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
