Re: [Condor-users] error compiling avida software

[Javier Forment Millet <jforment@xxxxxxxxxxxx>]

Hi all again... A couple of weeks ago I sent the message transcribed below to
the condor-users list. Somebody answered telling that I should use gcc-3.4
instead of gcc-4.1 in order to match the one used at compiling condor. I've
done that and I get the same error indicated below (obviously, with the
difference of errors pointing to gcc-3.4 instead of gcc-4.1).

The error arises only when trying to compile with condor_compile.

I'm using Ubuntu 7.10 in that machine.

Any idea?

Thanks very much,

Javier.



> Hi all.
>
> I have a Condor cluster with Pentium machines (i686) and Xeon machines
> (x86_64).
> I'm trying to compile AVIDA software (http://sourceforge.net/projects/avida)
> and
> get the following error:
>
> (...)
> Linking CXX executable ../../../bin/avida
> LINKING FOR CONDOR : /usr/bin/ld.real -L/usr/local/condor-6.8.6/lib -Bstatic
> --eh-frame-hdr -m elf_x86_64 --hash-style=both -export-dynamic
> -dynamic-linker
> /lib64/ld-linux-x86-64.so.2 -o ../../../bin/avida
> /usr/local/condor-6.8.6/lib/condor_rt0.o
> /usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/crti.o
> /usr/lib/gcc/x86_64-linux-gnu/4.1.2/crtbeginT.o
> -L/usr/local/avida-src-2.6.3/cbuild/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.1.2
> -L/usr/lib/gcc/x86_64-linux-gnu/4.1.2
> -L/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64 -L/lib/../lib64
> -L/usr/lib/../lib64 CMakeFiles/avida.dir/primitive.o -Bstatic -lmain
> -lclassification -lcpu -lanalyze -ldrivers -lcpu -ltools -lactions -lanalyze
> -Bdynamic -lpthread -Bstatic -ltcmalloc -lmain -Bdynamic
> /usr/local/condor-6.8.6/lib/libcondorsyscall.a
> /usr/local/condor-6.8.6/lib/libcondor_z.a
> /usr/local/condor-6.8.6/lib/libcomp_libstdc++.a
> /usr/local/condor-6.8.6/lib/libcomp_libstdc++.a -lm
> /usr/local/condor-6.8.6/lib/libcomp_libgcc.a
> /usr/local/condor-6.8.6/lib/libcomp_libgcc_eh.a -lcondor_c -lcondor_nss_files
> -lcondor_nss_dns -lcondor_resolv -lcondor_c -lcondor_nss_files
> -lcondor_nss_dns
> -lcondor_resolv -lcondor_c /usr/local/condor-6.8.6/lib/libcomp_libgcc.a
> /usr/local/condor-6.8.6/lib/libcomp_libgcc_eh.a
> /usr/lib/gcc/x86_64-linux-gnu/4.1.2/crtfastmath.o
> /usr/lib/gcc/x86_64-linux-gnu/4.1.2/crtend.o
> /usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/crtn.o
> /usr/local/condor-6.8.6/lib/libcondorsyscall.a(condor_file_agent.o): In
> function
> `CondorFileAgent::open(char const*, int, int)':
> /home/condor/execute/dir_16805/userdir/src/condor_ckpt/condor_file_agent.C:99:
> warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> /usr/local/condor-6.8.6/lib/libcondorsyscall.a(switches.o): In function
> `__gets_chk':
>
/home/condor/execute/dir_16805/userdir/src/condor_syscall_lib/switches.remap-LINUX.h:435:
> warning: the `gets' function is dangerous and should not be used.
> /usr/bin/ld.real: errno: TLS definition in /lib64/libc.so.6 section .tbss
> mismatches non-TLS definition in
> /usr/local/condor-6.8.6/lib/libcondor_c.a(errno.o) section .bss
> /lib64/libc.so.6: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[2]: *** [bin/avida] Error 1
> make[1]: *** [source/targets/avida/CMakeFiles/avida.dir/all] Error 2
> make: *** [all] Error 2
>
> It seems to be a problem with libc.so.6.
>
> Any idea?
>
> Thanks and cheers,
>
> Javier.
>
>
> --
> Javier Forment Millet
> Instituto de Biología Celular y Molecular de Plantas (IBMCP) CSIC-UPV
>  Ciudad Politécnica de la Innovación (CPI) Edificio 8 E, Escalera 7 Puerta E
>  Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain
> Tlf.:+34-96-3877858
> FAX: +34-96-3877859
> jforment@xxxxxxxxxxxx
>


-- 
Javier Forment Millet
Instituto de Biología Celular y Molecular de Plantas (IBMCP) CSIC-UPV
 Ciudad Politécnica de la Innovación (CPI) Edificio 8 E, Escalera 7 Puerta E
 Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain
Tlf.:+34-96-3877858
FAX: +34-96-3877859
jforment@xxxxxxxxxxxx