[Beowulf] static pvm library won't link anymore
landman at scalableinformatics.com
Thu Jul 5 16:58:25 PDT 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 ...
> broke my software that interfaces with those database
> 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
> 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
> lpvmpack.c:(.text+0x3bb8): undefined reference to `__ctype_b'
> 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
phone: +1 734 786 8423
fax : +1 866 888 3112
cell : +1 734 612 4615
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