John- There was an issue with the index data that we had generated. After rebuilding the indexes /w 1.3.9 everything works great!
Sorry for the false alarm. Thanks, Sean ________________________________________ From: [email protected] [[email protected]] on behalf of K. John Wu [[email protected]] Sent: Saturday, March 15, 2014 1:52 AM To: FastBit Users Subject: Re: [FastBit-users] fastbit query hangs on FUTEX_WAIT_PRIVATE Hi, Sean, Please check out SVN revision 706 and give it a try. Let us know if you continue to encounter problems. John PS: You can use the following command line to check out the latest code from SVN svn checkout https://codeforge.lbl.gov/anonscm/fastbit On 3/14/14, 2:26 PM, Sean McNamara wrote: > 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 > > > _______________________________________________ > FastBit-users mailing list > [email protected] > https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > _______________________________________________ FastBit-users mailing list [email protected] https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users _______________________________________________ FastBit-users mailing list [email protected] https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users
