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Driver JDBC, error rounding numeric value
by Luciano Sasso 25 Nov '15

25 Nov '15

Any idea, about error driver JDBC rounding error. Driver 2.18 run error, driver 2.1 run work ok. -- Luciano Sasso Vieira Data Scientist & Solutions Architect luciano(a)gsgroup.com.br <http://www.gsgroup.com.br> | tel: 17 3353-0833 | cel: 17 99706-9335 www.gsgroup.com.br <http://www.gsgroup.com.br> --- Este email foi escaneado pelo Avast antivírus. https://www.avast.com/antivirus

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Error driver JDBC
by Luciano Sasso 24 Nov '15

24 Nov '15

Hi, Iam use MonetDB JUL 2015-SPI, and driver JDBC 2.18, but error on load data, in rooud value, exampla, value 854 in source, load 850 in target. I am test with driver JDBC 2.1 and run word, value 845, load in target with 845. any idea !!! -- Luciano Sasso Vieira Data Scientist & Solutions Architect luciano(a)gsgroup.com.br <http://www.gsgroup.com.br> | tel: 17 3353-0833 | cel: 17 99706-9335 www.gsgroup.com.br <http://www.gsgroup.com.br> --- Este email foi escaneado pelo Avast antivírus. https://www.avast.com/antivirus

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Vacuum limitations
by Sébastien RAILLARD (PASSMAN) 24 Nov '15

24 Nov '15

Dear all, I have tried to call the vacuum function using this command: call sys.vacuum('my_schema','my_table'); I have a message telling me "vacuum not allowed on tables with indices". So, if I understand correctly, the table on which vacuum can be done must not have any index, even a primary key? Best regards, Sebastien -- Parc d'activité Tolstoï 4 rue Edouard Aynard 69100 Villeurbanne Tél. +33 (0)4 78 95 05 80 Fax +33 (0)4 78 95 00 17 www.passman.fr www.passman-hotels.com www.passman-camping.com www.passman-sante.com <https://www.facebook.com/PASSMAN-187787814053/>

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err incorrect checksum for freed object
by Lynn Carol Johnson 24 Nov '15

24 Nov '15

Hello - I had a working installation of monetdb on my MAC (OS x 10.9.5). Initially it was installed with the July 2015 release, I then updated to the july2015SP1. With the original version I was able to load a large (10G ) file without problems. For reasons relating to debugging a monetdb install on a red hat machine, I deleted the entries in the DB on my MAC and tried to re-add them. My commands were: > delete from annosites; > select count(*) from annosites; The db showed 0 items as expected. sql>\d annosites CREATE TABLE "testjeff"."annosites" ( "chr" INTEGER, "pos" INTEGER, "hapmap31_total_depth" INTEGER, "hapmap31_num_taxa" SMALLINT, "hapmap31_num_alleles" SMALLINT, "hapmap31_minor_allele_avg_depth" REAL, "hapmap31_minor_allele_avg_phred" REAL, "hapmap31_num_hets" SMALLINT, "hapmap31_ed_factor" REAL, "hapmap31_seg_test_p_value" REAL, "hapmap31_ibd_one_allele" BOOLEAN, "hapmap31_in_local_ld" BOOLEAN, "hapmap31_maf" REAL, "hapmap31_near_indel" BOOLEAN, "hapmap31_first_alt_allele_is_ins_or_del" BOOLEAN, "snpeff40e_effect_hapmap31" CHARACTER LARGE OBJECT, "snpeff40e_effectimpact_hapmap31" CHARACTER LARGE OBJECT, "snpeff40e_functionalclass_hapmap31" CHARACTER LARGE OBJECT, "gerp_neutral_tree_length" REAL, "gerp_score" REAL, "gerp_conserved" BOOLEAN, "mnase_low_minus_high_rpm_shoots" REAL, "mnase_bayes_factor_shoots" REAL, "mnase_hotspot_shoots" BOOLEAN, "mnase_low_minus_high_rpm_roots" REAL, "mnase_bayes_factor_roots" REAL, "mnase_hotspot_roots" BOOLEAN, "within_gene" BOOLEAN, "within_transcript" BOOLEAN, "within_exon" BOOLEAN, "within_cds" BOOLEAN, "within_cds_from_gff3" BOOLEAN, "within_five_prime_utr" BOOLEAN, "within_three_prime_utr" BOOLEAN, "codon_position" SMALLINT, "go_term_accession" CHARACTER LARGE OBJECT, "go_term_name" CHARACTER LARGE OBJECT ); But now, doing a "COPY INTO" continues to either hang with no error in the merovingian.log file , or to fail with the following error in the merovingian.log file. Most often it hangs. I have tried COPY into with and without the "records" option: sql> COPY INTO annosites from '/Users/lcj34/notes_files/machineLearningDB/annoDB_related/siteAnnoNoHdrsCol35Fixed_20151011.txt' USING DELIMITERS '\t','\n'; sql> sql>COPY 61000000 records INTO annosites from '/Users/lcj34/notes_files/machineLearningDB/annoDB_related/siteAnnoNoHdrsCol35Fixed_20151011.txt' USING DELIMITERS '\t','\n'; The merovingian.log file the one time it had an error: 015-11-23 15:02:55 MSG testJeff[752]: # loading sql script: 99_system.sql 2015-11-23 15:15:49 ERR testJeff[752]: mserver5(752,0x112908000) malloc: *** error for object 0x7fbe21a08208: incorrect checksum for freed object - object was probably modified after being freed. 2015-11-23 15:15:49 ERR testJeff[752]: *** set a breakpoint in malloc_error_break to debug 2015-11-23 15:15:50 MSG merovingian[747]: database 'testJeff' (752) was killed by signal SIGABRT Any idea what could be wrong? I tried stopping, then destroying the database and starting it over. This didn't help. I then created a new dbfarm, and new database, connect monetdbd to it, and tried again. While I can create this database of 37 columns, I am unable to load the file that previously was successfully loaded. Is this my a MAC issue? What else can I try on monetdb side? Is there any reason to re-install everything ? I'm still in the testing stage so would not be losing data. Thanks - Lynn

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commit failures with dbfarm on iSCSI LUN
by Roberto Cornacchia 24 Nov '15

24 Nov '15

Hi there, Do you have any experience with running a dbfarm over iSCSI? We have tried to use the NAS in our 1Gbit LAN for our largish daily experiments with MonetDB. It's a very handy setup and seems more suited than NFS. It seems to achieve reasonable performance, but we get quite regularly (though not predictably for now) commit failures during a rather long ETL. We do not get such commit failures when the same db and ETL are run on a local disk. Excerpt from merovingian.log (Jul2015-SP1): 2015-11-24 11:52:37 ERR trec01[19110]: !ERROR: bm_subcommit: commit failed 2015-11-24 11:52:37 ERR trec01[19110]: !ERROR: log_tend: write failed 2015-11-24 11:52:37 ERR trec01[19110]: !FATAL: 40000!COMMIT: transation commit failed (perhaps your disk is full?) exiting (kernel error: !ERROR: GDKsave: error on: name=07/717, ext=theap, mode=1 2015-11-24 11:52:37 ERR trec01[19110]: !OS: Input/output error 2015-11-24 11:52:37 ERR trec01[19110]: ) The disk is most definitely not full, 1.5 TB available (the same works on a local disk with less space available). It looks like iSCSI is the problem (which works perfectly except these random failures). Can you think of any reason why iSCSI could could fail where a real local block device would not? iscsi client (where MonetDB runs): libiscsi 1.11.0 iscsi storage (where the dbfarm is stored): iscsid 2.0-871 The iSCSI LUN is created as regular file with thin provisioning (a file that dynamically grows on the NAS). We haven't tried yet with a fixed-size block-level LUN (trying this today anyway) Hoping someone can have an idea already. Roberto

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String functions support in MonetDB
by Sébastien RAILLARD (PASSMAN) 24 Nov '15

24 Nov '15

Dear all, Is there a way to concatenate more than 2 strings at once? The CONCAT function only allow for concatenating 2 strings. Also, hhe JDBC driver for MonetDB reports that the following string functions are supported (see the list below). Are these functions documented somewhere? ascii char_length character_length code concat copyfrom difference editdistance editdistance2 get_value_for ilike index insert lcase left length levenshtein like locate lower lpad ltrim next_value_for not_ilike not_like octet_length patindex qgramnormalize repeat replace restart right rpad rtrim similarity soundex space splitpart strings substring trim truncate ucase upper Best regards, Sebastien -- Parc d'activité Tolstoï 4 rue Edouard Aynard 69100 Villeurbanne Tél. +33 (0)4 78 95 05 80 Fax +33 (0)4 78 95 00 17 www.passman.fr www.passman-hotels.com www.passman-camping.com www.passman-sante.com <https://www.facebook.com/PASSMAN-187787814053/>

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Making RPM packages for CentOS
by Sébastien RAILLARD (PASSMAN) 24 Nov '15

24 Nov '15

Dear all, Using a CentOS 6.7 x64 system, I was able to compile and make the RPM packages using the command "make rpm". The created packages were correctly installed and are working on the CentOS 6.7 x64 system. As I understand, the creation of the RPM packages process was made for Fedora systems: is-there any problem or limitation to be expected to create packages using "make rpm" for CentOS 6.x? Best regards, Sebastien -- Parc d'activité Tolstoï 4 rue Edouard Aynard 69100 Villeurbanne Tél. +33 (0)4 78 95 05 80 Fax +33 (0)4 78 95 00 17 www.passman.fr www.passman-hotels.com www.passman-camping.com www.passman-sante.com <https://www.facebook.com/PASSMAN-187787814053/>

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installing on redHat
by Lynn Carol Johnson 23 Nov '15

23 Nov '15

Hi all - I'm attempting to install on Redhat release 7.1 (Maipo) following the instructions here: https://www.monetdb.org/downloads/epel/ I have successfully executed : yum install http://dev.monetdb.org/downloads/epel/MonetDB-release-epel-1.1-1.monetdb.no… And rpm --import http://dev.monetdb.org/downloads/MonetDB-GPG-KEY But installing the server and client fail with the following message: [root@aztec Monetdb]# yum install MonetDB-SQL-server5 MonetDB-client Loaded plugins: langpacks, product-id, rhnplugin, subscription-manager This system is receiving updates from RHN Classic or Red Hat Satellite. http://dev.monetdb.org/downloads/epel/7Server/x86_64/repodata/repomd.xml: [Errno 14] HTTP Error 404 - Not Found Trying other mirror. One of the configured repositories failed (MonetDB 7Server - x86_64), and yum doesn't have enough cached data to continue. At this point the only safe thing yum can do is fail. There are a few ways to work "fix" this: 1. Contact the upstream for the repository and get them to fix the problem. 2. Reconfigure the baseurl/etc. for the repository, to point to a working upstream. This is most often useful if you are using a newer distribution release than is supported by the repository (and the packages for the previous distribution release still work). 3. Disable the repository, so yum won't use it by default. Yum will then just ignore the repository until you permanently enable it again or use --enablerepo for temporary usage: yum-config-manager --disable monetdb 4. Configure the failing repository to be skipped, if it is unavailable. Note that yum will try to contact the repo. when it runs most commands, so will have to try and fail each time (and thus. yum will be be much slower). If it is a very temporary problem though, this is often a nice compromise: yum-config-manager --save --setopt=monetdb.skip_if_unavailable=true failure: repodata/repomd.xml from monetdb: [Errno 256] No more mirrors to try. http://dev.monetdb.org/downloads/epel/7Server/x86_64/repodata/repomd.xml: [Errno 14] HTTP Error 404 - Not Found [root@aztec Monetdb]# When attempting to find this site from a browser I am unsuccessful. Should the repomd.xml file be grabbed from elsewhere? Any suggestions? Thanks - Lynn

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MonetDBLite issue: Compute() function not working
by Iain Wallace 23 Nov '15

23 Nov '15

Hi, Firstly, thanks for the wonderful MonetDBLite package. It certainly speeds up my analysis! I came acrros an issue that I thought you might want to be aware of. The compute() function doesn't appear to be working with MonetDBLite while collect() does Building from the example https://www.monetdb.org/blog/monetdblite-r library(MonetDB.R) ms <- src_monetdb(embedded=dbdir) x<-table(ms,"mtcars") y<-x%>%filter(gear==4) dim(y) [1] 12 11 compute(y) Source: MonetDB () From: lmsomncnjj [0 x 11] Error: n not greater than 0L I wasn't sure where to post this, so have also posted the issue on dplyr's github page: https://github.com/hadley/dplyr/issues/1533 Thanks Iain

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MonetDB Remote / Merge ( Distributed Query Processing ) Bug
by Brian Hood 19 Nov '15

19 Nov '15

Hi All, It seems when i run my SQL in sequence i can repeated break things with a MAL error. If this isn't a bug please can you point me in the right direction but looks like one with me. Master has 4 remote tables and a MERGE table ippacket with all the remote table added. All mserver5 instances are the same version / release. Welcome to mclient, the MonetDB/SQL interactive terminal (Jul2015-SP1) Database: MonetDB v11.21.11 (Jul2015-SP1), 'mapi:monetdb://mdb-master-01:50000/threatmonitor' Type \q to quit, \? for a list of available commands auto commit mode: on sql>\d MERGE TABLE threatmonitor.ippacket REMOTE TABLE threatmonitor.wifi_ippacket REMOTE TABLE threatmonitor.wifi_ippacket2 REMOTE TABLE threatmonitor.wifi_ippacket3 REMOTE TABLE threatmonitor.wifi_ippacket4 sql>select count(*) from ippacket limit 10; +------+ | L1 | +======+ | 951 | +------+ 1 tuple (44.499ms) sql>select guid, recv_date, ip_dst from ippacket limit 10 more>; (mapi:monetdb://monetdb@172.17.0.5/threatmonitor) 'user.l4' undefined in: (rmt3424_X_3_bat_oid_str:bat[:oid,:str],rmt3425_X_6_bat_oid_str:bat[:oid,:str],rmt3427_X_7_bat_oid_str:bat[:oid,:str]) := user.l4(); The second time i run the same query and its absolutely fine. sql>select guid, recv_date, ip_dst from ippacket limit 10 more>; +--------------------------------------+---------------------------+----------------+ | guid | recv_date | ip_dst | +======================================+===========================+================+ | 5f4c9bcb-e4b7-0af1-2919-fdef5623d20a | 2015-07-20 19:52:45 +0000 | 10.130.19.42 | | 2238c353-33cd-5174-31b6-ca57b4decade | 2015-07-20 19:52:45 +0000 | 216.58.209.227 | | 8ac3dde3-92ce-ff27-f6b1-f296b0d139f5 | 2015-07-20 19:52:45 +0000 | 10.130.19.42 | | 7a204771-8623-e498-5f45-ba1c58adb3da | 2015-07-20 19:52:45 +0000 | 85.25.200.151 | | 496ab33b-3ae9-56b5-9108-209413dcddeb | 2015-07-20 19:52:45 +0000 | 85.25.200.151 | | a1537072-8545-74eb-3b7e-9615a4c534ac | 2015-07-20 19:52:45 +0000 | 10.130.19.42 | | 91124c5a-0854-7f21-e60a-f175e45d68d1 | 2015-07-20 19:52:45 +0000 | 10.130.19.42 | | acefc01b-6ef8-6197-f5c0-27194e5749db | 2015-07-20 19:52:45 +0000 | 85.25.200.151 | | f0694ee8-2e7f-e019-a96e-450489ae8f37 | 2015-07-20 19:52:45 +0000 | 10.130.19.42 | | 78c246a9-eba2-79b5-fb87-59609f44a7d9 | 2015-07-20 19:52:45 +0000 | 85.25.200.151 | +--------------------------------------+---------------------------+----------------+ 10 tuples (63.443ms) sql> I've attached my example schema. Regards, Brian Hood

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MonetDB writing to disk?!
by Martin Schwitalla 19 Nov '15

19 Nov '15

Hi, I´m running some analysis on MonetDB and have quite bad results with MonetDB. At first I thought it would be the fault of the Operator-at-a-Time Modell. I could replicate the behaviour that predicates on more columns resulted in a linear growing in execution times. This is a direct consequence of the Operator-at-a-Time Modell. But know i realized that the behaviour heavily depends on the used disk in the system. If I have the database on my primary disk storage I get quite good results. But because the primary disk storage is quite limited in our experimental PC I have worked on an NAS with 11TB. When I launch the same query on the NAS the query doesn`t take 0,4s, but 25s! After further testing I could see with iotop that the mserver is constantly writing something to the disks. But why is that so? I`m running Ubuntu 14.04 64bit, with 2 Intel Xeon E5-2690 CPUs and 62GB RAM. I have installed the TPC-H benchmark and running select count(*) from lineitem where l_orderkey%2=0; on my primary disk storage took about 400ms. On the external disk storage it took about 23s. The table contains 149996355 tuple and I created the TPC-H database with a scaling factor of 25. While running this query SELECT anon_1.sample_id AS anon_1_sample_id, anon_1.variant_id AS anon_1_variant_id, anon_1.qual AS anon_1_qual, anon_1.is_heterozygous AS anon_1_is_heterozygous, anon_1.read_depth AS anon_1_read_depth, anon_1.ref_depth AS anon_1_ref_depth, anon_1.alt_depth AS anon_1_alt_depth, anon_1.strand_bias AS anon_1_strand_bias, anon_1.qual_by_depth AS anon_1_qual_by_depth, anon_1.mapping_qual AS anon_1_mapping_qual, anon_1.haplotype_score AS anon_1_haplotype_score, anon_1.mapping_qual_bias AS anon_1_mapping_qual_bias, anon_1.read_pos_bias AS anon_1_read_pos_bias, annotations.variant_id AS annotations_variant_id, annotations.feature_id AS annotations_feature_id, annotations.ref_codon AS annotations_ref_codon, annotations.alt_codon AS annotations_alt_codon, annotations.ref_acid AS annotations_ref_acid, annotations.alt_acid AS annotations_alt_acid, annotations.type AS annotations_type, annotations.region AS annotations_region, annotations.splice_dist AS annotations_splice_dist FROM (SELECT calls.sample_id AS sample_id, calls.variant_id AS variant_id, calls.qual AS qual, calls.is_heterozygous AS is_heterozygous, calls.read_depth AS read_depth, calls.ref_depth AS ref_depth, calls.alt_depth AS alt_depth, calls.strand_bias AS strand_bias, calls.qual_by_depth AS qual_by_depth, calls.mapping_qual AS mapping_qual, calls.haplotype_score AS haplotype_score, calls.mapping_qual_bias AS mapping_qual_bias, calls.read_pos_bias AS read_pos_bias FROM calls JOIN samples ON samples.id = calls.sample_id JOIN patients ON patients.id = samples.patient_id JOIN diseases ON diseases.id = samples.disease_id LEFT OUTER JOIN (SELECT calls.sample_id AS sample_id, calls.variant_id AS variant_id, calls.qual AS qual, calls.is_heterozygous AS is_heterozygous, calls.read_depth AS read_depth, calls.ref_depth AS ref_depth, calls.alt_depth AS alt_depth, calls.strand_bias AS strand_bias, calls.qual_by_depth AS qual_by_depth, calls.mapping_qual AS mapping_qual, calls.haplotype_score AS haplotype_score, calls.mapping_qual_bias AS mapping_qual_bias, calls.read_pos_bias AS read_pos_bias FROM calls WHERE calls.qual > 0 AND calls.sample_id IN (227, 230, 233, 234, 237, 190, 195, 198, 199, 203, 270, 273, 276, 189, 343, 366, 367, 368)) AS anon_2 ON anon_2.variant_id = calls.variant_id LEFT OUTER JOIN known ON known.variant_id = calls.variant_id AND known.source_id IN (1, 2, 20, 19, 46) WHERE samples.accession IN ('17041R5', '20195R', '21984R', '23273R', '23390R', '13264R', '18337R', '18533R', '19811R', '20039R', '21776R', '21809R', '22927R', '17294R', '17071R', '21016R', 'Greif1R', '18337T', '18533T', '19811T', '20039T', '21809T', '22927T', '20195T', '21984T', '23273T', '23390T', '17041T', '17294T', '17071T', '21016T', '13264T', '21776T', 'Greif1T1S') AND calls.qual >= 50 AND anon_2.variant_id IS NULL AND (known.variant_id IS NULL OR known.clinical AND (NOT known.clinical_significance = 2) OR known.precious OR known.locus_specific_db)) AS anon_1 JOIN variants ON variants.id = anon_1.variant_id JOIN annotations ON variants.id = annotations.variant_id JOIN features ON features.id = annotations.feature_id JOIN transcripts ON transcripts.id = features.transcript_id JOIN genes ON genes.id = transcripts.gene_id WHERE (variants.is_transition IS NULL OR variants.is_transversion IS NULL OR (variants.is_transition OR variants.is_transversion) AND (anon_1.strand_bias IS NULL OR anon_1.strand_bias <= 60.0) AND (anon_1.qual_by_depth IS NULL OR anon_1.qual_by_depth >= 2.0) AND (anon_1.mapping_qual IS NULL OR anon_1.mapping_qual >= 40.0) AND (anon_1.haplotype_score IS NULL OR anon_1.haplotype_score <= 13.0) AND (anon_1.mapping_qual_bias IS NULL OR anon_1.mapping_qual_bias >= -12.5) AND (anon_1.read_pos_bias IS NULL OR anon_1.read_pos_bias >= -8.0) OR NOT (variants.is_transition OR variants.is_transversion) AND (anon_1.strand_bias IS NULL OR anon_1.strand_bias <= 200.0) AND (anon_1.qual_by_depth IS NULL OR anon_1.qual_by_depth >= 2.0) AND (anon_1.read_pos_bias IS NULL OR anon_1.read_pos_bias >= -20.0)) AND (abs(annotations.splice_dist) <= 10 OR annotations.region = 2 AND (NOT annotations.type = 2) OR annotations.region = 3 OR annotations.region = 1); I could see that the mserver is constantly writing to the disks. So why is MonetDB constantly writing to the disks, even when the query is quite simpel like the one TPC-H query above? The data should fit into the memory without problems. Any ideas or suggestions? Kind Regards, Martin

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Using multiple COPY INTO inside a transaction from Java
by Gerardo Blanco 18 Nov '15

18 Nov '15

Hi, We are already using the COPY INTO bulk insert from Java via BufferedMCLWriter, as you suggest in your recipes book<https://www.monetdb.org/Documentation/Cookbooks/SQLrecipes/LoadingBulkData>, and based in the example<http://dev.monetdb.org/hg/MonetDB/file/tip/java/example/SQLcopyinto.java> you provided. I understood that each COPY INTO behaves as a single transaction. My question now is if there is a way to group two or more COPY INTO and make them behave as a single transaction. Thank you Gerardo

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publishing this november 30th
by Anthony Damico 17 Nov '15

17 Nov '15

some good news to go with the bad https://github.com/ajdamico/asdfree/tree/master/IPUMS%20International asdfree.com has had over 1,000 unique visitors per week since august. hopefully this will push even more users your way. thanks

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the majority of my monetdb programs broke between Jul2015 and Jul2015-SP1
by Anthony Damico 17 Nov '15

17 Nov '15

am i alone here? i'm very unhappy about this.. i'm sorry i'm being such a pain in the ass, but this has disrupted all of my work. all of my code worked on both unix and windows on prior versions. both the "american community survey" and "national incident based reporting system" bugs were introduced recently. [1] this bug [2] was also introduced after Jul2015, but luckily fixed before sp1's release. that had affected another two scripts. i am having a hell of a time reproducing a similar bug that's equally difficult to reproduce. it was a bit of a herculean effort for hannes to get 3828 isolated, the bug i am struggling with now is no different. [1] https://www.monetdb.org/bugzilla/buglist.cgi?bug_status=NEW&bug_status=ASSI… [2] https://www.monetdb.org/bugzilla/show_bug.cgi?id=3828

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what could i explore to create a reproducible example for a bug report?
by Anthony Damico 17 Nov '15

17 Nov '15

yellow highlight is the only difference > # this command works fine create table zp13 as select v.* , arf.fips , arf.county , arf.countyst , arf.msacode from v13 as v left join arf on v.state_code = arf.state_cd AND v.bene_county_cd = arf.cnty_cd WITH DATA; > # this command crashes mserver create table zp13 as select v.* , arf.fips , arf.county , arf.countyst , arf.msacode , arf.msaname from v13 as v left join arf on v.state_code = arf.state_cd AND v.bene_county_cd = arf.cnty_cd WITH DATA; i've attached the sys.columns for the two tables, not sure if attachments are allowed on the mailing list but i can send separately if needed. thanks!

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MonetDB concurrent commits exception
by Vijay Krishna 17 Nov '15

17 Nov '15

Hi, I am running a setup on MonetDB where in concurrent transactions take place. Everything works very fine but for a few transactions getting aborted due to SQLExceptions. I have set *auto commit to false* for all these transactions. I am getting frequent SQLExceptions with the message as *java.sql.SQLException: COMMIT: failed* But if I retry the same transaction, this works fine. Any idea on what would be the reason for frequent commit fails? When I set *auto commit to true* for the transactions, I get similarly frequent Exceptions but the message becomes *java.sql.SQLException: COMMIT: transaction is aborted because of concurrency conflicts* Is it like both the exception thrown be for the same cause? Any help much appreciated. Thanks in Advance. Vijayakrishna.P. Mobile : (+91) 9500402305.

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Chinese string and varchar size
by Mathieu Raillard 16 Nov '15

16 Nov '15

Hi all, Last week we find a strange case with chinese character and VARCHAR size. We have in our database a field defined with VARCHAR(5) and a chinese string "不要让早把" to be inserted. If we insert the string with SQL insert everything works find, but if we try to insert via BULK monet throw an error. I made several test and i need to extend the varchar from 5 to 10 to get the bulk insert working. It looks like BULK somehow counts bits and not characters ? I give you some infos if you want to reproduce the case: create table test.varcharsize4 ( id int, varchar105 varchar(4), primary key (id) ); create table test.varcharsize5 ( id int, varchar106 varchar(5), primary key (id) ); create table test.varcharsize9 ( id int, varchar200 varchar(8), primary key (id) ); create table test.varcharsize10 ( id int, varchar200 varchar(10), primary key (id) ); *Insert SQL :* insert into test.varcharsize4 values (1,'不要让早把'); insert into test.varcharsize5 values (1,'不要让早把'); insert into test.varcharsize9 values (1,'不要让早把'); insert into test.varcharsize10 values (1,'不要让早把'); *BULK Line to insert :* "1","不要让早把" *BULK executions :* COPY 10 RECORDS INTO test.varcharsize4 FROM '/root/test_varchar_chinois' USING DELIMITERS ',','\n','\"' NULL AS '\\N' ; Result : Failed to import table line 1 field 2 'varchar(4)' expected in '不要让早把' ------ COPY 10 RECORDS INTO test.varcharsize5 FROM '/root/test_varchar_chinois' USING DELIMITERS ',','\n','\"' NULL AS '\\N' ; Result : Failed to import table line 1 field 2 'varchar(5)' expected in '不要让早把' ------- COPY 10 RECORDS INTO test.varcharsize89 FROM '/root/test_varchar_chinois' USING DELIMITERS ',','\n','\"' NULL AS '\\N' ; Result : Failed to import table line 1 field 2 'varchar(9)' expected in '不要让早把' ------- COPY 10 RECORDS INTO test.varcharsize10 FROM '/root/test_varchar_chinois' USING DELIMITERS ',','\n','\"' NULL AS '\\N' ; OK Regards Mathieu

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Merge table; partition pruning?
by Bryan Senseman 13 Nov '15

13 Nov '15

Ok, I was all excited about MERGE TABLEs moving up into the SQL layer, unfortunately my enthusiasm might be misplaced as I don’t see any improvement in query performance. Let me explain: I have a fact table with ~300 M rows with 5 years of data. I created 5 yearly tables, ordering by my date_key (and also created a year column). Checked storage to verify MonetDB knew they were sorted. Created a Merge table over all 5 yearly tables. I then ran test queries with various year subsets (using direct fact column filter and joining from date dimension), from 1 to all 5 and well I didn’t see any improvement in query speed when a subset of the 5 years was queried. In fact I usually saw 10-20% degradation of performance. I am no MAL expert, but looking at the PLAN and the EXPLAIN/TRACE outputs it appears to me tables that shouldn’t have data for the query are still scanned. I ran this both on a 16GB 4 core Windows box and a 32GB 8 core EC2 Linux box, same behavior both places, using both July2015 and July2015SP1. Is this expected behavior? Am I missing some magic to have MonetDB do the Oracle concept of Partition Elimination? Or are Merge tables really just meant for data maintenance? Thanx, Bryan -- ------------------------------ This transmission is confidential and intended solely for the use of the recipient named above. It may contain confidential, proprietary, or legally privileged information. If you are not the intended recipient, you are hereby notified that any unauthorized review, use, disclosure or distribution is strictly prohibited. If you have received this transmission in error, please contact the sender by reply e-mail and delete the original transmission and all copies from your system.

4 3

Error starting a production database
by Juan Carlos Gastélum 13 Nov '15

13 Nov '15

Hi I'm getting the following error when a I try to start our production database: # builtin opt gdk_dbpath = /var/monetdb5/dbfarm/demo # builtin opt gdk_debug = 0 # builtin opt gdk_vmtrim = no # builtin opt monet_prompt = > # builtin opt monet_daemon = no # builtin opt mapi_port = 50000 # builtin opt mapi_open = false # builtin opt mapi_autosense = false # builtin opt sql_optimizer = default_pipe # builtin opt sql_debug = 0 # cmdline opt gdk_dbpath = /usr/local/monetdb/alm_dat_far # cmdline opt merovingian_uri = mapi:monetdb://farser07:50000/alm_dat_far # cmdline opt mapi_open = false # cmdline opt mapi_port = 0 # cmdline opt mapi_usock = /usr/local/monetdb/alm_dat_far/.mapi.sock # cmdline opt monet_vault_key = /usr/local/monetdb/alm_dat_far/.vaultkey # cmdline opt gdk_nr_threads = 6 # cmdline opt max_clients = 64 # cmdline opt sql_optimizer = default_pipe # cmdline opt monet_daemon = yes # cmdline opt gdk_debug = 10 # MonetDB 5 server v11.21.11 "Jul2015-SP1" # Serving database 'alm_dat_far', using 6 threads # Compiled for x86_64-pc-linux-gnu/64bit with 64bit OIDs and 128bit integers dynamically linked # Found 39.298 GiB available main-memory. # Copyright (c) 1993-July 2008 CWI. # Copyright (c) August 2008-2015 MonetDB B.V., all rights reserved # Visit http://www.monetdb.org/ for further information # Listening for UNIX domain connection requests on mapi:monetdb:///usr/local/monetdb/alm_dat_far/.mapi.sock # Start processing logs sql/sql_logs version 52200 !FATAL: Logger_new: cannot create seqs bats What can I do to solve it? I have been trying to recover a backup of the virtual machine where the instance of monetdb is but until now I have not been able to recover this database. Thanks in advance. Juan Carlos Gastelum

3 9

Merge and remote table errors
by Bart Lenoir 12 Nov '15

12 Nov '15

Hi, Just adding another finding: Using 1 MERGE TABLE (on Mac) with 2 REMOTE TABLEs (on Linux [physically remote, in another network]) COUNT, MIN, MAX are fine but AVG, MEDIAN, QUANTILE etc. make the server crash. Using 1 MERGE TABLE (on Linux) with 1 REMOTE TABLE (on Linux [physically together, in the same network]) and 1 local TABLE, all the above functions are fine except for the occasional error. sql>select sys.median(doubleDataType) from xxxxxxx; (mapi:monetdb://monetdb@192.168.1.212/xxxxxxx) 'user.l2' undefined in: (rmt3853_X_62_bat_oid_str:bat[:oid,:str],rmt3854_X_65_bat_oid_str:bat[:oid,:str],rmt3855_X_66_bat_oid_str:bat[:oid,:str ],rmt3856_X_67_bat_oid_str:bat[:oid,:str],rmt3857_X_68_bat_oid_dbl:bat[:oid,:dbl],rmt3858_X_70_bat_oid_dbl:bat[:oid,:d bl],rmt3859_X_71_bat_oid_dbl:bat[:oid,:dbl],rmt3860_X_72_bat_oid_dbl:bat[:oid,:dbl],rmt3861_X_73_bat_oid_dbl:bat[:oid ,:dbl],rmt3862_X_74_bat_oid_dbl:bat[:oid,:dbl],rmt3863_X_75_bat_oid_dbl:bat[:oid,:dbl],rmt3864_X_76_bat_oid_dbl:bat[: oid,:dbl],rmt3865_X_77_bat_oid_dbl:bat[:oid,:dbl],rmt3866_X_78_bat_oid_dbl:bat[:oid,:dbl],rmt3867_X_79_bat_oid_dbl:ba t[:oid,:dbl],rmt3868_X_80_bat_oid_dbl:bat[:oid,:dbl],rmt3869_X_81_bat_oid_dbl:bat[:oid,:dbl],rmt3870_X_82_bat_oid_dbl: bat[:oid,:dbl],rmt3871_X_83_bat_oid_dbl:bat[:oid,:dbl],rmt3872_X_84_bat_oid_dbl:bat[:oid,:dbl],rmt3873_X_85_bat_oid_d bl:bat[:oid,:dbl],rmt3874_X_86_bat_oid_dbl:bat[:oid,:dbl],rmt3875_X_87_bat_oid_dbl:bat[:oid,:dbl],rmt3876_X_88_bat_oid _dbl:bat[:oid,:dbl],rmt3877_X_89_bat_oid_dbl:bat[:oid,:dbl],rmt3878_X_90_bat_oid_dbl:bat[:oid,:dbl],rmt3879_X_91_bat_o id_dbl:bat[:oid,:dbl],rmt3880_X_92_bat_oid_dbl:bat[:oid,:dbl],rmt3881_X_93_bat_oid_dbl:bat[:oid,:dbl],rmt3882_X_94_ba t_oid_dbl:bat[:oid,:dbl],rmt3883_X_95_bat_oid_dbl:bat[:oid,:dbl],rmt3884_X_97_bat_oid_dbl:bat[:oid,:dbl],rmt3885_X_98_ bat_oid_dbl:bat[:oid,:dbl],rmt3886_X_99_bat_oid_dbl:bat[:oid,:dbl],rmt3887_X_100_bat_oid_dbl:bat[:oid,:dbl],rmt3888_X_ 101_bat_oid_dbl:bat[:oid,:dbl],rmt3889_X_103_bat_oid_dbl:bat[:oid,:dbl],rmt3890_X_104_bat_oid_dbl:bat[:oid,:dbl],rmt38 91_X_105_bat_oid_dbl:bat[:oid,:dbl],rmt3892_X_106_bat_oid_dbl:bat[:oid,:dbl],rmt3893_X_107_bat_oid_dbl:bat[:oid,:dbl],r mt3894_X_108_bat_oid_dbl:bat[:oid,:dbl],rmt3895_X_109_bat_oid_dbl:bat[:oid,:dbl],rmt3896_X_110_bat_oid_dbl:bat[:oid,: dbl],rmt3897_X_111_bat_oid_dbl:bat[:oid,:dbl],rmt3898_X_112_bat_oid_dbl:bat[:oid,:dbl],rmt3899_X_113_bat_oid_dbl:bat[: oid,:dbl],rmt3900_X_114_bat_oid_dbl:bat[:oid,:dbl],rmt3901_X_115_bat_oid_dbl:bat[:oid,:dbl],rmt3902_X_116_bat_oid_dbl: bat[:oid,:dbl],rmt3903_X_117_bat_oid_dbl:bat[:oid,:dbl],rmt3904_X_118_bat_oid_dbl:bat[:oid,:dbl],rmt3905_X_119_bat_oid _dbl:bat[:oid,:dbl],rmt3906_X_120_bat_oid_dbl:bat[:oid,:dbl],rmt3907_X_121_bat_oid_dbl:bat[:oid,:dbl],rmt3908_X_122_ba t_oid_dbl:bat[:oid,:dbl],rmt3909_X_123_bat_oid_dbl:bat[:oid,:dbl],rmt3910_X_124_bat_oid_dbl:bat[:oid,:dbl],rmt3911_X_12 5_bat_oid_dbl:bat[:oid,:dbl],rmt3912_X_126_bat_oid_bit:bat[:oid,:bit],rmt3913_X_128_bat_oid_bit:bat[:oid,:bit],rmt3914_X_ 130_bat_oid_oid:bat[:oid,:oid]) := user.l2(); Server version on Mac and Linux machines: MonetDB 5 server v11.21.5 "Jul2015" (64-bit, 64-bit oids, 128-bit integers) Thanks. Kind regards, Bart

1 0

Duplicate views problem
by Dennis Pallett 11 Nov '15

11 Nov '15

Hi all, We're having a problem whereby it's somehow possible in a MonetDB database to have multiple views with the same name. See attached screenshot of an example. Any ideas on how this is possible? Seems like a bug but unfortunately we can't reliably reproduce it. It just happens every now and then. Best regards, Dennis

2 2

Usage of pool
by poornima＠apakau.com 11 Nov '15

11 Nov '15

Hi, I am trying to use monetdb with Hikari Pool. I have set the connection timeout to 4500. I have 4 max connections. The query execution takes at the max 20 ms. I am testing with 250 threads and 100000 requests. But I get a connection time out as follows : 11 09:40:24 PST.DEBUG118*HikariPool~logPoolState@339: Timeout failure pool HikariPool-0 stats (total=4, active=3, idle=1, waiting=1) The waiting number increases to a large number as 139. The idle drops to 0 in just 4 such messages. My Hikari pool configuration is as follows _dataSource = new HikariDataSource(); _dataSource.setDriverClassName("nl.cwi.monetdb.jdbc.MonetDriver"); _dataSource.setJdbcUrl("jdbc:monetdb://" + _reg.getStrProp("tdbUrl")); _dataSource.setUsername(_reg.getStrProp("tdbUsr")); _dataSource.setPassword(_reg.getStrProp("tdbPswd")); _dataSource.setMaximumPoolSize(4); _dataSource.setConnectionTimeout(4500); _dataSource.addDataSourceProperty("cachePrepStmts", "true"); _dataSource.addDataSourceProperty("prepStmtCacheSize", "250"); _dataSource.addDataSourceProperty("prepStmtCacheSqlLimit", "2048"); Do I need to change the configuration ? Or am I supposed to change the pool ? Which is the pool that is used with monetdb JDBC driver ? Regards, Poornima.

1 0

thanks for BEST EFFORT
by Anthony Damico 11 Nov '15

11 Nov '15

1 0

Trying to understand select performance when returning many columns
by Ben Jeffery 09 Nov '15

09 Nov '15

I have a table of 93 columns and ~90M rows which is a 60GB "bat" directory on disk. Mostly I'm doing things with a few columns - Monet has been _amazing_ for those use cases so thanks for all your hard work. However sometimes I need to return all columns for a small subset of rows and I can't quite understand what Monet is doing or why it is taking a long time. Here's some timings for 'select * from table order by "unsorted_numerical_column" limit N;' caches all flushed before each query: N=1 907ms N=100 3105ms N=200 6782ms N=500 14656ms N=1000 30100ms N=10000 71093ms For the last two my 32GB ram is being completely filled with the cache. I'm clearly missing something in my understanding as I don't see why that should be needed. Surely you only need to read the whole of the sort column and then grab only N rows from all the other columns? Is there anything I can do to reduce the amount of data loaded? The output of "explain" is at https://gist.github.com/benjeffery/30e9f6173b625f5d0c31 <https://gist.github.com/benjeffery/30e9f6173b625f5d0c31if>. Thanks, Ben

1 0

MonetDB JDBC driver and IntelliJ IDEA 15
by Endre Palatinus 09 Nov '15

09 Nov '15

Dear MonetDB users, I would like to access my MonetDB (latest version: v1.7 (Jul2015-SP1)) database through JDBC (MonetDB JDBC driver version 2.18) using IntelliJ IDEA 15.0 under Mac OS X 10.9.5. The "Test connection" function succeeds, but the "Refresh" function crashes in the Database tool of the IDE with the Exception below. The same problem happened when I was trying to connect to PostgreSQL 9.4 with a PostgreSQL JDBC driver older than JDBC version 4.2. I guess that MonetDB's JDBC driver has JDBC version 4.0 only. Any ideas on how to fix this? Best regards, Endre Palatinus ===== Exception: ====== TABLE_TYPE unavailable java.lang.NullPointerException at nl.cwi.monetdb.jdbc.MonetResultSet.getObject(MonetResultSet.java:1945) at com.intellij.database.remote.jdbc.impl.RemoteResultSetImpl.getObject(RemoteResultSetImpl.java:77) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:323) at sun.rmi.transport.Transport$1.run(Transport.java:200) at sun.rmi.transport.Transport$1.run(Transport.java:197) at java.security.AccessController.doPrivileged(Native Method) at sun.rmi.transport.Transport.serviceCall(Transport.java:196) at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$254(TCPTransport.java:683) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler$$Lambda$2/490517473.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:276) at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:253) at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:162) at java.rmi.server.RemoteObjectInvocationHandler.invokeRemoteMethod(RemoteObjectInvocationHandler.java:194) at java.rmi.server.RemoteObjectInvocationHandler.invoke(RemoteObjectInvocationHandler.java:148) at com.sun.proxy.$Proxy130.getObject(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at com.intellij.execution.rmi.RemoteUtil.invokeRemote(RemoteUtil.java:124) at com.intellij.execution.rmi.RemoteUtil.access$100(RemoteUtil.java:36) at com.intellij.execution.rmi.RemoteUtil$RemoteInvocationHandler.invoke(RemoteUtil.java:229) at com.sun.proxy.$Proxy131.getObject(Unknown Source) at com.intellij.database.util.JdbcUtil.resultSetToListSafe(JdbcUtil.java:61) at com.intellij.database.dataSource.DatabaseModelLegacyLoader.getAllTableTypes(DatabaseModelLegacyLoader.java:966) at com.intellij.database.dataSource.DatabaseModelLegacyLoader.loadDataSourceStateInner(DatabaseModelLegacyLoader.java:127) at com.intellij.database.dataSource.DatabaseModelLegacyLoader.loadInner(DatabaseModelLegacyLoader.java:88) at com.intellij.database.dataSource.DatabaseModelLoader.performLegacyIntrospection(DatabaseModelLoader.java:197) at com.intellij.database.dataSource.DatabaseModelLoader.performIntrospection(DatabaseModelLoader.java:99) at com.intellij.database.dataSource.AbstractDataSource.refreshMetaData(AbstractDataSource.java:61) at com.intellij.database.dataSource.AbstractDataSource$1.perform(AbstractDataSource.java:36) at com.intellij.database.dataSource.AbstractDataSource$1.perform(AbstractDataSource.java:34) at com.intellij.database.dataSource.AbstractDataSource.performJdbcOperation(AbstractDataSource.java:116) at com.intellij.database.dataSource.AbstractDataSource.refreshMetaData(AbstractDataSource.java:34) at com.intellij.database.dataSource.DataSourceUiUtil$2.run(DataSourceUiUtil.java:188) at com.intellij.openapi.progress.impl.CoreProgressManager$TaskRunnable.run(CoreProgressManager.java:563) at com.intellij.openapi.progress.impl.CoreProgressManager$2.run(CoreProgressManager.java:142) at com.intellij.openapi.progress.impl.CoreProgressManager.a(CoreProgressManager.java:446) at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:392) at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:54) at com.intellij.openapi.progress.impl.CoreProgressManager.runProcess(CoreProgressManager.java:127) at com.intellij.openapi.progress.impl.ProgressManagerImpl$1.run(ProgressManagerImpl.java:126) at com.intellij.openapi.application.impl.ApplicationImpl$8.run(ApplicationImpl.java:365) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) at org.jetbrains.ide.PooledThreadExecutor$1$1.run(PooledThreadExecutor.java:55) and 8 duplicate reports

1 0