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
