[Debian-med-packaging] Bug#969608: Bug#969608: makeblastdb 2.10.x on 32-bit architectures

[Étienne Mollier]

Hi Aaron,

Aaron M. Ucko, on 2020-09-14 17:36:14 -0400:
> 
> Thanks for clarifying.  AFAICT, this environment imposes a tighter limit
> than native arm64 hardware, and versions 2.10.0-1 and 2.10.0-3 both hit
> it.  Rough bisection via the BLASTDB_LMDB_MAP_SIZE environment variable
> gives an empirical limit of 20,073,607,168 bytes (4,900,783 4K pages).
> This number isn't particularly round, so it presumably reflects what
> remains of some cumulative limit.  As such, the default should probably
> be at most 20,000,000,000 bytes (4,882,812½ pages ;-) to build in more
> of a margin.  That's 1/15 upstream's default, but with any luck should
> be plenty in practice, so I'm open to making that adjustment.  Also,
> this reduced limit would still be well more than we (can) allow on
> 32-bit architectures, which is in turn much more than upstream's trunk
> allows on Windows:
> 
> https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/include/objtools/blast/seqdb_writer/writedb_lmdb.hpp#L51

Wow, thanks for the comprehensive background information.  In
case someone else (me in a not so near future for instance)
stumbles upon this again, I keep note that reducing the size of
BLASTDB_LMDB_MAP_SIZE a bit might help:

	(sid-arm64-sbuild)$ makeblastdb -in NC_005816.faa -dbtype prot -hash_index -max_file_sz 20MB -parse_seqids -taxid 10
	
	
	Building a new DB, current time: 09/15/2020 19:37:37
	New DB name:   /tmp/NC_005816.faa
	New DB title:  NC_005816.faa
	Sequence type: Protein
	Deleted existing Protein BLAST database named /tmp/NC_005816.faa
	Keep MBits: T
	Maximum file size: 20000000B
	
	No volumes were created.
	
	Error: mdb_env_open: Cannot allocate memory

	(sid-arm64-sbuild)$ BLASTDB_LMDB_MAP_SIZE=10000000000 makeblastdb -in NC_005816.faa -dbtype prot -hash_index -max_file_sz 20MB -parse_seqids -taxid 10
	
	
	Building a new DB, current time: 09/15/2020 19:37:34
	New DB name:   /tmp/NC_005816.faa
	New DB title:  NC_005816.faa
	Sequence type: Protein
	Deleted existing Protein BLAST database named /tmp/NC_005816.faa
	Keep MBits: T
	Maximum file size: 20000000B
	Adding sequences from FASTA; added 10 sequences in 0.166301 seconds.

Kind Regards,
-- 
Étienne Mollier <etienne.mollier at mailoo.org>
Old rsa/3072: 5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
New rsa/4096: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/2, please excuse my verbosity.
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