[Condor-users] error compiling avida software

[Javier Forment Millet <jforment@xxxxxxxxxxxx>]

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 Biolog�Celular y Molecular de Plantas (IBMCP) CSIC-UPV
 Ciudad Polit�ica de la Innovaci�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