[FLASH-USERS] Compiling problem on SL6

[Christopher Daley]

Hi Seyit,

Did you ever resolve this problem?


These symbols exist in libpthread and libc.  Perhaps you are trying to
link statically and have not yet installed a static glibc for you
clean Scientific-Linux 6 installation:

$ repoquery --list glibc-static
/usr/lib64/libBrokenLocale.a
/usr/lib64/libanl.a
/usr/lib64/libc.a
/usr/lib64/libc_stubs.a
/usr/lib64/libcrypt.a
/usr/lib64/libdl.a
/usr/lib64/libm.a
/usr/lib64/libnsl.a
/usr/lib64/libpthread.a
/usr/lib64/libresolv.a
/usr/lib64/librt.a
/usr/lib64/libutil.a

If so, try installing the glibc-static package or remove the -static
option from your FLASH link options.


If the link still fails then you should test if it fails when you
remove the FLASH I/O library dependence, i.e. setup FLASH with +noio.

Chris


On 11/18/2011 05:06 AM, Seyit Hocuk wrote:
> Dear all,
>
> I have recently switched to Scientific Linux 6 (from CenOS 5), but now I
> cannot compile my code anymore. Below is a snippet of the error. It
> happens during the linking stage. Can anyone comment on this?
>
> I use my own fortran compiler (ifort 10.1.017)
> I use my own mpich (2.1.0.7)
> I use hdf5 version 1.8.1 (with api bindings for 1.6)
> These libraries are unchanged from Centos5 to SL6.
>
> I use the systems default gcc, which has changed from C5 to SL6.
>
> I've tried to reinstall ifort and mpich, even tried to use intelcc
> instead of gcc, but compiling still goes wrong. The problem lies surely
> in one of these. Is it gcc, mpich, or hdf5?
>
> Kind regards,
> Seyit
>
>
>
> ......tree.o umap.o user_coord_transfm.o ut_conversionInterface.o
> ut_convertToArrayIndicies.o ut_convertToMemoryOffset.o ut_fndpos.o
> ut_hunt.o ut_interpolationInterface.o ut_polint.o ut_quadraticInterpol.o
> ut_sortInterface.o ut_sortOnProcs.o workspace.o
> -L/net/ulubey/data/users/seyit/programmas/Libraries/lib64/hdf5-1.8.1/hdf5/lib
> -lhdf5 -lz -L
> /net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib
> -lmpich
>
> /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../lib64/crt1.o: In
> function `_start':
> (.text+0x12): undefined reference to `__libc_csu_fini'
> /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../lib64/crt1.o: In
> function `_start':
> (.text+0x19): undefined reference to `__libc_csu_init'
> /net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib/libmpich.a(abort.o):
> In function `MPI_Abort':
> abort.c:(.text+0x22a): undefined reference to `pthread_getspecific'
> abort.c:(.text+0x25a): undefined reference to `pthread_getspecific'
> abort.c:(.text+0x369): undefined reference to `pthread_setspecific'
> abort.c:(.text+0x3ae): undefined reference to `pthread_setspecific'
> /net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib/libmpich.a(initthread.o):
> In function `MPIR_Init_thread':
> initthread.c:(.text+0x32e): undefined reference to `pthread_getspecific'
> initthread.c:(.text+0x354): undefined reference to `pthread_setspecific'
> /net/ulubey/data/users/seyit/programmas/Libraries/lib64/mpich2-1.0.7/MPICH2/lib/libmpich.a(initthread.o):
> In function `MPI_Init_thread':
> initthread.c:(.text+0x3fa): undefined reference to `pthread_key_create'
> initthread.c:(.text+0x4d9): undefined reference to `pthread_key_delete'
> initthread.c:(.text+0x517): undefined reference to `pthread_getspecific'
> initthread.c:(.text+0x543): undefined reference to `pthread_setspecific'
> initthread.c:(.text+0x567): undefined reference to `pthread_getspecific'
> initthread.c:(.text+0x593): undefined reference to `pthread_setspecific'
> initthread.c:(.text+0x5bf): undefined reference to `pthread_getspecific'
> initthread.c:(.text+0x5dc): undefined reference to `pthread_setspecific'
> initthread.c:(.text+0x5ec): undefined reference to `pthread_getspecific'
> initthread.c:(.text+0x618): undefined reference to `pthread_setspecific'
> initthread.c:(.text+0x63d): undefined reference to `pthread_setspecific
> .... etc. etc.