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
