Re: [Swarm-Support] Swarm and opteron machines II

[David Camacho Trujillo]

Sorry, 
I have this ommitted
gcc 3.4.3 


Mensaje citado por: Paul Johnson <address@hidden>:

> OK, I'm just guessing in the dark, but I can see some obvious things to 
> fix before we get too excited.
> 
> Note that you never tell exactly which gcc version you are using.
> 
> David Camacho Trujillo wrote:
> > Many thanks for your response,
> > 
> > Here are some answers to your questions:
> > 
> > We have installed :
> > Blt-2.4.2-205.src.rpm
> > Blt2.4-patch 1
> > Blt2.4-patch 2 (see below)
> > 
> > Hdf55-1.6.2
> > Jdk 1.4.2-08
> > 
> > Here is what my colleague has write about the blt library:
> > 
> > building blt2.4z
> > for the opteron there is a bug and it is nessesary to patch the source
> code
> > 
> > go to the blt directory
> > 
> > patch -p0 < ../blt2.4z.patch
> > 
> > ./configure --prefix=/usr/local/blt --with-tcl=/usr/lib64/
> 
> I can't verify this because your blt build is not complete--no make, 
> make install.  I would suggest you make it easier on yourself and take 
> the src.rpm file and run "rpmbuild --rebuild blt**src.rpm" and let the 
> system do its magic, and then install that rpm.
> 
> > 
> > go to swarm directory
> > 
> > data/src/swarm-2.2 # ./configure --with-tclscriptdir=/usr/lib64/tcl8.4
> > --with-tkscriptdir=/usr/lib64/tk8.4 --with-bltdir=/usr/local/blt
> > --with-jdkdir=/usr/lib/jvm/java
> > 
> We do not recommend doing it this way.  Check the SwarmFaq where it 
> explains about NOT building in the source directory itself. 
> http://www.ku.edu/~pauljohn/SwarmFaq/SwarmOnlineFaq.html#2.4  It looks 
> to me as though your jdkdir is incorrect, if you installed the rpm for 
> j2sdk. You probably also need --prefix= and --with-defaultdir=.  I 
> notice below that you installed hdf5 someplace off to the side, in /data
> 
> or some such, and if you do that, swarm won't find it.
> 
> 
> If all else fails, try to build --without-jdkdir to see if the problem 
> is just in the objective C side.
> 
> You might take this swarm src.rpm I built on suse9.3
> 
> http://lark.cc.ku.edu/~pauljohn/Swarm/Swarm-2.2X_Suse9.3/swarm-2.2-
5_suse93.src.rpm
> 
> Install that, and then go to your SPEC directory and look through the 
> spec dir, see where the configure line is, fix the jdk directory.
> 
> After that, you could build the new rpm from that spec file.
> 
>  > rpmbuild -ba swarm-2.2.spec
> 
> 
> 
> > gcc-objc has to be installed
> > gperf has to be installed
> > 
> > ake[2]: Leaving directory `/data/src/hdf5-1.6.2/examples'
> > make[1]: Leaving directory `/data/src/hdf5-1.6.2'
> > PATH="$PATH:/sbin" ldconfig -n /data/src/hdf5-1.6.2/hdf5/lib
> > ----------------------------------------------------------------------
> > Libraries have been installed in:
> >    /data/src/hdf5-1.6.2/hdf5/lib
> > 
> > If you ever happen to want to link against installed libraries
> > in a given directory, LIBDIR, you must either use libtool, and
> > specify the full pathname of the library, or use the `-LLIBDIR'
> > flag during linking and do at least one of the following:
> >    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
> >      during execution
> >    - add LIBDIR to the `LD_RUN_PATH' environment variable
> >      during linking
> >    - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
> >    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
> > 
> > See any operating system documentation about shared libraries for
> > more information, such as the ld(1) and ld.so(8) manual pages.
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > Also, here is a longer info about the exit status from the
> installation:
> > 
> > bs && rm -f libswarm.so.0 && ln -s libswarm.so.0.0.0
> > libswarm.so.0)
> > (cd .libs && rm -f libswarm.so && ln -s libswarm.so.0.0.0
> > libswarm.so)
> > ar cru .libs/libswarm.a  SwarmEnvironment.o classList.o
> > ranlib .libs/libswarm.a
> > creating libswarm.la
> > (cd .libs && rm -f libswarm.la && ln -s ../libswarm.la
> > libswarm.la)
> > make[4]: Leaving directory `/data/src/swarm-2.2/src'
> > make[3]: Leaving directory `/data/src/swarm-2.2/src'
> > make[2]: Leaving directory `/data/src/swarm-2.2/src'
> > Making all in tools
> > make[2]: Entering directory `/data/src/swarm-2.2/tools'
> > if /bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..
> -I..
> > -I../libobjc -I../libobjc -I../src -I../src -I../src/collections -
> > I../src/defobj
> > -I../src/activity -I../src/objectbase -I../src/random
> -I../src/simtools
> > -I../src/gui -I../src/simtoolsgui -I../src/misc -I.  -DDLL_EXPORT -
> > D_GNU_SOURCE 
> > -g -O2 -fgnu-runtime -fno-strict-aliasing -Wall -Wno-import
> -Wno-protocol
> > -Wno-long-long -MT findImp.lo -MD -MP -MF ".deps/findImp.Tpo" -c -o
> > findImp.lo findImp.m; \
> > then mv -f ".deps/findImp.Tpo" ".deps/findImp.Plo"; else rm
> > -f ".deps/findImp.Tpo"; exit 1; fi
> > mkdir .libs
> >  gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../libobjc -I../libobjc
> -I../src
> > -I../src -I../src/collections -I../src/defobj -I../src/activity
> > -I../src/objectbase -I../src/random -I../src/simtools -I../src/gui
> > -I../src/simtoolsgui -I../src/misc -I. -DDLL_EXPORT -D_GNU_SOURCE -g
> -O2
> > -fgnu-runtime -fno-strict-aliasing -Wall -Wno-import -Wno-protocol
> > -Wno-long-long -MT findImp.lo -MD -MP -MF .deps/findImp.Tpo -c
> findImp.m  -fPIC
> > -DPIC -o .libs/findImp.o
> > findImp.m: In function `main':
> > findImp.m:45: warning: implicit declaration of function 
> > `swarm_force_references'
> >  gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../libobjc -I../libobjc
> -I../src
> > -I../src -I../src/collections -I../src/defobj -I../src/activity
> > -I../src/objectbase -I../src/random -I../src/simtools -I../src/gui
> > -I../src/simtoolsgui -I../src/misc -I. -DDLL_EXPORT -D_GNU_SOURCE -g
> -O2
> > -fgnu-runtime -fno-strict-aliasing -Wall -Wno-import -Wno-protocol
> > -Wno-long-long -MT findImp.lo -MD -MP -MF .deps/findImp.Tpo -c
> findImp.m -o
> > findImp.o >/dev/null 2>&1
> > /bin/sh ../libtool --mode=link gcc  -g -O2 -fgnu-runtime
> -fno-strict-aliasing
> > -Wall -Wno-import -Wno-protocol -Wno-long-long   -o findImp -L../src
> > -L../libobjc  findImp.lo -lswarm
> > gcc -g -O2 -fgnu-runtime -fno-strict-aliasing -Wall -Wno-import
> -Wno-protocol
> > -Wno-long-long -o .libs/findImp .libs/findImp.o 
> -L/data/src/swarm-2.2/src
> > -L/data/src/swarm-2.2/libobjc
> /data/src/swarm-2.2/src/.libs/libswarm.so
> > -L/data/src/swarm-2.2/src/space -L/data/src/swarm-2.2/src/analysis
> > -L/data/src/swarm-2.2/src/simtoolsgui
> -L/data/src/swarm-2.2/src/simtools
> > -L/data/src/swarm-2.2/src/random -L/data/src/swarm-2.2/src/tkobjc
> > -L/data/src/swarm-2.2/src/tclobjc -L/data/src/swarm-2.2/src/objectbase
> > -L/data/src/swarm-2.2/src/activity -L/data/src/swarm-2.2/src/defobj
> > -L/data/src/swarm-2.2/src/collections -L/data/src/swarm-2.2/src/misc
> > -L/usr/X11R6/lib64 /data/src/swarm-2.2/src/space/.libs/libspace.so
> > /data/src/swarm-2.2/src/analysis/.libs/libanalysis.so
> > /data/src/swarm-2.2/src/simtoolsgui/.libs/libsimtoolsgui.so
> > /data/src/swarm-2.2/src/simtools/.libs/libsimtools.so
> > /data/src/swarm-2.2/src/random/.libs/librandom.so
> > /data/src/swarm-2.2/src/tkobjc/.libs/libtkobjc.so /data/src/swarm!
> >  -2.2/src/tclobjc/.libs/libtclobjc.so
> > /data/src/swarm-2.2/src/objectbase/.libs/libobjectbase.so
> > /data/src/swarm-2.2/src/activity/.libs/libactivity.so
> > /data/src/swarm-2.2/src/defobj/.libs/libdefobj.so
> > /data/src/swarm-2.2/src/collections/.libs/libcollections.so
> > /data/src/swarm-2.2/src/misc/.libs/libmisc.so
> > /data/src/swarm-2.2/libobjc/.libs/libswarmobjc.so -lBLT24 -ltk8.4
> -ltcl8.4 -
> > lXpm
> > -lz -lX11 -lm -ldl
> > /data/src/swarm-2.2/src/.libs/libswarm.so: undefined reference to
> > `swarm_lookup_module'
> > collect2: ld returned 1 exit status
> > make[2]: *** [findImp] Error 1
> > make[2]: Leaving directory `/data/src/swarm-2.2/tools'
> > make[1]: *** [all-recursive] Error 1
> > make[1]: Leaving directory `/data/src/swarm-2.2'
> > make: *** [all] Error 2
> > 
> > 
> > Many thanks in advance,
> > David Camacho
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Support mailing list
> > address@hidden
> > http://www.swarm.org/mailman/listinfo/support
> 
> 
> -- 
> Paul E. Johnson                       email: address@hidden
> Dept. of Political Science            http://lark.cc.ku.edu/~pauljohn
> 1541 Lilac Lane, Rm 504
> University of Kansas                  Office: (785) 864-9086
> Lawrence, Kansas 66044-3177           FAX: (785) 864-5700
> _______________________________________________
> Support mailing list
> address@hidden
> http://www.swarm.org/mailman/listinfo/support
> 



David Camacho Ph.D. Student
Intelligent Bioinformatics Systems
German Cancer Research Center - DKFZ - TP3
www.dkfz.de
Im Neuenheimer Feld 580
69120 Heidelberg
DKFZPhone: +49 (0) 6221 42 2720
Fax:       +49 (0) 6221 42-3620