[Beowulf] static pvm library won't link anymore

David Mathog mathog at caltech.edu
Thu Jul 5 19:16:24 EDT 2007


In the land of dominoes...

The NCBI added another character or two to the allowed
list of letters that can be stored in BLAST databases

  which

broke my software that interfaces with those database

  which 

broke every program I use that reads sequence data through that interface.

That sort of change happens once or twice a year and so is par for the
course.  What is unusual this time is that when I tried to rebuild the
first one of these PVM based applications (hmmer 2.3.2 package by Sean
Eddy) the linker was very unhappy with the static pvm library:

/usr/common/pvm3/lib/LINUX/libpvm3.a(lpvmpack.o): In function `pvm_vpackf':
lpvmpack.c:(.text+0x36d4): undefined reference to `__ctype_b'
lpvmpack.c:(.text+0x36f8): undefined reference to `__ctype_b'
lpvmpack.c:(.text+0x3728): undefined reference to `__ctype_b'
lpvmpack.c:(.text+0x3747): undefined reference to `__ctype_b'
/usr/common/pvm3/lib/LINUX/libpvm3.a(lpvmpack.o): In function
`pvm_vunpackf':
lpvmpack.c:(.text+0x3bb8): undefined reference to `__ctype_b'
/usr/common/pvm3/lib/LINUX/libpvm3.a(lpvmpack.o):lpvmpack.c:(.text+0x3bd7):
more undefined references to `__ctype_b' follow
collect2: ld returned 1 exit status
make: *** [afetch] Error 1

In the spirit of leaving well enough alone the hmm applications have not
been modified in 3 years, and libpvm3.a has not been
touched since Oct 2002.  Apparently that library must now be rebuilt.
The source was PVM 3.4.4, it seems in the last 5 years they've released
3.4.5, so I guess it's time to update to that.

Anybody else seen this particular PVM/linker issue?
If so, is there anything else that needs to be done beyond
rebuilding PVM (applications and library)?

Thanks,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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