Hey John- I just tried the 1.3.9 release and I still see the same issue. The stacktrace is pasted below. I believe it is getting stuck in column.cpp line 737: ibis::util::mutexLock lock(&mutex, "column::getNullMask");
I can only reproduce the issue on ubuntu. If I can get the issue reproduced on my mac /w generated data I will send it your way in case you wouldn't mind examining. Btw- I am building with c++0x instead of c++0x11 on ubuntu since it has an older gcc that doesn't support 0x11. Thanks again, Sean #0 0x00007ffff59d989c in __lll_lock_wait () from /lib/x86_64-linux-gnu/libpthread.so.0 (gdb) bt #0 0x00007ffff59d989c in __lll_lock_wait () from /lib/x86_64-linux-gnu/libpthread.so.0 #1 0x00007ffff59d5065 in _L_lock_858 () from /lib/x86_64-linux-gnu/libpthread.so.0 #2 0x00007ffff59d4eba in pthread_mutex_lock () from /lib/x86_64-linux-gnu/libpthread.so.0 #3 0x00007ffff708e613 in ibis::column::getNullMask(ibis::bitvector&) const () from /usr/local/lib/libfastbit.so.0 #4 0x00007ffff79573d0 in ibis::direkte::direkte(ibis::column const*, unsigned int, unsigned int) () from /usr/local/lib/libfastbit.so.0 #5 0x00007ffff77f2ec3 in ibis::category::fillIndex(char const*) const () from /usr/local/lib/libfastbit.so.0 #6 0x00007ffff77f6c68 in ibis::category::prepareMembers() const () from /usr/local/lib/libfastbit.so.0 #7 0x00007ffff77fbd85 in ibis::category::getDictionary() const () from /usr/local/lib/libfastbit.so.0 #8 0x00007ffff6fe085d in ibis::bord::bord(char const*, char const*, ibis::selectClause const&, std::vector<ibis::part const*, std::allocator<ibis::part const*> > const&) () from /usr/local/lib/libfastbit.so.0 #9 0x00007ffff78b0c69 in ibis::filter::sift2(ibis::selectClause const&, std::vector<ibis::part const*, std::allocator<ibis::part const*> > const&, ibis::whereClause const&) () from /usr/local/lib/libfastbit.so.0 #10 0x00007ffff78b8c28 in ibis::table::select(std::vector<ibis::part const*, std::allocator<ibis::part const*> > const&, char const*, char const*) () from /usr/local/lib/libfastbit.so.0 #11 0x00007ffff771513b in ibis::mensa::select(char const*, char const*) const () from /usr/local/lib/libfastbit.so.0 ________________________________ From: [email protected] [[email protected]] on behalf of Sean McNamara [[email protected]] Sent: Friday, March 14, 2014 12:19 PM To: FastBit Users Subject: Re: [FastBit-users] fastbit query hangs on FUTEX_WAIT_PRIVATE John- Unfortunately I cannot share this dataset. I may try to make a dataset that I can share if I can repo the issue. In case it is helpful here is a stacktrace: http://pastebin.com/FT3qsLH6 I tried pulling the data down to my local machine and it works fine there, no issues whatsoever. (I have a newer version of fastbit installed locally). So first I will try deploying the latest and greatest on our cluster. I will let you know how that goes. Thanks again! Sean ________________________________ From: [email protected] [[email protected]] on behalf of John [[email protected]] Sent: Friday, March 14, 2014 12:04 PM To: FastBit Users Subject: Re: [FastBit-users] fastbit query hangs on FUTEX_WAIT_PRIVATE Hi, Sean, Thanks for bring this issue up. It appears to be some sort of deadlock. I could look into further if you can share the sample data. Is the link you give the data or the log messages? -- John -- On Mar 14, 2014, at 10:53 AM, Sean McNamara <[email protected]<mailto:[email protected]>> wrote: Hi- I¹m trying to troubleshoot an issue that I just started seeing. Queries seem to hang, but only for certain columns and it¹s not clear to me why. If it¹s any help, I am using fastbit a few commits after 692. Here is the strace for the query: strace ibis -d /mnt/data/test -q "select daily_binned_datetime² http://pastebin.com/xczKJVWL Here is the tail of what ibis is doing with verbosity: fileManager::storage(0x258e630, 0) cleared array_t<i>::freeMemory this=0x24421a0 actual=0x24515f0 and m_begin=0 (active references: 0, past references: 1) fileManager::storage(0x24515f0, 0) cleared fileManager::flushFile will do nothing because "/mnt/data/explore/keyidx/35000/rp13/2014/02/03/daily_binned_datetime.idx" is not tracked by the file manager fileManager::storage(0x24515f0, 0) initialization completed array_t<i> constructed at 0x2451350 with actual=0x24515f0, m_begin=0 and m_end=0 fileManager::storage(0x258e630, 0) initialization completed array_t<l> constructed at 0x2451368 with actual=0x258e630, m_begin=0 and m_end=0 fileManager::storage(0x2451170, 0) initialization completed array_t<PN4ibis9bitvectorE> constructed at 0x2451380 with actual=0x2451170, m_begin=0 and m_end=0 array_t<PN4ibis9bitvectorE>::freeMemory this=0x2451380 actual=0x2451170 and m_begin=0 (active references: 0, past references: 1) fileManager::storage(0x2451170, 0) cleared fileManager::storage(0x2451170, 0x2451290) added 16 bytes to increase totalBytes to 80192 fileManager::storage(0x2451170, 0x2451290) initialization completed with 16 elements fileManager::storage(0x24512e0, 0) initialization completed array_t<j> constructed at 0x24512c0 with actual=0x24512e0, m_begin=0 and m_end=0 bitvector (0x24512b0) constructed with m_vec at 0x24512c0 <‹ hangs here Does anyone have any insight? Thanks, Sean _______________________________________________ FastBit-users mailing list [email protected]<mailto:[email protected]> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users
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