[Beowulf] static pvm library won't link anymore

Joe Landman landman at scalableinformatics.com
Thu Jul 5 19:58:25 EDT 2007


David Mathog wrote:
> 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

Yeah ... breaks my parsers every now and then ...

> 
>   which
> 
> broke my software that interfaces with those database

:)

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

You should see what they did to the code itself.  Just go try to build 
it in a non-GCC linux environment on x86_64.  It will complain, badly. 
I have patches for that in my latest RPMs 
(http://downloads.scalableinformatics.com/downloads/ncbi/).  Annoying.

> That sort of change happens once or twice a year and so is par for the

Progress ...

> 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

Been modified by some :) to make them go faster.  Also there is a nice 
MPI version out now (no PVM vs MPI here, just pointing it out) at 
http://code.google.com/p/mpihmmer/ .  Dev team are good guys :)

> 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?

I think this could be due to some libs being built with older glibc/gcc 
bits.  Library mismatch is best guess.

> If so, is there anything else that needs to be done beyond
> rebuilding PVM (applications and library)?

Possibly any dependencies.



-- 

Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
        http://jackrabbit.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 866 888 3112
cell : +1 734 612 4615

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