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
