"chomsri upkaew" writes:
>Dear All,
>
>Did anyone compile sander with parallel on Linux cluster machine? I can't
>compile it. My machine is Linux SuSE 6.2 containing absoft, f77, pgf77,
>pgf90 and g77 compilers, including mpich-1.2.0 library.
>
>When I compiled with machine file 'Machine.g77_mpich', I obtained error
>message as below.
>
>.
>.
>.
>checksz.o: warning: multiple common of `misc5i_'
>lesmain.o: warning: previous common is here
>checksz.o: warning: multiple common of `misc6i_'
>lesmain.o: warning: previous common is here
>../lib/mexit.o: In function `mexit_':
>../lib/mexit.o(.text+0x36): undefined reference to `mpi_abort__'
>../lib/mexit.o(.text+0x46): undefined reference to `mpi_finalize__'
>../lib/mexit.o(.data+0x0): undefined reference to `mpi_dup_fn__'
>../lib/mexit.o(.data+0x4): undefined reference to `mpi_null_delete_fn__'
>../lib/mexit.o(.data+0x8): undefined reference to `mpi_null_copy_fn__'
>collect2: ld returned 1 exit status
>make[1]: *** [addles] Error 1
>make[1]: Leaving directory `/users/siriwong/amber6/src/addles'
>make: *** [install] Error 2
Actually, addles doesn't need to be compiled in parallel. But the specific error
you're having has to do with "second underscores".
If I run "nm" (symbol table lister) on the MPICH libray on my system, I see:
dek_at_warhol:~
:nm /opt/mpich-1.2.0/lib/libmpich.a|grep mpi_abort
00000000 W mpi_abort__
00000000 T pmpi_abort__
so my symbols have "second underscores", "__" at the end of their names.
Now, I expect, if you were to run nm on your mpich, you wouldn't see
the second underscore.
I would try adding "-fno-second-underscore" to the compile and link options
for AMBER in the Machine.g77_mpich file, and recompiling.
Be careful- ../lib/mexit.o doesn't get cleaned up if you do a "make clean"
in the sander subdirectory. You have to "make clean" in the top-level src
directory, or "make clean" in lib.
But again note, addless doesn't need to be compiled parallel. Only sander
really needs to (or would benefit from) parallelization. So focus your time
on getting sander compiled parallel :-)
Received on Fri Mar 16 2001 - 09:28:06 PST
