Update:

Tried running this again this morning. I’m trying to remember if I have successfully loaded this large file since applying the July2015SP1. I might not have. Regardless, this morning when trying to load anew, my merovingian.log file shows:

2015-11-24 07:28:33 MSG merovingian[18398]: database 'jeffTest' (24708) was killed by signal 8

Signal 8 indicates a floating point exception happened in the program. Are there known issues with floating points? I was able to successfully load this file before the upgrade to SP1.

Since nothing was loaded into the database (select count(*) on table shows 0 records), I tried another “COPY INTO” with a smaller version of the input file. This time it fails with a data message:

sql>COPY 61000000 records INTO annosites FROM '/home/lcj34/monetdbFiles/sites10000Jeff.txt' USING DELIMITERS '\t','\n';

Failed to import table Leftover data 'componentof nuclearinner membrane;molecular_function;biological_process;endoplasmicreticulum'

sql>

These are not column headers in my table – does it indicate a particular place in the software that importing the file had a problem?

Thanks – Lynn

From: users-list <users-list-bounces+lcj34=cornell.edu@monetdb.org> on behalf of Lynn Carol Johnson <lcj34@cornell.edu>
Reply-To: Communication channel for MonetDB users <users-list@monetdb.org>
Date: Monday, November 23, 2015 at 3:48 PM
To: Communication channel for MonetDB users <users-list@monetdb.org>
Subject: err incorrect checksum for freed object

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