August 2020 - users-list

[MonetDB-users] Proofreading your professional documents
by Richard Hounslow 24 Feb '24

24 Feb '24

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2 2

SELinux problems
by Arjen P. de Vries 29 Dec '21

29 Dec '21

Hi all, Not really a bug report because I did not manage to figure out the cause. However, after upgrading from FC31 to FC32 I could not login any more, due to SELinux problems. Auto-relabeling did not work, nothing really... ... until I did dnf uninstall MonetDB-selinux. I came to this point because trying to give systemd services the correct labels with restorecon failed with an error referencing a monetdb specific file. I do not have the details unfortunately, but if you get problems, beware that MonetDB SELinux package and systemd may interfere in some way beyond my knowledge of these services. Best regards, Arjen PS: Some output from logs: sudo ausearch -c monetdb -m AVC,SELINUX_ERR [..] ---- time->Sat May 2 20:57:01 2020 type=AVC msg=audit(1588445821.693:203): avc: denied { open } for pid=1232 comm="monetdbd" path="/etc/resolv.conf" dev="dm-0" ino=3409775 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:default_t:s0 tclass=file permissive=1 ---- time->Sat May 2 21:12:56 2020 type=AVC msg=audit(1588446776.043:1194): avc: denied { execute } for pid=2861 comm="(monetdbd)" name="monetdbd" dev="dm-0" ino=2147256 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:unlabeled_t:s0 tclass=file permissive=1 trawcon="unconfined_u:object_r:monetdbd_exec_t:s0" ---- time->Sat May 2 21:12:56 2020 type=AVC msg=audit(1588446776.043:1195): avc: denied { execute_no_trans } for pid=2861 comm="(monetdbd)" path="/usr/bin/monetdbd" dev="dm-0" ino=2147256 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:unlabeled_t:s0 tclass=file permissive=1 trawcon="unconfined_u:object_r:monetdbd_exec_t:s0" ---- time->Sat May 2 21:12:56 2020 type=AVC msg=audit(1588446776.044:1196): avc: denied { map } for pid=2861 comm="monetdbd" path="/usr/bin/monetdbd" dev="dm-0" ino=2147256 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:unlabeled_t:s0 tclass=file permissive=1 trawcon="unconfined_u:object_r:monetdbd_exec_t:s0" ---- time->Sat May 2 21:12:56 2020 type=AVC msg=audit(1588446776.714:1197): avc: denied { remove_name } for pid=1232 comm="monetdbd" name="merovingian.pid" dev="tmpfs" ino=34369 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:unlabeled_t:s0 tclass=dir permissive=1 trawcon="system_u:object_r:monetdbd_var_run_t:s0" ---- time->Sat May 2 21:12:56 2020 type=AVC msg=audit(1588446776.714:1198): avc: denied { unlink } for pid=1232 comm="monetdbd" name="merovingian.pid" dev="tmpfs" ino=34369 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:unlabeled_t:s0 tclass=file permissive=1 ---- time->Sat May 2 21:12:56 2020 type=AVC msg=audit(1588446776.714:1199): avc: denied { write } for pid=1232 comm="monetdbd" name=".merovingian_lock" dev="dm-0" ino=5899443 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:unlabeled_t:s0 tclass=file permissive=1 trawcon="system_u:object_r:monetdbd_lock_t:s0" ---- time->Sat May 2 21:13:15 2020 type=AVC msg=audit(1588446795.214:1209): avc: denied { read } for pid=2925 comm="(monetdbd)" name="passwd" dev="dm-0" ino=524514 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:var_t:s0 tclass=file permissive=1 ---- time->Sat May 2 21:13:15 2020 type=AVC msg=audit(1588446795.214:1210): avc: denied { open } for pid=2925 comm="(monetdbd)" path="/var/lib/sss/mc/passwd" dev="dm-0" ino=524514 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:var_t:s0 tclass=file permissive=1 ---- time->Sat May 2 21:13:15 2020 type=AVC msg=audit(1588446795.214:1211): avc: denied { map } for pid=2925 comm="(monetdbd)" path="/var/lib/sss/mc/passwd" dev="dm-0" ino=524514 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:var_t:s0 tclass=file permissive=1 ---- time->Sat May 2 21:14:24 2020 type=AVC msg=audit(1588446864.487:1281): avc: denied { read } for pid=3072 comm="(monetdbd)" name="passwd" dev="dm-0" ino=524514 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:var_t:s0 tclass=file permissive=1 ---- time->Sat May 2 21:14:24 2020 type=AVC msg=audit(1588446864.487:1282): avc: denied { open } for pid=3072 comm="(monetdbd)" path="/var/lib/sss/mc/passwd" dev="dm-0" ino=524514 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:var_t:s0 tclass=file permissive=1 ---- time->Sat May 2 21:14:24 2020 type=AVC msg=audit(1588446864.487:1283): avc: denied { map } for pid=3072 comm="(monetdbd)" path="/var/lib/sss/mc/passwd" dev="dm-0" ino=524514 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:var_t:s0 tclass=file permissive=1 -- ==================================================================== ICIS, office M1.00.05 Radboud University Mercator 1 Faculty of Science Toernooiveld 212 arjen(a)cs.ru.nl NL-6525 EC Nijmegen, The Netherlands +31-(0)24-365 2354 ===================== http://www.informagus.nl/ ==================== -- ==================================================================== ICIS, office M1.00.05 Radboud University Mercator 1 Faculty of Science Toernooiveld 212 arjen(a)cs.ru.nl NL-6525 EC Nijmegen, The Netherlands +31-(0)24-365 2354 ===================== http://www.informagus.nl/ ====================

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Bad query performance after lots of updates
by Daniel Glöckner 01 Sep '20

01 Sep '20

Hi, select count(*) from table where field = 'some value'; --> a few ms update table set field = 'value'; --> update 2 million rows out of 1 billion rows select count(*) from table where field = 'some value'; --> almost a minute :( Analyze did not help and sys.vacuum could not be used as the table has indexes (foreign key). Re-starting the DB helped ;) What's the recommended way to make MonetDB perform well after lots of updates? Kind regards, Daniel

2 1

custom joins in Jun2020
by Roberto Cornacchia 27 Aug '20

27 Aug '20

This is a question about join order. In general, about how it changed from Nov2019 to Jun2020 releases. In particular, with respect to custom joins (filter functions). With a schema: CREATE TABLE t1(s string); CREATE TABLE t2(s string); Consider the following 2 queries, which only differ for having swapped conditions: Q1: SELECT t1.s, t2.s FROM t1, t2 WHERE t1.s <> t2.s AND [t1.s] maxlevenshtein [t2.s, 1]; Q2: SELECT t1.s, t2.s FROM t1, t2 WHERE [t1.s] maxlevenshtein [t2.s, 1] AND t1.s <> t2.s; [t1.s] maxlevenshtein [t2.s, 1] is equivalent to levenshtein(t1.s, t2.s) <=1 (i.e. the two strings have a levenshtein distance at most 1) This is a relatively expensive and selective function. In Nov2019, both Q1 and Q2 are translated to: - "maxlevenshtein" custom join - "!=" selection on the result In Jun2020, the two queries happen to be evaluated in the same order as they are written. Which means that Q2 is evaluated as: - "!=" join - "maxlevenshtein" selection This last evaluation plan is unfortunately not viable at all. The first join is not very selective, and the "maxlevenshtein" selection is run on way too many pairs, without the optimizations that can be exploited in a join (in a join, it is possible to skip the actual levenshtein computation for most combinations). Q2 in Jun2020 is 2 orders of magnitude slower than Q1, which quickly leads to unreasonably long query times. Of course, this is just one specific case. A very unfortunate one, due to the combination of a couple of factors: - The "!=" join is not selective enough - The custom function is an expensive one I guess my real questions are: - Is it by chance (or, as a by-product of more generic join ordering rules) that Nov2019 executes custom joins first in both Q1 and Q2, or was it an intentional choice to first execute custom joins? - What would a reasonable approach be? Is it reasonable to assume that if one writes a custom join, this is expected to use an expensive comparison function and that the join implementation can be much more efficient than the selection implementation (by skipping unnecessary comparisons)? If no assumptions can be made, can there be a way to annotate custom implementations with information on selectivity and cost? Thanks for you input, Roberto

1 1

Loading timestamps via Python loader functions
by Daniel Glöckner 26 Aug '20

26 Aug '20

Hi, there seems to be a limitation for Python-based loader functions wrt timestamps. Looking at the implementation in sql/backends/monet5/UDF/pyapi3/convert_loops.h suggests that timestamps are indeed not covered. Both of the the 2 following examples fail with "Failed conversion: MALException:pyapi3.eval:PY000!Unrecognized type. Could not convert to NPY_UNICODE.". CREATE LOADER array_loader() LANGUAGE PYTHON { from datetime import datetime _emit.emit( { 'a': [1,2,3], 'b': [datetime.utcnow(), datetime.utcnow(), datetime.utcnow()], 'c': ['1', '2', '3']}) }; CREATE LOADER array_loader() LANGUAGE PYTHON { import numpy as np from datetime import datetime dt = datetime.utcnow() _emit.emit( { 'a': [1,2,3], 'b': np.array([dt, dt, dt], dtype=np.datetime64), 'c': ['1', '2', '3']}) }; Is anyone aware of a workaround? An obvious workaround is to insert the timestamps as strings and convert them via SQL but that's much less efficient. Kind regards, Daniel

1 0

result properties in pcre.c
by Roberto Cornacchia 25 Aug '20

25 Aug '20

Hi, I was looking at pcre.c for some inspiration and found something suspicious. At the end of both pcre_likeselect() and re_likeselect(): if (bn && !msg) { BATsetcount(bn, BATcount(bn)); /* set some properties */ bn->tsorted = true; bn->trevsorted = bn->batCount <= 1; bn->tkey = true; bn->tseqbase = bn->batCount == 0 ? 0 : bn->batCount == 1 ? * (oid *) Tloc(bn, 0) : oid_nil; } Which I read as: if everything went well, then the result is sorted and key. But I miss why it should be sorted and key. Roberto

2 2

Re: Re: MonetDB on IBM Power architecture
by Daniel Glöckner 20 Aug '20

20 Aug '20

Hi, This looks very promising so far. Building on Power 8 was easy, just following the official guide from the wiki. https://www.monetdb.org/wiki/MonetDB:Building_from_sources So far I’ve only loaded larger amounts of data and the timings look good. Will perform more tests over the next days but overall this looks like absolutely usable for production. Kind regards, Daniel

1 0

JDBC Driver
by Walter Weinmann 19 Aug '20

19 Aug '20

Including the JDBC driver with gradle implementation 'monetdb:monetdb-java-lite:2.38' gives me: FAILURE: Build failed with an exception. * Where: Build file 'D:\SoftDevelopment\Projects\Konnexions\db_seeder\build.gradle' line: 66 * What went wrong: Could not determine the dependencies of task ':fatJar'. > Could not resolve all files for configuration ':runtimeClasspath'. > Could not find monetdb:monetdb-jdbc-new:2.37-SNAPSHOT. Searched in the following locations: - https://jcenter.bintray.com/monetdb/monetdb-jdbc-new/2.37-SNAPSHOT/maven-me… - https://jcenter.bintray.com/monetdb/monetdb-jdbc-new/2.37-SNAPSHOT/monetdb-… - https://repo.maven.apache.org/maven2/monetdb/monetdb-jdbc-new/2.37-SNAPSHOT… - https://repo.maven.apache.org/maven2/monetdb/monetdb-jdbc-new/2.37-SNAPSHOT… - https://jitpack.io/monetdb/monetdb-jdbc-new/2.37-SNAPSHOT/maven-metadata.xml - https://jitpack.io/monetdb/monetdb-jdbc-new/2.37-SNAPSHOT/monetdb-jdbc-new-… - http://maven.cubrid.org/monetdb/monetdb-jdbc-new/2.37-SNAPSHOT/maven-metada… - http://maven.cubrid.org/monetdb/monetdb-jdbc-new/2.37-SNAPSHOT/monetdb-jdbc… Required by: project : > monetdb:monetdb-java-lite:2.38 * Try: Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

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Re: Re: MonetDB on IBM Power architecture
by Daniel Glöckner 19 Aug '20

19 Aug '20

Hi, Thanks a lot for confirming this. We’ll perform some basic tests on our Power 8 system to see if we’re able to build and run it. Kind regards, Daniel

1 0

MonetDB on IBM Power architecture
by Daniel Glöckner 19 Aug '20

19 Aug '20

Hi folks, I was wondering if one could run MonetDB on IBM Power architecture (Power 8 and later). I guess there's no official build for this? Did anyone try this out? Kind regards, Daniel

2 1