Hi Aaron, Aaron M. Ucko, on 2020-09-13 22:44:00 -0400: > Étienne Mollier <etienne.mollier@mailoo.org> writes: > > > regression looks still there in version 2.10.0-3, at least on > > arm64 architecture. > > How can I reproduce it? I worked within an arm64 schroot built with sbuild-createchroot, on a native amd64 machine. The reproducer is the test from Biopython stored in Tests/test_NCBI_BLAST_tools.py, which boils down to running the command: makeblastdb \ -in NC_005816.faa \ -dbtype prot \ -hash_index \ -max_file_sz 20MB \ -parse_seqids \ -taxid 10 where NC_005816.faa can be obtained from the Biopython test suite on Salsa: https://salsa.debian.org/med-team/python-biopython/-/raw/master/Tests/GenBank/NC_005816.faa When I run it within that arm64 environment, I get the following output, and the error code 255 sent back to the shell: Building a new DB, current time: 09/14/2020 18:35:05 New DB name: /tmp/NC_005816.faa New DB title: NC_005816.faa Sequence type: Protein Keep MBits: T Maximum file size: 20000000B No volumes were created. Error: mdb_env_open: Cannot allocate memory while specifying "-blastdb_version 4" in additions restores the former behavior: Building a new DB, current time: 09/14/2020 18:44:51 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 0.0821829 seconds. I haven't straced the execution of the program to check the amount of memory in map, so maybe the issue is different but with similar symptoms as previously? > AFAICT python-biopython's autopkgtest boils > down to the upstream test suite, which runs fine as part of a build of > revision 15084ca (immediately preceding your patch to drop back to > version 4 on selected architectures) on the porterbox amdahl. Perhaps > system limits come into play in some other environments, but then I > expect they would have done the same on 2.10.0-1. Also, the telltale > warning > > /<<PKGBUILDDIR>>/c++/include/objtools/blast/seqdb_writer/writedb_lmdb.hpp:52:59: warning: integer overflow in expression of type ‘int’ results in ‘-647710720’ [-Woverflow] > > occurs only in the logs for 2.10.0-2. Ouch, looks good to know, thank you for the warning. Kind Regards, -- Étienne Mollier <etienne.mollier@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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