vsyscall ()
> #1 0xf71053fa in __GI_epoll_pwait (epfd=7, events=0x578ea930, maxevents=32, timeout=-1, set=0x0)
> at ../sysdeps/unix/sysv/linux/epoll_pwait.c:42
> #2 0xf710569a in epoll_wait (epfd=7, events=0x578ea930, maxevents=32, timeout=-1)
> at ../sysdeps/unix/sysv/linux/epoll_wait.c:30
> #3 0xf5ca199a in epoll_dispatch (base=0x578ea7a0, tv=0x0) at epoll.c:407
> #4 0xf5ca59e9 in opal_libevent2022_event_base_loop (base=<optimized out>, flags=<optimized out>) at event.c:1630
> #5 0xf5af23eb in progress_engine (obj=0x578ea7a0) at src/util/progress_threads.c:52
> #6 0xf5df6316 in start_thread (arg=0xf5ac5b40) at pthread_create.c:465
> #7 0xf7105296 in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:108
>
> Thread 1 (Thread 0xf5b4fe00 (LWP 29002)):
> #0 0xf7ed67f5 in ?? ()
> #1 0xf7ed6b43 in __vdso_clock_gettime ()
> #2 0xf7112961 in __GI___clock_gettime (clock_id=1, tp=0xffb74194) at ../sysdeps/unix/clock_gettime.c:115
> #3 0xf5cc3297 in opal_timer_linux_get_usec_clock_gettime () at timer_linux_component.c:197
> #4 0xf5c669c3 in opal_progress () at runtime/opal_progress.c:197
> #5 0xf74b5e05 in sync_wait_st (sync=<optimized out>) at ../opal/threads/wait_sync.h:80
> #6 ompi_request_default_wait_all (count=2, requests=0xffb742e4, statuses=0x0) at request/req_wait.c:221
> #7 0xf750640d in ompi_coll_base_allreduce_intra_recursivedoubling (sbuf=0x57951030, rbuf=0x57a9b400, count=2,
> dtype=0xf7565140 <ompi_mpi_unsigned>, op=0xf7573e60 <ompi_mpi_op_sum>, comm=0xf7569520 <ompi_mpi_comm_world>,
> module=0x57976fa0) at base/coll_base_allreduce.c:225
> #8 0xe991f640 in ompi_coll_tuned_allreduce_intra_dec_fixed (sbuf=0x57951030, rbuf=0x57a9b400, count=2,
> dtype=0xf7565140 <ompi_mpi_unsigned>, op=0xf7573e60 <ompi_mpi_op_sum>, comm=0xf7569520 <ompi_mpi_comm_world>,
> module=0x57976fa0) at coll_tuned_decision_fixed.c:66
> #9 0xf74c5b77 in PMPI_Allreduce (sendbuf=0x57951030, recvbuf=0x57a9b400, count=2,
> datatype=0xf7565140 <ompi_mpi_unsigned>, op=0xf7573e60 <ompi_mpi_op_sum>, comm=0xf7569520 <ompi_mpi_comm_world>)
> at pallreduce.c:107
> #10 0xf7b476cf in boost::mpi::detail::all_reduce_impl<unsigned int, std::plus<unsigned int> > (comm=...,
> in_values=0x57951030, n=n at entry=2, out_values=0x57a9b400) at /usr/include/boost/mpi/collectives/all_reduce.hpp:36
> #11 0xf7b58fc0 in boost::mpi::all_reduce<unsigned int, std::plus<unsigned int> > (out_values=<optimized out>, n=2,
> in_values=<optimized out>, comm=..., op=...) at /usr/include/boost/mpi/collectives/all_reduce.hpp:93
> #12 rheolef::mpi_assembly_begin<std::multimap<unsigned int, unsigned int, std::less<unsigned int>, rheolef::heap_allocator<std::pair<unsigned int, unsigned int> > >, rheolef::disarray_rep<rheolef::index_set, rheolef::distributed, std::allocator<rheolef::index_set> >::message_type, rheolef::apply_iterator<std::_Rb_tree_iterator<std::pair<unsigned int const, unsigned int> >, rheolef::first_op<std::pair<unsigned int const, unsigned int> > > > (stash=..., first_stash_idx=...,
> last_stash_idx=..., ownership=..., receive=..., send=...) at ../../include/rheolef/mpi_assembly_begin.h:113
> #13 0xf7b5a346 in rheolef::disarray_rep<rheolef::index_set, rheolef::distributed, std::allocator<rheolef::index_set> >::dis_entry_assembly_begin<rheolef::index_set_add_op<rheolef::index_set> > (this=0x57acab70, my_set_op=...)
> at ../../include/rheolef/disarray_mpi.icc:223
> #14 rheolef::disarray<rheolef::index_set, rheolef::distributed, std::allocator<rheolef::index_set> >::dis_entry_assembly_begin (this=<optimized out>) at ../../include/rheolef/disarray.h:592
> #15 rheolef::disarray<rheolef::index_set, rheolef::distributed, std::allocator<rheolef::index_set> >::dis_entry_assembly (this=<optimized out>) at ../../include/rheolef/disarray.h:594
> #16 rheolef::geo_rep<double, rheolef::distributed>::set_element_side_index (this=<optimized out>,
> side_dim=<optimized out>) at geo_mpi_get.cc:461
> #17 0xf7b5f25a in rheolef::geo_rep<double, rheolef::distributed>::get (this=<optimized out>, ips=...)
> at geo_mpi_get.cc:965
> #18 0xf7b60a48 in rheolef::geo_rep<double, rheolef::distributed>::load (this=<optimized out>, filename=..., comm=...)
> at geo_mpi_get.cc:989
> #19 0xf7b3030a in rheolef::geo_load<double, rheolef::distributed> (name=...) at geo.cc:172
> #20 0x56592bf8 in rheolef::geo_basic<double, rheolef::distributed>::geo_basic (comm=...,
> name="\360\265\225W\030\000\000\000\030\000\000\000\227 at YV\320<ZV\002\000\000\000\000\060\bn\003\000\000\000y+YV at K\267\377\000\000\000\000\000\360\035\367\000\000\000\000\000\000\000\000\203w\002\367\000\360\035\367\000\360\035\367\000\000\000\000\203w\002\367\003\000\000\000\324K\267\377\344K\267\377dK\267\377\003\000\000\000\324K\267\377\000\360\035\367\352w\356\367\001\000\000\000\000\000\000\000\000\360\035\367\000\000\000\000\000\000\000\000Tl\324\tEf\254c", '\000' <repeats 12 times>, "\320K\267\377\000\200\355\367\354\202\355\367\350\210\355\367\003\000\000\000\320<ZV\003\000\000\000\310 at YV\000\000\000\000\371 at YV`+YV\003\000\000\000\324K\267\377"..., this=0xffb74ac0)
> at ../../include/rheolef/geo.h:1460
> #21 main (argc=<optimized out>, argv=<optimized out>) at space_tst.cc:26
>
>
>
>
> Thread 3 (Thread 0xf51ffb40 (LWP 29033)):
> #0 0xf7fb7db9 in __kernel_vsyscall ()
> #1 0xf71dbbd3 in __GI___poll (fds=0xf48005d0, nfds=2, timeout=3600000) at ../sysdeps/unix/sysv/linux/poll.c:29
> #2 0xf5d8fd4a in poll (__timeout=3600000, __nfds=2, __fds=0xf48005d0) at /usr/include/i386-linux-gnu/bits/poll2.h:46
> #3 poll_dispatch (base=0x57eef9c0, tv=0xf51f9bfc) at poll.c:165
> #4 0xf5d869e9 in opal_libevent2022_event_base_loop (base=<optimized out>, flags=<optimized out>) at event.c:1630
> #5 0xf5d4c3bd in progress_engine (obj=0x57eef950) at runtime/opal_progress_threads.c:105
> #6 0xf5ed7316 in start_thread (arg=0xf51ffb40) at pthread_create.c:465
> #7 0xf71e6296 in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:108
>
> Thread 2 (Thread 0xf5ba6b40 (LWP 29030)):
> #0 0xf7fb7db9 in __kernel_vsyscall ()
> #1 0xf71e63fa in __GI_epoll_pwait (epfd=7, events=0x57eee930, maxevents=32, timeout=-1, set=0x0) at ../sysdeps/unix/sysv/linux/epoll_pwait.c:42
> #2 0xf71e669a in epoll_wait (epfd=7, events=0x57eee930, maxevents=32, timeout=-1) at ../sysdeps/unix/sysv/linux/epoll_wait.c:30
> #3 0xf5d8299a in epoll_dispatch (base=0x57eee7a0, tv=0x0) at epoll.c:407
> #4 0xf5d869e9 in opal_libevent2022_event_base_loop (base=<optimized out>, flags=<optimized out>) at event.c:1630
> #5 0xf5bd33eb in progress_engine (obj=0x57eee7a0) at src/util/progress_threads.c:52
> #6 0xf5ed7316 in start_thread (arg=0xf5ba6b40) at pthread_create.c:465
> #7 0xf71e6296 in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:108
>
> Thread 1 (Thread 0xf5c30e00 (LWP 29003)):
> #0 0xf7fb77f5 in ?? ()
> #1 0xf7fb7b43 in __vdso_clock_gettime ()
> #2 0xf71f3961 in __GI___clock_gettime (clock_id=1, tp=0xffa8c4b4) at ../sysdeps/unix/clock_gettime.c:115
> #3 0xf5da4297 in opal_timer_linux_get_usec_clock_gettime () at timer_linux_component.c:197
> #4 0xf5d479c3 in opal_progress () at runtime/opal_progress.c:197
> #5 0xf7596e05 in sync_wait_st (sync=<optimized out>) at ../opal/threads/wait_sync.h:80
> #6 ompi_request_default_wait_all (count=2, requests=0xffa8c604, statuses=0x0) at request/req_wait.c:221
> #7 0xf75e740d in ompi_coll_base_allreduce_intra_recursivedoubling (sbuf=0x5809b980, rbuf=0x580805b0, count=139,
> dtype=0xf7646140 <ompi_mpi_unsigned>, op=0xf7655660 <ompi_mpi_op_max>, comm=0xf764a520 <ompi_mpi_comm_world>, module=0x57f74810)
> at base/coll_base_allreduce.c:225
> #8 0xf1a05640 in ompi_coll_tuned_allreduce_intra_dec_fixed (sbuf=0x5809b980, rbuf=0x580805b0, count=139, dtype=0xf7646140 <ompi_mpi_unsigned>,
> op=0xf7655660 <ompi_mpi_op_max>, comm=0xf764a520 <ompi_mpi_comm_world>, module=0x57f74810) at coll_tuned_decision_fixed.c:66
> #9 0xf75a6b77 in PMPI_Allreduce (sendbuf=0x5809b980, recvbuf=0x580805b0, count=139, datatype=0xf7646140 <ompi_mpi_unsigned>,
> op=0xf7655660 <ompi_mpi_op_max>, comm=0xf764a520 <ompi_mpi_comm_world>) at pallreduce.c:107
> #10 0xf7c2862f in boost::mpi::detail::all_reduce_impl<unsigned int, boost::mpi::maximum<unsigned int> > (comm=..., in_values=0x5809b980, n=139,
> out_values=0x580805b0) at /usr/include/boost/mpi/collectives/all_reduce.hpp:36
> #11 0xf7c4019f in boost::mpi::all_reduce<unsigned int, boost::mpi::maximum<unsigned int> > (out_values=<optimized out>, n=<optimized out>,
> in_values=<optimized out>, comm=..., op=...) at /usr/include/boost/mpi/collectives/all_reduce.hpp:93
> #12 rheolef::geo_rep<double, rheolef::distributed>::get (this=<optimized out>, ips=...) at geo_mpi_get.cc:942
> #13 0xf7c41a48 in rheolef::geo_rep<double, rheolef::distributed>::load (this=<optimized out>, filename=..., comm=...) at geo_mpi_get.cc:989
> #14 0xf7c1130a in rheolef::geo_load<double, rheolef::distributed> (name=...) at geo.cc:172
> #15 0x5658abf8 in rheolef::geo_basic<double, rheolef::distributed>::geo_basic (comm=...,
> name="\000\327\365W\030\000\000\000\030\000\000\000\227\300XV\320\274YV\002\000\000\000\000\240x1\003\000\000\000y\253XV\360\313\250\377\000\000\000\000\000\000,\367\000\000\000\000\000\000\000\000\203\207\020\367\000\000,\367\000\000,\367\000\000\000\000\203\207\020\367\003\000\000\000\204\314\250\377\224\314\250\377\024\314\250\377\003\000\000\000\204\314\250\377\000\000,\367\352\207\374\367\001\000\000\000\000\000\000\000\000\000,\367\000\000\000\000\000\000\000\000\276\"\333\071\257HBI", '\000' <repeats 12 times>, "\200\314\250\377\000\220\373\367\354\222\373\367\350\230\373\367\003\000\000\000\320\274YV\003\000\000\000\310\300XV\000\000\000\000\371\300XV`\253XV\003\000\000\000\204\314\250\377"...,
> this=0xffa8cb70) at ../../include/rheolef/geo.h:1460
> #16 main (argc=<optimized out>, argv=<optimized out>) at space_tst.cc:26
>
> --
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