-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Hi, Mike,
Glad that you found a work around. Feel free to let us know if you have any additional questions. John On 8/12/14 5:32 AM, Mike Carter wrote: > Finally I found the problem. I had to set the LD_LIBRARY_PATH to > …/fastbit-ibis-3.8 > > Thank you for your Help Mike > > > > 2014-07-29 19:06 GMT+02:00 Mike Carter <[email protected] > <mailto:[email protected]>>: > > > Hi John > > The OS is CentOS 6.5 and I installed the 'Development Tools' > package. > > Mike > > > 2014-07-29 17:38 GMT+02:00 K. John Wu <[email protected] > <mailto:[email protected]>>: > > Hi, Mike, > > I am looking into this now. > > Seems like you are on a system that I have not tried recently, > would you mind tell me your setup, mostly the type and the > version of the compiler you are using, so that I can reproduce > your errors and not have you report each one separately. > > Alternatively, you might run 'make -k' and send me the report. > > Thanks. > > John > > > > On 7/29/14 8:24 AM, Mike Carter wrote: >> Hi John, >> >> thank you again! I got a new error while compiling. >> >> make[2]: *** [dictionary.lo] Error 1 make[2]: Leaving directory >> `/root/fastbit/src' make[1]: *** [all] Error 2 make[1]: Leaving >> directory `/root/fastbit/src' >> >> Mike >> >> >> >> 2014-07-29 16:23 GMT+02:00 K. John Wu <[email protected] > <mailto:[email protected]>>: >> >>> Hi, Mike, >>> >>> Thanks for the report. I see the compilation problem now. > It should >>> be fixed in SVN Revision 741. Please give it a try. >>> >>> John >>> >>> >>> On 7/29/14 1:01 AM, Mike Carter wrote: >>>> Hi John >>>> >>>> I appended the make and configure - process "logs" . >>>> >>>> Mike >>>> >>>> >>>> 2014-07-28 16:58 GMT+02:00 K. John Wu <[email protected] > <mailto:[email protected]>>: >>>> >>>>> Hi, Mike, >>>>> >>>>> Thanks for the report of compilation problem. Would it > be possible >>>>> for you to capture the whole error message from make? > The lines you >>>>> included shows something about stl_map.h, which is a > standard header >>>>> file. It would be more useful to me to see where in > FastBit code this >>>>> error originates. >>>>> >>>>> John >>>>> >>>>> >>>>> On 7/28/14 5:23 AM, Mike Carter wrote: >>>>>> Hi John, >>>>>> >>>>>> thank you for your help. I tried it with following > command from the >>> new >>>>>> svn version (revision 740) >>>>>> >>>>>> ./configure --with-java=/usr/java/jdk1.8.0_11 ... >>>>>> checking if /usr/java/jdk1.8.0_11/bin/java works... >>>>>> yes checking jni.h usability... yes checking jni.h >>>>>> presence... yes checking for jni.h... yes ... >>>>>> >>>>>> After the configuration I got an error by using make >>>>>> >>>>>> >>>>> >>> > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_map.h:581: > > >>>>> note: typename std::_Rb_tree<_Key, > std::pair<const >>> _Key, >>>>>> _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, > _Compare, typename >>>>>> _Alloc::rebind<std::pair<const _Key, _Tp> >> ::other>::size_type >>>>>> std::map<_Key, _Tp, _Compare, _Alloc>::erase(const > _Key&) [with _Key = >>>>>> const char*, _Tp = ibis::part*, _Compare = >>>>>> ibis::lessi, > _Alloc = >>>>>> std::allocator<std::pair<const char* const, >>>>>> ibis::part*> >] >>>>>> >>>>> >>> > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_map.h:596: > > >>>>> note: void std::map<_Key, _Tp, _Compare, >>>>>> _Alloc>::erase(typename std::_Rb_tree<_Key, > std::pair<const _Key, _Tp>, >>>>>> std::_Select1st<std::pair<const _Key, _Tp> >, >>>>>> _Compare, > typename >>>>>> _Alloc::rebind<std::pair<const _Key, _Tp> >> ::other>::iterator, typename >>>>>> std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, >>>>>> std::_Select1st<std::pair<const _Key, _Tp> >, >>>>>> _Compare, > typename >>>>>> _Alloc::rebind<std::pair<const _Key, _Tp> >> ::other>::iterator) [with >>>>> _Key = >>>>>> const char*, _Tp = ibis::part*, _Compare = >>>>>> ibis::lessi, > _Alloc = >>>>>> std::allocator<std::pair<const char* const, >>>>>> ibis::part*> >] make[2]: *** [capi.lo] Error 1 make[2]: >>>>>> Leaving directory `/root/fastbit/src' make[1]: *** >>>>>> [all] Error 2 make[1]: Leaving directory >>>>>> `/root/fastbit/src' make: *** [all-recursive] Error 1 >>>>>> >>>>>> >>>>>> >>>>>> Mike >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 2014-07-27 9:43 GMT+02:00 K. John Wu <[email protected] > <mailto:[email protected]>>: >>>>>> >>>>>>> Hi, Mike, >>>>>>> >>>>>>> Thanks for your interest in our work. There was a > problem in >>>>>>> detecting whether you javac could be used safely in > configure.ac <http://configure.ac>. >>>>>>> This problem should be fixed in the code from the >>>>>>> SVN > archive. Would >>>>>>> you mind check out the source code with >>>>>>> >>>>>>> svn checkout >>>>>>> https://codeforge.lbl.gov/anonscm/fastbit >>>>>>> >>>>>>> and give it another try. >>>>>>> >>>>>>> One thing to watch for is that when you run >>>>>>> configure > script (for >>>>>>> example, through runconf), you will notice something >>>>>>> like >>>>>>> >>>>>>> checking for jni.h... yes >>>>>>> >>>>>>> If you don't see this like, it means that the >>>>>>> configure > script has not >>>>>>> figured out how to deal with JNI stuff on your >>>>>>> system. > In which case, >>>>>>> you might tell it where to find you JDK installation >>>>>>> by > giving the >>>>>>> following option to the configure script >>>>>>> >>>>>>> --with-java=path-to-jdk >>>>>>> >>>>>>> Hope this helps. >>>>>>> >>>>>>> John >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 7/18/14 6:50 AM, Mike Carter wrote: >>>>>>>> Hello everybody! >>>>>>>> >>>>>>>> After installing Fastbit successfully on CentOS, I > tried to run the >>>>> milky >>>>>>>> example by using the command [java milky > ../tests/tmp/t1 "a>10 and c >>>>>>>> between 50 and 70"]. >>>>>>>> >>>>>>>> [root@vm001 java]# java milky ../tests/tmp/t1 >>>>>>>> "a>10 > and c between 50 >>>>>>> and 70" >>>>>>>> Exception in thread "main" > java.lang.UnsatisfiedLinkError: no >>>>> fastbitjni >>>>>>> in >>>>>>>> java.library.path at > java.lang.ClassLoader.loadLibrary(ClassLoader.java:1857) >>>>>>>> at > java.lang.Runtime.loadLibrary0(Runtime.java:870) >>>>>>>> at java.lang.System.loadLibrary(System.java:1119) >>>>>>>> at > gov.lbl.fastbit.FastBit.<clinit>(FastBit.java:188) >>>>>>>> at milky.main(milky.java:69) >>>>>>>> >>>>>>>> So I was looking for the file "libfastbitjni.so", >>>>>>>> but > I couldn't find >>>>> it. >>>>>>>> It doesn't exist in the folder fastbit/src/.libs >>>>>>>> nor > in the folder >>>>>>>> /usr/local/lib (the java.library.path). In the >>>>>>>> documentation I found the following command to > produce the >>>>>>>> libfastbitjni.so. I'm not sure how to use it to >>>>>>>> produce >>>>> libfastbitjni.so. >>>>>>>> Additionally, the libfastbitjni.so doesn't exist >>>>>>>> in > the folder >>>>> src/.libs, >>>>>>>> which is a presumption to run this command. >>>>>>>> >>>>>>>> >>>>>>>> gcc -O -shared -o libfastbitjni.so > -Wl,-soname,libfastbitjni.so \ >>>>>>>> -I/export/home/jdk1.2/include \ >>>>>>>> -I/export/home/jdk1.2/include/linux FastBit.c \ >>>>>>>> ..\src\libfastbit.lo -lm >>>>>>>> >>>>>>>> Any hints and advices? What I am doing wrong? I >>>>>>>> unpacket fastbit-ibis1.3.8.tar.gz and first I >>>>>>>> executed. Ibis > and ardea works, >>>>> but >>>>>>> I >>>>>>>> need to access fastbit through Java. >>>>>>>> >>>>>>>> ./configure gmake -j 3 all make install >>>>>>>> >>>>>>>> Thank you! Mike Carter >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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] > <mailto:[email protected]> >>>>>>> > https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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] > <mailto:[email protected]> >>>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > >>>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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] > <mailto:[email protected]> >>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users > >>> >> >> >> >> >> _______________________________________________ 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] > <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 > -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) Comment: GPGTools - https://gpgtools.org iF4EAREKAAYFAlPqoZYACgkQ4I69U3+CTfxXewD/e3yWvWtKDCGSnsHJeKuthmVx Ey9DTB1inQmtE3/mDbAA/3ZBn1hka2KWPia5dIvX7y9QLOin5xVge29re0kpuHFt =Dwtw -----END PGP SIGNATURE----- _______________________________________________ FastBit-users mailing list [email protected] https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users
