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]>: > > 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]>: > > 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]>: >> > >> >> 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]>: >> >>> >> >>>> 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]>: >> >>>>> >> >>>>>> 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. >> >>>>>> 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] >> >>>>>>> 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 >> >>>> >> >>> >> >>> >> >>> >> >>> _______________________________________________ >> >>> 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 >> > >> _______________________________________________ >> FastBit-users mailing list >> [email protected] >> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >> > >
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