64bit Solaris compile of SRS v5.10?

Tim Cutts timc at chiark.greenend.org.uk
Thu Nov 18 10:22:35 EST 1999


In article <8103vh$1ui$1 at flotsam.uits.indiana.edu>,
Don Gilbert <gilbertd at bio.indiana.edu> wrote:
>When I try building SRS 5.10 on a 64 bit Solaris system using
>Sun's 64bit compiler (cc -xarch=v9), I get binaries that fail with
>bus errors.
>
>The system is newly installed Solaris 2.7 Ultrasparc, and the compiler
>is newly installed (Sun WorkShop 98/12/15 C 5.0, with all patches).
>I have tested other software, gzip, in a 64bit compile -- it works.
>
>Has anyone built SRS okay with this configuration (is it my system
>or an incompatibility of SRS to 64 bit systems)?
>
>-- one reason for a 64bit SRS is the Genbank daily update file has 
>grown over 2 GB and 32bit SRS won't open it :(  

SRS 5.x uses the Int4 type (i.e 32-bit integers) all over the place.  I'm
not at all surprised it doesn't compile as a 64-bit program; on 32-bit
systems any assumptions that certain system types are 32-bits (off_t in
filesystem access routines, for example) are the same as int and the
same as Int4 are fine, but on 64-bit systems this is liable to lead to
segmentation faults and bus errors.

SRS 6.x might compile 64-bit, but then again it might not - I haven't
seen it.

My solution to your problem is to split the cumulative update file into
chunks.  You then generate an appropriate genbank.i file on the fly, for
the right number of chunks, run srssection, and then re-build your
indices.

This works fine.  I can send you my scripts for doing this, if you are
interested.

Tim.






More information about the Bio-srs mailing list