First thoughts on mysql-4.0.3
Hi, after upgrading, I had two problems: /usr/local/mysql/bin/mysqld: ERROR: unknown variable 'query_buffer_size=32M' I had to comment out this variable, it seems it got renamed. I have to figure out what's the new name. 020828 17:30:12 mysqld started 020828 17:30:12 Can't find messagefile 'mysql-4.0.3-beta-pc-linux-gnu-i686/share/mysql/english/errmsg.sys' 020828 17:30:12 Aborting 020828 17:30:12 mysqld ended This I've already posted once. My fix is: # cd /usr/local/mysql(/usr/local/mysql is a link to /usr/local/mysql-4.0.3-beta-pc-linux-gnu-i686) # ln -s . mysql-4.0.3-beta-pc-linux-gnu-i686 # /etc/rc3.d/S98mysql start Hope this helps -- Martin Mokrejs [EMAIL PROTECTED], [EMAIL PROTECTED] PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3683 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: mysql 4.0.2 startup problems
Hi, it's a bit late reply, to my original mail sent to bugs list. Now the problem reappeared as the box got rebooted. I was receiving in $hostname.err: 020812 11:34:20 mysqld started 020812 11:34:20 Can't find messagefile 'mysql-4.0.2-alpha-pc-linux-gnu-i686/share/mysql/english/errmsg.sys' 020812 11:34:20 Aborting 020812 11:34:20 mysqld ended $ diff -u -w mysql-4.0.2-alpha-pc-linux-gnu-i686/support-files/mysql.server /etc/init.d/mysql --- mysql-4.0.2-alpha-pc-linux-gnu-i686/support-files/mysql.server Mon Jul 1 14:52:15 2002 +++ /etc/init.d/mysql Mon Aug 12 11:42:30 2002 @@ -29,11 +29,11 @@ # If you want to affect other MySQL variables, you should make your changes # in the /etc/my.cnf or other configuration files. -PATH=/sbin:/usr/sbin:/bin:/usr/bin +PATH=/sbin:/usr/sbin:/bin:/usr/bin:/usr/local/mysql/bin export PATH # Set some defaults -datadir=/usr/local/mysql/data +datadir=/data1/mysql basedir= pid_file= if test -z $basedir @@ -45,7 +45,7 @@ fi if test -z $pid_file then - pid_file=$datadir/`@HOSTNAME@`.pid + pid_file=$datadir/jerboas.pid else case $pid_file in /* ) ;; @@ -116,7 +116,7 @@ then # Give extra arguments to mysqld with the my.cnf file. This script may # be overwritten at next upgrade. - $bindir/mysqld_safe --datadir=$datadir --pid-file=$pid_file + $bindir/mysqld_safe --skip-innodb --datadir=$datadir --pid-file=$pid_file # Make lock for RedHat / SuSE if test -w /var/lock/subsys then On Wed, 17 Jul 2002, Alexander Keremidarski wrote: Martin MOKREJ wrote: How-To-Repeat: /usr/local/mysql/log# cp /dev/null jerboas.log /usr/local/mysql/log# cp /dev/null jerboas.err /usr/local/mysql/log# /etc/rc3.d/S98mysql start /usr/local/mysql/log# Starting mysqld daemon with databases from /data1/mysql 020716 20:21:26 mysqld ended Use mysql.server script from 4.0.2 tree. It knows where to find mysqld_safe Thanks, I copied that file over. See above the diff. cp mysql.server /etc/rc.d/initd/mysql chmod +x /etc/rc.d/initd/mysql chkconfig --add mysql or use your favorite method to link it in appropriate runlevel dirs. I've suspected that mysqld operates in unexpected current directory, and this really helped: cd /usr/local/mysql (which is a symlink to /usr/local/mysql-4.0.2-alpha-pc-linux-gnu-i686) ln -s . mysql-4.0.2-alpha-pc-linux-gnu-i686 Now when mysqld is in /usr/local/mysql and want's to see mysql-4.0.2-alpha-pc-linux-gnu-i686/share*, it can get it. Please note that I dod not re-set $bindir inside /etc/my.cnf. However, $basedir is reported by 'mysqladmin variables' to be set to 'mysql-4.0.2-alpha-pc-linux-gnu-i686/'. Maybe that's my problem? TIA Please Cc: me in replies, if possible. -- Martin Mokrejs [EMAIL PROTECTED] PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3683 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
MYISAM Compressed table corruption
Hi, I've observed some table corruption: How-To-Repeat: no idea, but maybe you might have one ;) $ mysql -hxxx Escherichia_coli_O157_H7 Reading table information for completion of table and column names You can turn off this feature to get a quicker startup with -A Didn't find any fields in table 'intergenome' Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 327 to server version: 3.23.49a Type 'help;' or '\h' for help. Type '\c' to clear the buffer. mysql check table intergenome; +--+---+--+---+ | Table| Op| Msg_type | Msg_text | | +--+---+--+---+ | Escherichia_coli_O157_H7.intergenome | check | warning | Table is marked as crashed |and last repair failed | | Escherichia_coli_O157_H7.intergenome | check | error| Can't read indexpage from |filepos: -1 | | Escherichia_coli_O157_H7.intergenome | check | error| Corrupt | | +--+---+--+---+ 3 rows in set (1.20 sec) mysql flush tables; Query OK, 0 rows affected (0.03 sec) mysql lock table intergenome write; ERROR 1016: Can't open file: 'intergenome.MYD'. (errno: 144) mysql Oh yes, it was compressed before the crash. :( # /usr/local/mysql/bin/myisamchk -dvv intergenome MyISAM file: intergenome Record format: Compressed Character set: latin1 (8) File-version:1 Creation time: 2002-03-23 19:38:55 Recover time:2002-03-26 0:03:32 Status: crashed Checksum: 1999381211 Data records: 1712335 Deleted blocks: 0 Datafile parts:1712335 Deleted data: 0 Datafile pointer (bytes):4 Keyfile pointer (bytes):3 Datafile length: 200889622 Keyfile length: 12134400 Max datafile length:4294967294 Max keyfile length: 17179868159 Recordlength: 1019 table description: Key Start Len Index Type Rec/key Root Blocksize 1 2 3 unique uint24 1 12133376 1024 2 211 255 multip. char packed stripped 02048 3 753 255 multip. char packed stripped 02048 4 111 100 multip. char packed stripped 01024 5 5 3 multip. uint24 01024 6 8 3 multip. uint24 01024 Field Start Length Nullpos Nullbit Type Huff tree Bits 1 1 1 constant 1 0 2 2 3 2 9 3 5 3 zerofill(1) 3 9 4 8 3 always zero 2 9 5 11100constant 4 0 6 111 100no endspace 5 5 7 211 255no endspace 6 9 8 466 4 table-lockup 7 0 9 470 255no endspace 8 6 10725 4 no zeros, zerofill(3)9 1 11729 4 table-lockup10 0 12733 4 table-lockup11 0 13737 4 zerofill(2) 12 9 14741 2 table-lockup13 0 15743 2 table-lockup14 0 16745 4 zerofill(2) 15 9 17749 4 zerofill(2) 16 9 18753 255no endspace 17 9 191008 10 1 1 blob 2 9 201018 1 1 2 always zero 2 9 211019 1 1 4 always zero 2 9 # /usr/local/mysql/bin/myisamchk -r -v intergenome.MYI - recovering (with sort) MyISAM-table 'intergenome.MYI' Data records: 1712335 - Fixing index 1 - Searching for keys, allocating buffer for 1525193 keys - Last merge and dumping keys - Fixing index 2 - Searching for keys, allocating buffer for 63069 keys - Last merge and dumping keys - Fixing index 3 - Searching for keys,
Re: Error in accept: Invalid argument and Duplicate entry '0' forkey
Hi, Victoria Reznichenko wrote: VR Martin, VR Wednesday, April 03, 2002, 5:45:00 PM, you wrote: VR VR MM would anyone please explain me what are these error messages? VR VR MM 020327 12:29:26 mysqld started VR MM 020327 12:29:26 Warning: listen() on TCP/IP failed with error 98 VR MM /usr/local/mysql/bin/mysqld: ready for connections VR MM /usr/local/mysql/bin/mysqld: ready for connections VR MM 020327 12:29:26 Error in accept: Invalid argument VR MM 020327 12:29:26 Error in accept: Invalid argument VR MM [There're plenty of those Error in accept messages.] VR VR # perror 98 VR Error code 98: Address already in use VR Is your mysql server box behind a firewall? Perhaps firewall to keep VR out MySQL server. No firewall between those machines. I was told later by people the machine had load 20 so probably safe_mysqld restarted mysqld and it retried to start mysqld twice at the same time. I don't know why that happened so quickly, all within one second. VR VR [...] VR VR MM Actually there's a hit in old docs in Solaris section(maybe I missed that VR MM in current docs?): VR MM http://www.google.de/search?q=cache:XowJDknOOI4C:theoryx5.uwinnipeg.ca/mysql/manual_4.html+mysql+Error+in+accept:+Invalid+argumenthl=de VR MM If too many processes try to connect very rapidly to mysqld, you will see this VR error in the MySQL log: VR MM Error in accept: Protocol error VR MM You might try starting the server with the --set-variable back_log=50 option VR as a workaround for this. VR VR How does 'Error in accept: Protocol error' belong to error that you VR received? Probably no relation, that was just the only Google hit I had. Maybe few words in the offcial documentation about this kind of errors? Possible causes, solutions? VR MM ERROR 1036 at line 46: Table 'intergenome' is read only VR MM Failed to dump Synechocystis_PCC6803.intergenome VR MM ERROR 1062 at line 46: Duplicate entry '0' for key 1 VR MM Failed to dump Tmaritima.intergenome VR VR Looks like you have corrupted indexes. And speaking about 'table is VR read-only' it means that you have no permissions to write ih those VR files, but it can make problems in dump ... Unfortunately none of them are true, but Michael is looking into this already. Thanks. -- Martin Mokrejs [EMAIL PROTECTED] PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Error in accept: Invalid argument and Duplicate entry '0' for key1
Hi, would anyone please explain me what are these error messages? 020327 12:29:26 mysqld started 020327 12:29:26 Warning: listen() on TCP/IP failed with error 98 /usr/local/mysql/bin/mysqld: ready for connections /usr/local/mysql/bin/mysqld: ready for connections 020327 12:29:26 Error in accept: Invalid argument 020327 12:29:26 Error in accept: Invalid argument [There're plenty of those Error in accept messages.] Looking into official searchable documnetation gives me no hits. Google search returns old thread from mysql archives - suggestion was to recompile because the binaries were compiled on other box with different. As I use official binaries ... :( Actually there's a hit in old docs in Solaris section(maybe I missed that in current docs?): http://www.google.de/search?q=cache:XowJDknOOI4C:theoryx5.uwinnipeg.ca/mysql/manual_4.html+mysql+Error+in+accept:+Invalid+argumenthl=de If too many processes try to connect very rapidly to mysqld, you will see this error in the MySQL log: Error in accept: Protocol error You might try starting the server with the --set-variable back_log=50 option as a workaround for this. That might be a solution, but the cause for my error is Invalid argument! And what about the error 98? I can't say much what happened, I's dumping large MyISAM tables to this servers during easters and this is what I've found(but might be totally unrelated): ERROR 1062 at line 46: Duplicate entry '0' for key 1 Failed to dump Mthermoautotrophicum.intergenome ERROR 1062 at line 46: Duplicate entry '0' for key 1 Failed to dump Pyrococcus_abyssi_GE5.intergenome ERROR 1062 at line 46: Duplicate entry '0' for key 1 Failed to dump Pyrococcus_horikoshii_OT3.intergenome ERROR 1062 at line 46: Duplicate entry '0' for key 1 Failed to dump Rprowazekii.intergenome ERROR 1062 at line 46: Duplicate entry '0' for key 1 Failed to dump Sulfolobus_solfataricus_P2.intergenome ERROR 1036 at line 46: Table 'intergenome' is read only Failed to dump Synechocystis.intergenome ERROR 1036 at line 46: Table 'intergenome' is read only Failed to dump Synechocystis_PCC6803.intergenome ERROR 1062 at line 46: Duplicate entry '0' for key 1 Failed to dump Tmaritima.intergenome Actually this problem I've already seen once, but forgot to report. ;) There're couple of interresting things: 1. I'm using `--add-drop-table' argument to dump each table using mysqldump. 2. Source tables aren't compressed. MyISAM file: /data/mysql/Sulfolobus_solfataricus_P2/intergenome.MYI Record format: Packed Character set: latin1 (8) File-version:1 Creation time: 2002-01-25 9:52:45 Status: changed Data records: 976106 Deleted blocks: 0 Datafile parts:1952210 Deleted data: 0 Datafile pointer (bytes):4 Keyfile pointer (bytes):4 Datafile length: 235019464 Keyfile length: 66795520 Max datafile length:4294967294 Max keyfile length: 4398046510079 Recordlength: 1019 table description: Key Start Len Index Type Rec/key Root Blocksize 1 2 3 unique uint24 1 59776000 1024 2 211 255 multip. char packed stripped 0 12270592 2048 3 753 255 multip. char packed stripped 0 7548928 2048 4 111 100 multip. char packed stripped 0 39867392 1024 5 5 3 multip. uint24 0 59780096 1024 6 8 3 multip. uint24 0 59784192 1024 MyISAM file: /data/mysql/Synechocystis/intergenome.MYI Record format: Packed Character set: latin1 (8) File-version:1 Creation time: 2002-01-26 1:28:24 Status: changed Data records: 1138312 Deleted blocks: 0 Datafile parts:1518104 Deleted data: 0 Datafile pointer (bytes):4 Keyfile pointer (bytes):4 Datafile length: 241362564 Keyfile length: 77243392 Max datafile length:4294967294 Max keyfile length: 4398046510079 Recordlength: 1019 table description: Key Start Len Index Type Rec/key Root Blocksize 1 2 3 unique uint24 1 61722624 1024 2 211 255 multip. char packed stripped 0 10539008 2048 3 753 255 multip. char packed stripped 0 8295424 2048 4 111 100 multip. char packed stripped 0 44457984 1024 5 5 3 multip. uint24 0 61726720 1024 6 8 3 multip. uint24 0 61730816 1024 3. On the target I do compress tables, but they should be dropped first if present. So, it's not clear to me what cause the problem that entry for key 0 is duplicated. CHECK TABLE on
--extended-insert vs. performance
Hi, sorry to bother you with this, but one thing one might look into is: When table was dumped with --extended-insert option, that the server importing the table does NOT perform well. In the output from `vmstat 1` each second there's a lot of I/O, and at least on linux 2.4.19-pre1 it runs more easily out of memory. On the other hand, when omitting --extended-insert, I get: 1 0 0 19520 9552 19216 922272 0 0 0 4692 1852 3323 23 10 67 1 0 0 19520 9460 19220 922300 4 0 4 0 1850 3385 27 6 67 1 0 0 19520 9472 19220 922260 0 0 0 0 1789 3206 21 8 71 1 0 0 19520 9440 19220 922240 0 0 0 0 2040 3879 33 7 60 1 0 0 19520 9440 19220 922216 0 0 0 0 1994 3747 26 7 67 1 0 0 19520 9504 19264 922064 0 0 0 3668 1784 3268 22 7 70 0 0 0 19520 9520 19264 922004 0 0 0 0 1810 3323 28 10 62 1 0 0 19520 9516 19268 921956 0 0 0 0 2125 3105 25 6 68 1 0 0 19520 9536 19268 921892 0 0 0 0 2096 3136 23 6 71 1 0 0 19520 9440 19268 921964 0 0 0 0 2076 3066 25 6 69 1 0 0 19520 9552 19312 921756 0 0 0 3796 2081 3105 24 8 68 procs memoryswap io system cpu r b w swpd free buff cache si sobibo incs us sy id 1 0 0 19520 9564 19316 921700 0 0 0 0 2012 3097 25 8 67 1 0 0 19520 9456 19316 921760 0 0 0 0 1992 3140 24 7 69 1 0 0 19520 9468 19316 921712 0 0 0 0 1835 3171 26 12 61 1 0 0 19520 9472 19316 921680 0 0 0 0 2032 3287 18 5 76 0 0 0 19520 9508 19364 921544 0 0 0 3796 2375 3221 23 9 68 0 0 0 19520 9448 19364 921564 0 0 0 0 2424 3187 23 9 68 0 0 0 19520 9508 19364 921460 0 0 0 0 2467 3199 22 9 68 0 0 0 19520 9516 19364 921416 0 0 0 0 2207 3301 23 7 69 0 0 0 19520 9484 19364 921404 0 0 0 0 1879 3327 30 7 63 1 0 0 19520 9524 19412 921276 0 0 0 4316 1874 3294 24 8 68 1 0 0 19520 9692 19408 921068 0 0 0 0 1822 3389 26 7 67 0 0 0 19520 9608 19408 921228 0 0 4 0 2002 3623 29 9 62 1 0 0 19516 9832 19240 921256 0 0 0 0 1826 3385 26 8 66 1 0 0 19516 9764 18904 921636 0 0 0 0 1794 3348 26 8 66 1 0 0 19516 9976 18232 922060 0 0 0 4316 2358 3489 21 9 70 0 0 0 19736 10544 17592 922160 0 0 0 0 2253 3470 26 4 70 I do not want to stop my import script to send you the output what happens in case 1 above. Sorry, that's just a note. So just time to time we read data(and/or) write them. I guess read is via network. Checking iostat output tells me, that every about 4 seconds a lot of data is written to the disk and zero activity at all in between. --- Second point would be, that there's a lot of table locks issued when importing table. It looks every row equals to one lock ( I use mysqldump | mysql ) to import data. The shell command is executed on remote host, I'm talking about mysqld on target, not source. And, once I have seen: ++--++---+-+--++--+ | Id | User | Host | db| Command | Time | |State | Info || ++--++---+-+--++--+ | 4 | pedant | xx | Bordetella_pertussis_Tohama_I | Query | 0| |Locked | INSERT INTO `blast` VALUES (42171,5097,0,'BP','orf188','PIR:A49936',319,'9e-86',39,54,56,595,540,550 | | 7 | bioadmin | 127.0.0.1 | | Query | 0| || show processlist | | ++--++---+-+--++--+ I can exclude the possibility that someone else had locked this table temporarily as the traffic on server who query usually this box is redirected to another db server. My question is initiated because the number of Table_locks_immediate is growing very fast while importing data. Maybe both my question are poor misunderstanding. Please Cc: me in replies. TIA. (tested on Linux 2.4.19-pre1 and 3.23.49a) -- Martin Mokrejs - PGP5.0i key is at
Lost primary key from table
Hi, I've really interresting topic this time: our application stopped getting data. It turned out these queries were unexpectedly slow while operating on MyISAM tables: ++---+---+--+-+--+++ | Id | User | Host | db | Command | Time | State | | Info | | ++---+---+--+-+--+++ | 16 | wwwpedant | localhost | Saccharomyces_cerevisiae | Query | 0| Sorting |result | select descr,hitcode,pval,score from blast where prot_data_id=180 and |pval0.5 order by 4 desc | In case of other databases same applications and same mysqld operated normally. I think I see the problem why it's so slow: Instead of having: +--+--+--+-+-+---+ | Field| Type | Null | Key | Default | Extra | +--+--+--+-+-+---+ | id | int(11) | | PRI | 0 | | | prot_data_id | int(11) | | MUL | 0 | | | contig_data_id | int(11) | | MUL | 0 | | | contig_data_code | varchar(100) | | | | | | code | varchar(100) | | MUL | | | | hitcode | varchar(255) | | MUL | | | | score| int(11) | | | 0 | | | pval | varchar(255) | | | | | | ident| int(11) | | | 0 | | | posit| int(11) | | | 0 | | | begin| int(11) | | | 0 | | | end | int(11) | | | 0 | | | length | int(11) | | | 0 | | | hitlength| int(11) | | | 0 | | | hitstart | int(11) | | | 0 | | | hitstop | int(11) | | | 0 | | | descr| varchar(255) | YES | MUL | NULL| | | aln | longtext | YES | | NULL| | | conf | varchar(6) | YES | | NULL| | | manual | char(3) | YES | | NULL| | +--+--+--+-+-+---+ we have in one case: +--+--+--+-+-+---+ | Field| Type | Null | Key | Default | Extra | +--+--+--+-+-+---+ | id | int(11) | | | 0 | | | prot_data_id | int(11) | | | 0 | | | contig_data_id | int(11) | | | 0 | | | contig_data_code | varchar(100) | | | | | | code | varchar(100) | | | | | | hitcode | varchar(255) | | | | | | score| int(11) | | | 0 | | | pval | varchar(255) | | | | | | ident| int(11) | | | 0 | | | posit| int(11) | | | 0 | | | begin| int(11) | | | 0 | | | end | int(11) | | | 0 | | | length | int(11) | | | 0 | | | hitlength| int(11) | | | 0 | | | hitstart | int(11) | | | 0 | | | hitstop | int(11) | | | 0 | | | descr| varchar(255) | YES | | NULL| | | aln | longtext | YES | | NULL| | | conf | varchar(6) | YES | | NULL| | | manual | char(3) | YES | | NULL| | +--+--+--+-+-+---+ Actually, here's the diff: 4,6c4,6 | id | int(11) | | | 0 | | | prot_data_id | int(11) | | | 0 | | | contig_data_id | int(11) | | | 0 | | --- | id | int(11) | | PRI | 0 | | | prot_data_id | int(11) | | MUL | 0 | | | contig_data_id | int(11) | | MUL | 0 | | 8,9c8,9 | code | varchar(100) | | | | | | hitcode | varchar(255) | | | | | --- | code | varchar(100) | | MUL | | | |
RE: Cannot import mysql dump
On Mon, 28 Jan 2002, Sinisa Milivojevic wrote: =?iso-8859-2?Q?Martin MOKREJ=A9?= writes: On Mon, 28 Jan 2002, Sinisa Milivojevic wrote: Hi, I am retrying to an answer to my question from January. Could please someone from the developers have a look into this? http://lists.mysql.com/cgi-ez/ezmlm-cgi?1:mss:97726:200201:ljpgbhblfacaahpnemag The problem still persists, namely when I try to dump some tables on mysql-3.23.42 (linux binary distrib.), I get: My script: Just dumping Bordetella_pertussis_Tohama_I.nonglob_data ERROR 1064 at line 12: You have an error in your SQL syntax near 'PRIMARY (id), KEY contig_data_id (contig_data_id), KEY contig_data_id_2 (con' at line 9 My script: Failed to dump Bordetella_pertussis_Tohama_I.nonglob_data My script: Just dumping Brucella_melitensis_16M.nonglob_data ERROR 1064 at line 12: You have an error in your SQL syntax near 'PRIMARY (id), KEY contig_data_id (contig_data_id), KEY contig_data_id_2 (con' at line 9 My script: Failed to dump Brucella_melitensis_16M.nonglob_data My script: Just dumping Brucella_melitensis_16M.scop2_data ERROR 1064 at line 12: You have an error in your SQL syntax near 'PRIMARY (id), KEY contig_data_id (contig_data_id), KEY contig_data_id_2 (con' at line 9 My script: Failed to dump Brucella_melitensis_16M.scop2_data The problem is either in mysqld exporting data in wrong format or in mysqld 3.23.47 (see mails from january) or 3.23.49a when importing dumps into the database. The only conclusion from January is that the PRIMARY KEY syntax used in dumps is wrong. Dump of usable table using 3.23.42 client, but the dumps is not importable: # MySQL dump 8.16 # # Host: localhost.Database: Bordetella_pertussis_Tohama_I # # Server version3.23.42-log # # Table structure for table 'nonglob_data' # CREATE TABLE nonglob_data ( id int(11) NOT NULL default '0', contig_data_id int(11) NOT NULL default '0', contig_data_code varchar(100) NOT NULL default '', code varchar(100) NOT NULL default '', descr varchar(255) default NULL, dat longtext, created varchar(100) NOT NULL default '', UNIQUE KEY PRIMARY (id), KEY contig_data_id (contig_data_id), KEY contig_data_id_2 (contig_data_id), KEY contig_data_code (contig_data_code), KEY contig_data_id_3 (contig_data_id), KEY code (code), KEY contig_data_id_4 (contig_data_id), KEY descr (descr), KEY contig_data_code_2 (contig_data_code), KEY contig_data_code_3 (contig_data_code), KEY code_2 (code), KEY contig_data_code_4 (contig_data_code), KEY code_3 (code), KEY contig_data_id_5 (contig_data_id), KEY contig_data_id_6 (contig_data_id), KEY code_4 (code), KEY descr_2 (descr), KEY descr_3 (descr), KEY contig_data_code_5 (contig_data_code), KEY contig_data_code_6 (contig_data_code), KEY descr_4 (descr), KEY contig_data_id_7 (contig_data_id), KEY contig_data_id_8 (contig_data_id), KEY contig_data_code_7 (contig_data_code), KEY contig_data_code_8 (contig_data_code), KEY code_5 (code), KEY descr_5 (descr), KEY code_6 (code), KEY code_7 (code), KEY descr_6 (descr), KEY code_8 (code), KEY descr_7 (descr) ) TYPE=MyISAM; Dump of usable table using 3.23.42 client (this dump is importable): # MySQL dump 8.16 # # Host: localhost.Database: Aeropyrum_pernix_K1 # # Server version3.23.42-log # # Table structure for table 'nonglob_data' # CREATE TABLE nonglob_data ( id mediumint(8) unsigned NOT NULL default '0', contig_data_id mediumint(8) unsigned NOT NULL default '0', contig_data_code varchar(100) NOT NULL default '', code varchar(100) NOT NULL default '', descr varchar(255) NOT NULL default '', dat longtext, created varchar(100) default NULL, PRIMARY KEY (id), KEY code (code), KEY descr (descr), KEY contig_data_id (contig_data_id), KEY contig_data_code (contig_data_code) ) TYPE=MyISAM; mysql use Bordetella_pertussis_Tohama_I; mysql describe nonglob_data; +--+--+--+-+-+---+ | Field| Type | Null | Key | Default | Extra | +--+--+--+-+-+---+ | id | int(11) | | PRI | 0 | | | contig_data_id | int(11) | | MUL | 0 | | | contig_data_code | varchar(100) | | MUL | | | | code | varchar(100) | | MUL | | | | descr| varchar(255) | YES | MUL | NULL| | | dat | longtext | YES | | NULL| | | created | varchar(100) | | | | | +--+--+--+-+-+---+ mysql use Aeropyrum_pernix_K1; mysql describe nonglob_data; +--+---+--+-+-+---+ | Field| Type
Setting net_buffer_length
Hi, we have 3.23.42 official binaries running on Linux 2.4.17. It seems mysqld does not read in from /etc/my.cnf the value for net_buffer_length. When having in the config file: [mysqld] set-variable= net_buffer_length=16M set-variable= max_allowed_packet=16M [...] I get | net_buffer_length | 1047552 | max_allowed_packet | 16776192 Another approach: [mysqld] set-variable= net_buffer_length=16776176 set-variable= max_allowed_packet=16776192 show variables reports: | max_allowed_packet | 16775168 | net_buffer_length | 1047552 It seems mysqld manipulates the numbers set in the config file and ignores somehow the net_buffer_length settings? I started to be curious, if we have to set the net_buffer_length before setting the max_allowed_packet, because of The maximum size of one packet. The message buffer is initialised to net_buffer_length bytes, but can grow up to at http://www.mysql.com/doc/S/H/SHOW_VARIABLES.html But as you see, I already tried this but no luck. Also, the above page shows: | net_buffer_length| 16384 is that in kB ? Or was the number that low in 3.23.29a ? When trying to hope that I can first set the net_buffer_length huge and then set max_allowed_packet to it's maximum: [mysqld] set-variable= net_buffer_length=18M set-variable= max_allowed_packet=16M | net_buffer_length | 1047552 | max_allowed_packet | 16776192 So far, I'm not able to raise the net_buffer_length value in server at all. -- Regarding the client side, when I have in /etc/my.cnf or ~/.my.cnf: [client] port= 3306 socket = /tmp/mysql.sock set-variable= net_buffer_length=16M set-variable= max_allowed_packet=16M I get: $ mysqladmin variables | grep buffer No variable match for: -O 'net_buffer_length=16M' $ Any ideas what I'm doing wrong? Please Cc: me in replies. Thanks. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
RE: Cannot import mysql dump
On Mon, 28 Jan 2002, Sinisa Milivojevic wrote: Hi, This is not OK according to syntax as PRIMARY is a reserved word. UNIQUE KEY PRIMARY (id) Why don't you just say PRIMARY KEY (id) ?? Hmm, well because that's just a mysqldump of a database which already exists in mysql and it turned out that I cannot reimport it into mysql back. It looks to me as a bug in mysqldump (look for the version of mysqdump in the original post, I think it was 3.23.44). I don't have such a problem with 3.23.42 for example. TIA -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
RE: Cannot import mysql dump
On Mon, 28 Jan 2002, Sinisa Milivojevic wrote: Are you sure that the above is the output from mysqldump ?? What server version ?? Look into the original posting on Jan 9 2002 for complete description. ;-) -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
RE: Cannot import mysql dump
On Mon, 28 Jan 2002, Sinisa Milivojevic wrote: =?iso-8859-2?Q?Martin_MOKREJ=A9?= writes: On Mon, 28 Jan 2002, Sinisa Milivojevic wrote: Hi, Hmm, well because that's just a mysqldump of a database which already exists in mysql and it turned out that I cannot reimport it into mysql back. It looks to me as a bug in mysqldump (look for the version of mysqdump in the original post, I think it was 3.23.44). I don't have such a problem with 3.23.42 for example. TIA -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 It is possible that PRIMARY was a keyword before, but I can not find that info in the Changelog. Dont know, but maybe you could check that yourself: quoted from my original mail: I've uploaded these two files into /pub/mysql/secret: Bordetella_pertussis_Tohama_I.nonglob_data.sql.gz Bordetella_pertussis_Tohama_I.tmhmm_data.sql.gz Hope they're still there. I can create currently dumps from same tables using 3.23.42 if you need them. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
RE: Cannot import mysql dump
Hi, can someone from the mysql developers tell me what i did wrong, if this is a bug? I converted back to 3.23.42 to be on the safe side. ;) TIA -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 -- Forwarded message -- Date: Wed, 9 Jan 2002 21:08:09 +0100 From: Roger Baklund [EMAIL PROTECTED] To: [EMAIL PROTECTED] Cc: Martin MOKREJ [EMAIL PROTECTED] Subject: RE: Cannot import mysql dump * Martin MOKREJ I have a problem to re-import sql dump from Linux 2.2.19 running mysql Ver 11.15 Distrib 3.23.44, for pc-linux-gnu (i686) into the same mysqld under different database. while running the same commandline on the source at least. $ mysqldump --extended-insert Bordetella_pertussis_Tohama_I nonglob_data | mysql mmo ERROR 1064 at line 11: You have an error in your SQL syntax near 'PRIMARY (id), KEY contig_data_id (contig_data_id), KEY contig_data_id_2 (con' at line 9 $ Could someone explain me where is the error? I don't know why this happens, but read below... The dump looks like: $ mysqldump --extended-insert Bordetella_pertussis_Tohama_I nonglob_data | less # MySQL dump 8.16 # # Host: xxxDatabase: Bordetella_pertussis_Tohama_I # # Server version3.23.44-log # # Table structure for table 'nonglob_data' # CREATE TABLE nonglob_data ( id int(11) NOT NULL default '0', contig_data_id int(11) NOT NULL default '0', contig_data_code varchar(100) NOT NULL default '', code varchar(100) NOT NULL default '', descr varchar(255) default NULL, dat longtext, created varchar(100) NOT NULL default '', UNIQUE KEY PRIMARY (id), The error message suggests the problem is in the above line. From the documentation: create_definition: col_name type [NOT NULL | NULL] [DEFAULT default_value] [AUTO_INCREMENT] [PRIMARY KEY] [reference_definition] orPRIMARY KEY (index_col_name,...) orKEY [index_name] (index_col_name,...) orINDEX [index_name] (index_col_name,...) orUNIQUE [INDEX] [index_name] (index_col_name,...) orFULLTEXT [INDEX] [index_name] (index_col_name,...) or[CONSTRAINT symbol] FOREIGN KEY [index_name] (index_col_name,...) [reference_definition] orCHECK (expr) You can have UNIQUE, KEY or PRIMARY KEY, but not all at the same time... I have no idea why mysqldump creates this statement. But there is more... KEY contig_data_id (contig_data_id), KEY contig_data_id_2 (contig_data_id), KEY contig_data_code (contig_data_code), KEY contig_data_id_3 (contig_data_id), Why are there multiple indexes for the same fields? KEY code (code), KEY contig_data_id_4 (contig_data_id), KEY descr (descr), KEY contig_data_code_2 (contig_data_code), KEY contig_data_code_3 (contig_data_code), KEY code_2 (code), KEY contig_data_code_4 (contig_data_code), KEY code_3 (code), KEY contig_data_id_5 (contig_data_id), KEY contig_data_id_6 (contig_data_id), KEY code_4 (code), KEY descr_2 (descr), KEY descr_3 (descr), KEY contig_data_code_5 (contig_data_code), KEY contig_data_code_6 (contig_data_code), KEY descr_4 (descr), KEY contig_data_id_7 (contig_data_id), KEY contig_data_id_8 (contig_data_id), KEY contig_data_code_7 (contig_data_code), KEY contig_data_code_8 (contig_data_code), KEY code_5 (code), KEY descr_5 (descr), KEY code_6 (code), KEY code_7 (code), KEY descr_6 (descr), KEY code_8 (code), KEY descr_7 (descr) ) TYPE=MyISAM; A lot of them, actually... can anyone explain this? -- Roger - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: mysql warnings when write locking compressed table
On Fri, 25 Jan 2002, Sinisa Milivojevic wrote: Hi, sorry, I didn't get it. As far as I know there's no way yet how to uncompress table my using SQL command. I have to uncompress using `myisamchk --unpack *.MYI`, right? =?iso-8859-2?Q?Martin_MOKREJ=A9?= writes: Hi, when I'm trying to lock multiple tables and some of the are Compressed, mysql warn's me only about the first-one being Compressed. It either reports the first Compressed table only from the list, or it checks only the first-one in the list of tables to be locked: mysql use Escherichia_coli_O157_H7_EDL933 Database changed mysql lock table blast_data write; write, blimps_data write, cogs_data write, coils_data write, contig_data write, funcat_data write, intragenome_data write, known3d_data write, nonglob_data write, orf_data write, pfam_data write, prd_data write, pros_data write, prot_data write, scop1_data write, scop2_data write, seg_data write, tmhmm_data write; ERROR 1036: Table 'blast_data' is read only mysql `myisamchk -f -d ' reports on those tables their status, and most of them were Compressed. I don't think it make's sense to paste the output here. I don't know if it's really `ERROR', because I'm locking the tables to FLUSH TABLES and then in the backgroung run `myisamchk --unpack *.MYI'. ;)[B Linux 2.4.17, /usr/local/mysql/bin/mysqld Ver 3.23.42 for pc-linux-gnu on i686 -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 Please do not run myisamchk while the server is running. Use CHECK TABLE to check tables ... -- Regards, __ ___ ___ __ / |/ /_ __/ __/ __ \/ /Mr. Sinisa Milivojevic [EMAIL PROTECTED] / /|_/ / // /\ \/ /_/ / /__ MySQL AB, Fulltime Developer /_/ /_/\_, /___/\___\_\___/ Larnaca, Cyprus ___/ www.mysql.com -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Cannot import mysql dump
Hi, I have a problem to re-import sql dump from Linux 2.2.19 running mysql Ver 11.15 Distrib 3.23.44, for pc-linux-gnu (i686) into the same mysqld under different database. while running the same commandline on the source at least. $ mysqldump --extended-insert Bordetella_pertussis_Tohama_I nonglob_data | mysql mmo ERROR 1064 at line 11: You have an error in your SQL syntax near 'PRIMARY (id), KEY contig_data_id (contig_data_id), KEY contig_data_id_2 (con' at line 9 $ Could someone explain me where is the error? The dump looks like: $ mysqldump --extended-insert Bordetella_pertussis_Tohama_I nonglob_data | less # MySQL dump 8.16 # # Host: xxxDatabase: Bordetella_pertussis_Tohama_I # # Server version3.23.44-log # # Table structure for table 'nonglob_data' # CREATE TABLE nonglob_data ( id int(11) NOT NULL default '0', contig_data_id int(11) NOT NULL default '0', contig_data_code varchar(100) NOT NULL default '', code varchar(100) NOT NULL default '', descr varchar(255) default NULL, dat longtext, created varchar(100) NOT NULL default '', UNIQUE KEY PRIMARY (id), KEY contig_data_id (contig_data_id), KEY contig_data_id_2 (contig_data_id), KEY contig_data_code (contig_data_code), KEY contig_data_id_3 (contig_data_id), KEY code (code), KEY contig_data_id_4 (contig_data_id), KEY descr (descr), KEY contig_data_code_2 (contig_data_code), KEY contig_data_code_3 (contig_data_code), KEY code_2 (code), KEY contig_data_code_4 (contig_data_code), KEY code_3 (code), KEY contig_data_id_5 (contig_data_id), KEY contig_data_id_6 (contig_data_id), KEY code_4 (code), KEY descr_2 (descr), KEY descr_3 (descr), KEY contig_data_code_5 (contig_data_code), KEY contig_data_code_6 (contig_data_code), KEY descr_4 (descr), KEY contig_data_id_7 (contig_data_id), KEY contig_data_id_8 (contig_data_id), KEY contig_data_code_7 (contig_data_code), KEY contig_data_code_8 (contig_data_code), KEY code_5 (code), KEY descr_5 (descr), KEY code_6 (code), KEY code_7 (code), KEY descr_6 (descr), KEY code_8 (code), KEY descr_7 (descr) ) TYPE=MyISAM; [...] I've uploaded these two files into /pub/mysql/secret: Bordetella_pertussis_Tohama_I.nonglob_data.sql.gz Bordetella_pertussis_Tohama_I.tmhmm_data.sql.gz Thanks. Please Cc: me in replies. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Swapped out mysqld on linux 2.4.17-rc2 with INSERT DELAYED data
Hi, I'm using INSERT DELAYED to insert about 120GB of data into mysql from mysqldumpped data from remote server. After the weekend I've found such output from our perl script (after was dumped let's say 60GB): Just dumping Mthermoautotrophicum.orf Just dumping Mthermoautotrophicum.orf_data Just dumping Mthermoautotrophicum.pfam Just dumping Mthermoautotrophicum.pfam_data ERROR 1135 at line 30: Can't create a new thread (errno 11). If you are not out of available memory, you can consult the manual for a possible OS-dependent bug Failed to dump Mthermoautotrophicum.pfam_data Just dumping Mthermoautotrophicum.pirkw ERROR 1135 at line 46: Can't create a new thread (errno 11). If you are not out of available memory, you can consult the manual for a possible OS-dependent bug Failed to dump Mthermoautotrophicum.pirkw Just dumping Mthermoautotrophicum.prd ERROR 1135 at line 31: Can't create a new thread (errno 11). If you are not out of available memory, you can consult the manual for a possible OS-dependent bug Failed to dump Mthermoautotrophicum.prd [...] DBI-connect failed: Can't create a new thread (errno 11). If you are not out of available memory, you can consult the manual for a possible OS-dependent bug at /home/bioadmin/bin/dump_tables.pl line 252 FATAL ERROR: Unable to connect to jerboas: Can't create a new thread (errno 11). If you are not out of available memory, you can consult the manual for a possible OS-dependent bug at /home/bioadmin/bin/dump_tables.pl line 252. Can't call method func without a package or object reference at /home/bioadmin/bin/dump_tables.pl line 254. shell$ The machine is linux 2.4.17-rc2 running /usr/local/mysql/bin/mysql Ver 11.15 Distrib 3.23.42, for pc-linux-gnu (i686). The machine runs SMP kernel on 2 Intel Pentium III processor box with 1GB of memory. I rerun our script to continue dumps and managed to dump about 60 tables, and then same problem: arrose Just dumping Mycoplasma_genitalium_G37.cogs_data ERROR 1135 at line 30: Can't create a new thread (errno 11). If you are not out of available memory, you can consult the manual for a possible OS-dependent bug Failed to dump Mycoplasma_genitalium_G37.cogs_data shell$ mysqladmin extended-status +--++ | Variable_name| Value | +--++ | Aborted_clients | 196| | Aborted_connects | 23 | | Bytes_received | 1584472794 | | Bytes_sent | 1311517| | Connections | 11826 | | Created_tmp_disk_tables | 0 | | Created_tmp_tables | 0 | | Created_tmp_files| 0 | | Delayed_insert_threads | 4089 | | Delayed_writes | 78047350 | | Delayed_errors | 3591775| | Flush_commands | 1 | | Handler_delete | 0 | | Handler_read_first | 1 | | Handler_read_key | 0 | | Handler_read_next| 2 | | Handler_read_prev| 0 | | Handler_read_rnd | 0 | | Handler_read_rnd_next| 418| | Handler_update | 0 | | Handler_write| 85799969 | | Key_blocks_used | 249376 | | Key_read_requests| 2092226517 | | Key_reads| 21218 | | Key_write_requests | 542944973 | | Key_writes | 10606554 | | Max_used_connections | 4 | | Not_flushed_key_blocks | 0 | | Not_flushed_delayed_rows | 0 | | Open_tables | 4318 | | Open_files | 28192 | | Open_streams | 0 | | Opened_tables| 10989 | | Questions| 25236 | | Select_full_join | 0 | | Select_full_range_join | 0 | | Select_range | 0 | | Select_range_check | 0 | | Select_scan | 0 | | Slave_running| OFF| | Slave_open_temp_tables | 0 | | Slow_launch_threads | 0 | | Slow_queries | 949| | Sort_merge_passes| 0 | | Sort_range | 0 | | Sort_rows| 0 | | Sort_scan| 0 | | Table_locks_immediate| 10247 | | Table_locks_waited | 0 | | Threads_cached | 3 | | Threads_created | 16 | | Threads_connected| 4090 | | Threads_running | 1 | | Uptime | 1445845| +--++ shell$ mysqladmin processlist gives me: | 11711 | DELAYED | localhost | Mthermoautotrophicum | |Delayed_insert | 981| Waiting on cond | scop2 | | 11713 | DELAYED | localhost | Mthermoautotrophicum | |Delayed_insert |
RE: Got error 127 when reading table
Hi, I have another example of this strange behaviour. I've managed to dump most of the table and then after certain row got the error 127. This machine is linux 2.2.17 in this particular example operating on table close to the 2GB limit. mysql Ver 11.15 Distrib 3.23.44, for pc-linux-gnu (i686) I'm running following command: From my copy script I got: /usr/local/mysql/bin/mysqldump: Error 1030: Got error 127 from table handler when dumping table 'intragenome_data' at row: 5585 When checking the table on the target host, where I thought would be empty table, it appeared that the table in fine and contains first 5585 rows and contains data as expected. mysql describe intragenome_data; +--+--+--+-+-+---+ | Field| Type | Null | Key | Default | Extra | +--+--+--+-+-+---+ | id | int(11) | | PRI | 0 | | | contig_data_id | int(11) | | MUL | 0 | | | contig_data_code | varchar(100) | | MUL | | | | code | varchar(100) | | MUL | | | | descr| varchar(255) | YES | MUL | NULL| | | dat | longtext | YES | | NULL| | | created | varchar(100) | | | | | +--+--+--+-+-+---+ 7 rows in set (0.02 sec) mysql Then I checked the table on source host (from which I got the sql dump data) the logfile and table itself: 011209 05:48:19 mysqld started /usr/local/mysql/libexec/mysqld: ready for connections 011210 14:47:02 Warning: Found 24646 of 0 rows when repairing './Burkholderia_pseudomallei_K96243/known3d_data' 011211 13:09:28 read_const: Got error 127 when reading table ./hemi_prot/prot_data 011211 13:09:59 read_const: Got error 127 when reading table ./hemi_prot/prot_data 011211 13:11:27 read_const: Got error 127 when reading table ./hemi_prot/prot_data 011211 13:11:32 read_const: Got error 127 when reading table ./hemi_prot/prot_data 011211 13:11:32 read_const: Got error 127 when reading table ./hemi_prot/prot_data 011211 13:11:32 read_const: Got error 127 when reading table ./hemi_prot/prot_data 011211 13:11:33 read_const: Got error 127 when reading table ./hemi_prot/prot_data 011211 13:11:33 read_const: Got error 127 when reading table ./hemi_prot/prot_data 011211 13:15:43 read_const: Got error 127 when reading table ./Listeria_monocytogenes_EGD/orf_data 011211 13:16:03 read_const: Got error 127 when reading table ./Listeria_monocytogenes_EGD/orf_data 011213 11:37:32 read_const: Got error 127 when reading table ./Saccharomyces_cerevisiae/funcat_data 011213 11:41:40 read_const: Got error 127 when reading table ./Saccharomyces_cerevisiae/funcat_data 011213 19:14:13 read_const: Got error 127 when reading table ./Agrobacterium_tumefaciens_C58_pAT/blast_data 011213 19:23:21 read_const: Got error 127 when reading table ./Agrobacterium_tumefaciens_C58_pAT/blast_data 011219 16:47:28 read_const: Got error 127 when reading table ./Spombe/blast_data 020102 19:50:28 read_const: Got error 127 when reading table ./Pasteurella_multocida_PM70/blast_data 020103 15:32:09 read_const: Got error 127 when reading table ./Agrobacterium_tumefaciens_C58_pAT/funcat_data 020104 16:39:01 Warning: Found 5585 of 5586 rows when repairing './Arabidopsis_thaliana/intragenome_data' ---^ yes, I already had this problems with this table 2 days ago and ran REPAIR on it. No-one should modify the table, no-one should even run myisampack/myisamchk/flush-tables commands, so this time I'm rather sure only mysqld is involved. 020107 12:12:33 read_const: Got error 127 when reading table ./Arabidopsis_thaliana/intragenome_data kulan$ mysql Arabidopsis_thaliana Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 97806 to server version: 3.23.44-log Type 'help;' or '\h' for help. Type '\c' to clear the buffer. mysql check table intragenome_data; +---+---+--+---+ | Table | Op| Msg_type | Msg_text || +---+---+--+---+ | Arabidopsis_thaliana.intragenome_data | check | warning | Table is marked as |crashed| | Arabidopsis_thaliana.intragenome_data | check | error| Size of datafile is: |2147483647 Should be: 2152589024 | | Arabidopsis_thaliana.intragenome_data | check | error| Corrupt || +---+---+--+---+ 3 rows in
Compiling mysql-3.23.46 on OSF1
Hi,
did someone manage to compile mysql on OSF1 4.0[D-F] series using
Digital's cc and cxx compilers? Please Cc: me in reply, thanks.
CC=cc CXX=cxx CFLAGS='-non_shared -O3 -tune-host' CXXFLAGS='-non_shared
-O3 -tune-host' ./configure --with-libwrap
--with-mysqld-ldflags=-all-static --enable-assembler
--prefix=/usr/local/mysql-3.23.46 --with-charset=latin1 --enable-thread-safe-client
--disable-shared
I have problems linking against -lpthread. There's /usr/shlib/libpthread.so
Configure thinks DEC threads are installed, so it bumps at the libm.a, but
in real again because of missing -lpthread (which it should realize
already some steps sooner).
checking for crypt in -lcrypt... no
checking for crypt... yes
checking if libz with compress... no
checking for tcpd.h... no
checking for int8... no
checking LinuxThreads... Not found
checking DEC threads... yes
checking named thread libs:... -lpthread -lmach -lexc
checking for strtok_r in -lpthread... no
checking for strtok_r in -lc_r... no
checking for strtok_r... no
checking for pthread_init... no
checking for dlopen in -ldl... no
checking for restartable system calls... no
checking need of special linking flags... none
checking for working const... yes
checking for inline... __inline
checking for off_t... yes
checking for st_rdev in struct stat... yes
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking size of char... 0
configure: error: No size for char type.
A likely cause for this could be that there isn't any
static libraries installed. You can verify this by checking if you have libm.a
in /lib, /usr/lib or some other standard place. If this is the problem,
install the static libraries and try again. If this isn't the problem,
examine config.log for possible errors. If you want to report this, use
'scripts/mysqlbug' and include at least the last 20 rows from config.log!
mmokrejs@prfdec$ ls -la /usr/lib/libm.a
lrwxrwxrwx 1 root system17 Feb 23 1998 /usr/lib/libm.a -
../ccs/lib/libm.a
mmokrejs@prfdec$ ls -la /usr/ccs/lib/libm.a
-rw-r--r-- 1 bin bin 666208 Jan 5 1998 /usr/ccs/lib/libm.a
mmokrejs@prfdec$
from the config.log:
configure:5503: checking DEC threads
configure:5780: checking named thread libs:
configure:5904: checking for strtok_r in -lpthread
configure:5923: cc -std1 -o conftest -non_shared -O3 -tune-hostconftest.c
-lpthread -lpthread -lmach -lexc
-lm -lpthread -lmach -lexc 15
ld:
Can't locate file for: -lpthread
configure: failed program was:
#line 5912 configure
#include confdefs.h
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
char strtok_r();
int main() {
strtok_r()
; return 0; }
configure:5955: checking for strtok_r in -lc_r
configure:5974: cc -std1 -o conftest -non_shared -O3 -tune-hostconftest.c -lc_r
-lpthread -lmach -lexc -lm
-lpthread -lmach -lexc 15
ld:
Can't locate file for: -lpthread
configure: failed program was:
#line 5963 configure
#include confdefs.h
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
char strtok_r();
int main() {
strtok_r()
; return 0; }
configure:6008: checking for strtok_r
BTW: from the configure script:
5412 *netbsd*)
5413 echo Adding flag -Dunix
5414 CFLAGS=$CFLAGS -Dunix
5415 CXXFLAGS=$CXXFLAGS -Dunix
5416 OVERRIDE_MT_LD_ADD=\$(top_srcdir)/mit-pthreads/obj/libpthread.a
5417 ;;
How does the netbsd relate to -Dunix ?
I found that I can compile using cxx -lpthread or just cc without
using -lpthread. I compiled in such way the example from
http://www.tru64unix.compaq.com/docs/base_doc/DOCUMENTATION/V40F_HTML/AQ2DPDTK/DOCU_008.HTM#c_example
The libpthread is only shared library, there's no static binary
available (at least I cannot find it). How can I create static binary in
such case?
I've solved part of my problems:
1. removing the -lpthread string occurencies from configure where
relates to OSF1, so only -lmach -lexc are retained (they're present as
static libs).
2. I've changed mysql-3.23.46/libtool this way:
- hardcode_libdir_flag_spec=\${wl}-rpath \${wl}\$libdir
+ hardcode_libdir_flag_spec=
It looks to me it's designed for gcc, but not for cc.
Next problem I faced is that config.status contains:
s%@AWK@%gawk%g
s%@CC@%cc -std1%g
s%@CXX@%cxx%g
Note that I did not use -std1 CFLAGS at all while calling configure.
This option makes cc more strict and thus exit. Removing -std1 helps in
many cases, but here's one example:
Making all in libmysql_r
make[2]: Entering directory `/scratch/mmokrejs/mysql-3.23.46/libmysql_r'
/bin/sh ../libtool --mode=compile cc -std1
-DDEFAULT_CHARSET_HOME=\/usr/local/mysql-3.23.46\
Re: Compiling mysql-3.23.46 on OSF1
On Thu, 20 Dec 2001, Martin MOKREJ wrote: Hi, did someone manage to compile mysql on OSF1 4.0[D-F] series using Digital's cc and cxx compilers? Please Cc: me in reply, thanks. CC=cc CXX=cxx CFLAGS='-non_shared -O3 -tune-host' CXXFLAGS='-non_shared -O3 -tune-host' ./configure --with-libwrap --with-mysqld-ldflags=-all-static --enable-assembler --prefix=/usr/local/mysql-3.23.46 --with-charset=latin1 --enable-thread-safe-client --disable-shared I have problems linking against -lpthread. There's /usr/shlib/libpthread.so Just a folloup: I cannot compile nor with gcc 2.95.2. CC=gcc CXX=g++ CFLAGS='-O3 -felide-constructors -fno-exceptions -fno-rtti' CXXFLAGS='-O3 -felide-constructors -fno-exceptions -fno-rtti' ./configure --with-libwrap --with-mysqld-ldflags=-all-static --enable-assembler --prefix=/usr/local/mysql-3.23.46 --with-charset=latin1 --enable-thread-safe-client --disable-shared /bin/sh ../libtool --mode=link g++ -O3 -DDBUG_OFF -O3 -felide-constructors -fno-exceptions -fno-rtti -fno-implicit-templates -fno-exceptions -fno-rtti -o mysqld sql_lex.o item.o item_sum.o item_buff.o item_func.o item_cmpfunc.o item_strfunc.o item_timefunc.o thr_malloc.o item_create.o field.o key.o sql_class.o sql_list.o net_serv.o violite.o net_pkg.o lock.o my_lock.o sql_string.o sql_manager.o sql_map.o mysqld.o password.o hash_filo.o hostname.o convert.o sql_parse.o sql_yacc.o sql_base.o table.o sql_select.o sql_insert.o sql_update.o sql_delete.o procedure.o item_uniq.o sql_test.o log.o log_event.o init.o derror.o sql_acl.o unireg.o time.o opt_range.o opt_sum.o opt_ft.o records.o filesort.o handler.o ha_heap.o ha_myisam.o ha_myisammrg.o ha_berkeley.o ha_innobase.o ha_gemini.o ha_isam.o ha_isammrg.o sql_db.o sql_table.o sql_rename.o sql_crypt.o sql_load.o mf_iocache.o field_conv.o sql_show.o sql_udf.o sql_analyse.o sql_cache.o slave.o sql_repl.o mini_client.o mini_client_errors.o md5.o stacktrace.o -all-/bin/sh ../libtool --mode=link g++ -O3 -DDBUG_OFF -O3 -felide-constructors -fno-exceptions -fno-rtti -fno-implicit-templates -fno-exceptions -fno-rtti -o mysqld sql_lex.o item.o item_sum.o item_buff.o item_func.o item_cmpfunc.o item_strfunc.o item_timefunc.o thr_malloc.o item_create.o field.o key.o sql_class.o sql_list.o net_serv.o violite.o net_pkg.o lock.o my_lock.o sql_string.o sql_manager.o sql_map.o mysqld.o password.o hash_filo.o hostname.o convert.o s g++ -O3 -DDBUG_OFF -O3 -felide-constructors -fno-exceptions -fno-rtti -fno-implicit-templates -fno-exceptions -fno-rtti -o mysqld sql_lex.o item.o item_sum.o item_buff.o item_func.o item_cmpfunc.o item_strfunc.o item_timefunc.o thr_malloc.o item_create.o field.o key.o sql_class.o sql_list.o net_serv.o violite.o net_pkg.o lock.o my_lock.o sql_string.o sql_manager.o sql_map.o mysqld.o password.o hash_filo.o hostname.o convert.o sql_parse.o sql_yacc.o sql_base.o table.o sql_select.o sql_insert.o sql_update.o sql_delete.o procedure.o item_uniq.o sql_test.o log.o log_event.o init.o derror.o sql_acl.o unireg.o time.o opt_range.o opt_sum.o opt_ft.o records.o filesort.o handler.o ha_heap.o ha_myisam.o ha_myisammrg.o ha_berkeley.o ha_innobase.o ha_gemini.o ha_isam.o ha_isammrg.o sql_db.o sql_table.o sql_rename.o sql_crypt.o sql_load.o mf_iocache.o field_conv.o sql_show.o sql_udf.o sql_analyse.o sql_cache.o slave.o sql_repl.o mini_client.o mini_client_errors.o md5.o stacktrace.o -static ../isam/libnisam.a ../merge/libmg++ -O3 -DDBUG_OFF -O3 -felide-constructors -fno-exceptions -fno-rtti -fno-implicit-templates -fno-exceptions -fno-rtti -o mysqld sql_lex.o item.o item_sum.o item_buff.o item_func.o item_cmpfunc.o item_strfunc.o item_tim/usr/bin/ld: Can't locate file for: -lpthread collect2: ld returned 1 exit status make[3]: *** [mysqld] Error 1 make[3]: Leaving directory `/scratch/mmokrejs/mysql-3.23.46-gcc/sql' Please Cc: me. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Got error 127 when reading table
Hi,
once I've reported here problems that somehow randomly we get these
errors in mysql's log file. It looks, that when user drops a table, a
table isn't dropped or somehow remains in cache. The when user tries to
create the table again from scratch, he get's the error 127.
Please note that the error is clearly NOT loggeg in mysqld's error
logfile. Flushing logs or hosts or threads doesn't help to get this error
written to disk.
From what has the user reported, from such a dropped improperly
recreated table he can only select using the first column and doesn't get
the data from other columns at all. While I was flushing table cache few
times per day, he found that possibly this fixed his problem.
I'm curious why he gets the error when adding index to table's column.
Why not when trying to create the table already?
We are trying to get more out from this. ;)
kulan$ tail /usr/local/mysql/log/kulan.gsf.de.err
011211 13:11:32 read_const: Got error 127 when reading table ./hemi_prot/prot_data
011211 13:11:33 read_const: Got error 127 when reading table ./hemi_prot/prot_data
011211 13:11:33 read_const: Got error 127 when reading table ./hemi_prot/prot_data
011211 13:15:43 read_const: Got error 127 when reading table
./Listeria_monocytogenes_EGD/orf_data
011211 13:16:03 read_const: Got error 127 when reading table
./Listeria_monocytogenes_EGD/orf_data
011213 11:37:32 read_const: Got error 127 when reading table
./Saccharomyces_cerevisiae/funcat_data
011213 11:41:40 read_const: Got error 127 when reading table
./Saccharomyces_cerevisiae/funcat_data
011213 19:14:13 read_const: Got error 127 when reading table
./Agrobacterium_tumefaciens_C58_pAT/blast_data
011213 19:23:21 read_const: Got error 127 when reading table
./Agrobacterium_tumefaciens_C58_pAT/blast_data
011219 16:47:28 read_const: Got error 127 when reading table ./Spombe/blast_data
kulan$ /home/w3/pedant2/mips/PEDANT2/soft/PEDANT2/PERL/parse.pl -table intergenome -db
Saccharomyces_cerevisiae
DBD::mysql::st execute failed: Got error 127 from table handler at
/home/w3/pedant2/mips/PEDANT2/soft/PEDANT2/PERL/Database_Pro_MySQL.pm line 292.
Can not execute SQL statement: 'alter table intergenome add index (hitcode)' at
/home/w3/pedant2/mips/PEDANT2/soft/PEDANT2/PERL/Database_Pro_MySQL.pm line 292
Database_Pro_MySQL::PrepEx('Database_Pro_MySQL=HASH(0x8594fc8)', 'alter table
intergenome add index (hitcode)') called at
/home/w3/pedant2/mips/PEDANT2/soft/PEDANT2/PERL/Database_Pro_MySQL.pm line 277
Database_Pro_MySQL::AddIndex('Database_Pro_MySQL=HASH(0x8594fc8)',
'intergenome', 'hitcode') called at
/home/w3/pedant2/mips/PEDANT2/soft/PEDANT2/PERL/Parse_Pro.pm line 393
Parse_Pro::_IndexTable('Parse_Pro=HASH(0x841b2d8)') called at
/home/w3/pedant2/mips/PEDANT2/soft/PEDANT2/PERL/Parse_Pro.pm line 373
Parse_Pro::_SetTable('Parse_Pro=HASH(0x841b2d8)') called at
/home/w3/pedant2/mips/PEDANT2/soft/PEDANT2/PERL/Parse_Pro.pm line 307
Parse_Pro::new('Parse_Pro', 'SET', 'Saccharomyces_cerevisiae', 'METH',
'intergenome') called at /home/w3/pedant2/mips/PEDANT2/soft/PEDANT2/PERL/parse.pl line
177
Database handle destroyed without explicit disconnect.
kulan$ tail /usr/local/mysql/log/kulan.gsf.de.err
011211 13:11:32 read_const: Got error 127 when reading table ./hemi_prot/prot_data
011211 13:11:33 read_const: Got error 127 when reading table ./hemi_prot/prot_data
011211 13:11:33 read_const: Got error 127 when reading table ./hemi_prot/prot_data
011211 13:15:43 read_const: Got error 127 when reading table
./Listeria_monocytogenes_EGD/orf_data
011211 13:16:03 read_const: Got error 127 when reading table
./Listeria_monocytogenes_EGD/orf_data
011213 11:37:32 read_const: Got error 127 when reading table
./Saccharomyces_cerevisiae/funcat_data
011213 11:41:40 read_const: Got error 127 when reading table
./Saccharomyces_cerevisiae/funcat_data
011213 19:14:13 read_const: Got error 127 when reading table
./Agrobacterium_tumefaciens_C58_pAT/blast_data
011213 19:23:21 read_const: Got error 127 when reading table
./Agrobacterium_tumefaciens_C58_pAT/blast_data
011219 16:47:28 read_const: Got error 127 when reading table ./Spombe/blast_data
kulan$
--
Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs
MIPS / Institute for Bioinformatics http://mips.gsf.de
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
tel.: +49-89-3187 3616 , fax:+49-89-3187 3585
-
Before posting, please check:
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http://lists.mysql.com/ (the list archive)
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RE: Got error 127 when reading table
On Thu, 20 Dec 2001, Almar van Pel wrote: I believe this error is assigned to a crashed table. try repair table and afterwards optimize. Eh, I forgot to mention that I've done CHECK TABLE a bit too late, when the user came and said that the problem got fixed itself, and asked me what I did. We came to the conclusion it's because of the flush tables command. Next time he has to run the check table himself and grab the table files before doing anything, and I plan to do then check table, grab files again and then flush tables and then again grab the table files. I wish there will be a difference in file sizes or timestamps or just something. In principal, there should be if he accessing somehow first row from already deleted table and claiming there's same amount of rows. But to answer your question, when I check those tables referred in errorlog, CHECK TABLE says OK. :( And no-one did any repair table on them, for sure. Currently we still don't know how to reproduce it, but at least the approach with dropping table gives an idea about cache handling. But, those errors are on the other hand haven't been logged in the errorlog, although the user received, the error through perl DBI. However, those examples from errolog are examples, when those tables aren't ever modified. They're just in the errolog file and I never found a corrupted table in such case when if I do run CHECK TABLE on them, (they're OK), as I've said above. So it looks taht at some random situations mysql cannot operate on some tables. It doesn't look to be related to size of the table at all, and all of them are MyISAM. So the approach drop/create isn't what happens usually here and what's logged in the errrolog. However, probably with right amount of threads operating on same database/tables would show the problem. But I've seen these 127 erros posted to list by others also, if I remeber, so maybe I'm not the only-one. It happens on Linux 2.2.19 with 3.23.44, but those errors 127 we have also on 2.4.11 if I remember right the kernel version. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Introducing hidden row having duplicated primary key
Hello,
I think I've found a bug. Just by playing with REPLACE and INSERT, the
following happened. I'm including full log, demonstrating that I don't
understand sql at all. ;-) Can someone explain me what 2 rows affected
means? How can I select the second row from the table? How can I delete it?
Please CC me in reply. Thanks.
mysql select * from Upd;
++-+
| Tab| Time|
++-+
| prot_data | 2001-07-20 00:45:44 |
| contig_data| 2001-07-20 00:45:47 |
| orf_data | 2001-07-20 00:45:48 |
| blast_data | 2001-11-12 15:19:13 |
| seg_data | 2001-11-12 15:19:29 |
| nonglob_data | 2001-11-12 15:19:35 |
| pfam_data | 2001-11-12 15:33:25 |
| scop_data | 2001-11-12 15:33:41 |
| mem_data | 2001-11-12 15:33:47 |
| coils_data | 2001-11-12 15:33:54 |
| funcat_data| 2001-11-12 15:34:15 |
| cogs_data | 2001-11-12 15:34:59 |
| known3d_data | 2001-11-12 15:35:11 |
| blimps_data| 2001-11-12 15:37:55 |
| pros_data | 2001-11-12 15:38:08 |
| prd_data | 2001-11-12 15:39:16 |
| scop1_data | 2001-09-02 16:34:01 |
| scop2_data | 2001-09-02 17:05:52 |
| blast_crossupdate_data | 2001-08-23 18:05:12 |
| blast_self_data| 2001-10-03 05:15:48 |
| intergenome_data | 2001-10-23 20:56:48 |
++-+
21 rows in set (0.02 sec)
mysql replace into Upd Tab=test Time=NOW();
ERROR 1064: You have an error in your SQL syntax near 'Tab=test Time=NOW()' at line 1
mysql replace into Upd Tab=test Time=2;
ERROR 1064: You have an error in your SQL syntax near 'Tab=test Time=2' at line 1
mysql replace into Upd Tab=test Time=NOW();
ERROR 1064: You have an error in your SQL syntax near 'Tab=test Time=NOW()' at line 1
mysql replace into Upd set Tab=test Time=NOW();
ERROR 1064: You have an error in your SQL syntax near 'Time=NOW()' at line 1
mysql replace into Upd (Tab,Time) values ('test', NOW());
Query OK, 1 row affected (0.02 sec)
mysql update into Upd (Tab,Time) values ('test', NOW());
ERROR 1064: You have an error in your SQL syntax near 'into Upd (Tab,Time) values
('test', NOW())' at line 1
mysql update Upd (Tab,Time) values ('test', NOW());
ERROR 1064: You have an error in your SQL syntax near '(Tab,Time) values ('test',
NOW())' at line 1
mysql update Upd set Time=NOW() where Tab=test;
Query OK, 1 row affected (0.02 sec)
Rows matched: 1 Changed: 1 Warnings: 0
mysql replace into Upd (Tab,Time) values ('test', NOW());
Query OK, 2 rows affected (0.02 sec)
mysql select * from Upd;
++-+
| Tab| Time|
++-+
| prot_data | 2001-07-20 00:45:44 |
| contig_data| 2001-07-20 00:45:47 |
| orf_data | 2001-07-20 00:45:48 |
| blast_data | 2001-11-12 15:19:13 |
| seg_data | 2001-11-12 15:19:29 |
| nonglob_data | 2001-11-12 15:19:35 |
| pfam_data | 2001-11-12 15:33:25 |
| scop_data | 2001-11-12 15:33:41 |
| mem_data | 2001-11-12 15:33:47 |
| coils_data | 2001-11-12 15:33:54 |
| funcat_data| 2001-11-12 15:34:15 |
| cogs_data | 2001-11-12 15:34:59 |
| known3d_data | 2001-11-12 15:35:11 |
| blimps_data| 2001-11-12 15:37:55 |
| pros_data | 2001-11-12 15:38:08 |
| prd_data | 2001-11-12 15:39:16 |
| scop1_data | 2001-09-02 16:34:01 |
| scop2_data | 2001-09-02 17:05:52 |
| blast_crossupdate_data | 2001-08-23 18:05:12 |
| blast_self_data| 2001-10-03 05:15:48 |
| intergenome_data | 2001-10-23 20:56:48 |
| test | 2001-11-13 22:39:40 |
++-+
22 rows in set (0.02 sec)
mysql insert into Upd (Tab,Time) values ('test', NOW());
ERROR 1062: Duplicate entry 'test' for key 1
mysql select * from Upd;
++-+
| Tab| Time|
++-+
| prot_data | 2001-07-20 00:45:44 |
| contig_data| 2001-07-20 00:45:47 |
| orf_data | 2001-07-20 00:45:48 |
| blast_data | 2001-11-12 15:19:13 |
| seg_data | 2001-11-12 15:19:29 |
| nonglob_data | 2001-11-12 15:19:35 |
| pfam_data | 2001-11-12 15:33:25 |
| scop_data | 2001-11-12 15:33:41 |
| mem_data | 2001-11-12 15:33:47 |
| coils_data | 2001-11-12 15:33:54 |
| funcat_data| 2001-11-12 15:34:15 |
| cogs_data | 2001-11-12 15:34:59 |
| known3d_data | 2001-11-12 15:35:11 |
|
Re: Introducing hidden row having duplicated primary key
On Tue, 13 Nov 2001, Gerald Clark wrote: Looks correct to me. What do you think is the problem? 2 rows were affected by the replace. One row was deleted, and one was inserted, Both rows had a value of 'test' for column 'Tab'. Cool, thanks to Jeremy Zawodny and you, now I know even more that I do not know sql. Well, I told you that. ;) I thought that REPLACE replaces only fields which are different, so if a line is missing, behaves as an insert, if the line is present, behaves as an updates on columns which differ. This means that I was hoping that UPDATE updates/rewrites all specified columns on line; REPLACE has some logic to figure out that we do not have to rewrite a column with the same data and so we do not have to recreate an index for such column. If I guess right, deleting a row means marking it as deleted, right, so the REPLACE in my case marked the old line/row deleted and appended a new row to the table? That would mean it's better to use UPDATE then REPLACE, right? ;) -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany tel.: +49-89-3187 3616 , fax:+49-89-3187 3585 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Missing binaries in 3.23.42 release binary dist.
Hi, I've found there are missing binaries at least in mysql-3.23.42-pc-linux-gnu-i686.tar.gz Those are: isamlog, myisamlog, mysql_install_db, mysqlbinlog I've checked that in the tar archive again, but not luck. Am I totally blind? ;-) -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
3.23.42 and some errors in logfile
Hi, so I've tried the binary distribution for linux and I have these errors in logfile (I've seen them already under 3.23.41, under which I compressed the tables): 010910 18:12:20 mysqld started /usr/local/mysql/bin/mysqld: ready for connections 010910 18:13:52 read_const: Got error 127 when reading table ./Ncrassa/contig_data Running myisamchk without options does not show any errors. Here are some details: $ myisamchk -dvvv /data/mysql/Ncrassa/contig_data.MYI MyISAM file: /data/mysql/Ncrassa/contig_data.MYI Record format: Compressed Character set: latin1 (8) File-version:1 Creation time: 2001-08-29 5:45:44 Recover time:2001-08-30 0:08:31 Status: checked,analyzed,optimized keys,sorted index pages Checksum: 2185832194 Data records: 247 Deleted blocks: 0 Datafile parts:247 Deleted data: 0 Datafile pointer (bytes):4 Keyfile pointer (bytes):2 Datafile length: 4562802 Keyfile length: 15360 Max datafile length:4294967294 Max keyfile length: 67107839 Recordlength:55929 table description: Key Start Len Index Type Rec/key Root Blocksize 1 2 3 unique uint24 1 1024 1024 2 108 100 multip. char packed stripped 1 4096 1024 3 208 255 multip. char packed stripped 247 7168 2048 4 8 100 multip. char packed stripped 1 9216 1024 5 5 3 multip. uint24 prefix 112288 1024 Field Start Length Nullpos Nullbit Type Huff tree Bits 1 1 1 constant 1 0 2 2 3 zerofill(2) 2 9 3 5 3 zerofill(2) 2 9 4 8 100no endspace 2 9 5 108 100no endspace 2 9 6 208 255constant 3 0 7 463 12 1 1 blob 4 3 CHECK TABLE CONTIG_DATA says that the table is also OK. My question is: because I compressed the table under broken 3.23.41, shouldn't I uncpress the table and compress again? Or at least recreate the index. The problem is, that I don't know how to repeat this problem. I can work with table (i.e. SELECTs work). However, the message in logfile is weird. It happens (and happened even before this upgrade) with other tables: 010910 16:08:04 read_const: Got error 127 when reading table ./Athaliana_II/contig_data 010910 16:12:28 read_const: Got error 127 when reading table ./Campylobacter_jejuni_NCTC_11168/blast_data You may want to check pub/mysql/secret/compressed.tgz or delete it as junk. ;) Thanks! -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: ERROR 1054 at line 52: Unknown column 'nan' in 'field list'
On Sun, 2 Sep 2001, Michael Widenius wrote:
Hi,
Sinisa == Sinisa Milivojevic [EMAIL PROTECTED] writes:
Sinisa =?iso-8859-2?Q?Martin_MOKREJ=A9?= writes:
And should say that
update rep set low='0.00' where id=148;
solved my problem for command:
mysqldump -f --socket=/tmp/mysql.sock --add-drop-table --extended-insert
--quick --databases Cmuridarum rep | mysql -f --host=pednew -C Cmuridarum
... to be complete. ;)
--
Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs
MIPS / Institute for Bioinformatics http://mips.gsf.de
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
Sinisa Yes, I saw this. Still, we should fix it.
MySQL should never allow you to insert 'nan' into a column.
It would be nice to know how this value was inserted in the first
place.
Hmm, I did not write this code and can't find it quickly, but hust trying
to repeat it works:
mysql show columns from rep;
+--+---+--+-+-+---+
| Field| Type | Null | Key | Default | Extra |
+--+---+--+-+-+---+
| id | mediumint(8) unsigned | | PRI | 0 | |
| prot_data_id | mediumint(8) unsigned | | MUL | 0 | |
| contig_data_id | mediumint(8) unsigned | | MUL | 0 | |
| contig_data_code | varchar(100) | | | | |
| code | varchar(100) | | MUL | | |
| length | int(11) | | | 0 | |
| mw | float(10,2) | | | 0.00| |
| pI | float(10,2) | | | 0.00| |
| class| varchar(255) | | MUL | | |
| mem | int(11) | | | 0 | |
| low | float(10,2) | | | 0.00| |
| nonglob | float(10,2) | | | 0.00| |
| coil | float(10,2) | | | 0.00| |
| sigp | int(11) | | | 0 | |
| loc | varchar(255) | | MUL | | |
| summary | text | YES | | NULL| |
| geneid | varchar(255) | | MUL | | |
| classification | varchar(255) | | MUL | | |
| pubmed | varchar(255) | | MUL | | |
| comments | text | YES | | NULL| |
| remarks | text | YES | | NULL| |
| descr| varchar(255) | | MUL | | |
| manual | enum('yes','no') | YES | | NULL| |
+--+---+--+-+-+---+
mysql update rep set low='nan' where id=148;
Query OK, 1 row affected (0.07 sec)
Rows matched: 1 Changed: 1 Warnings: 1
'mysqladmin version' gives:
mysqladmin Ver 8.21 Distrib 3.23.41, for pc-linux-gnu on i686
Copyright (C) 2000 MySQL AB MySQL Finland AB TCX DataKonsult AB
This software comes with ABSOLUTELY NO WARRANTY. This is free software,
and you are welcome to modify and redistribute it under the GPL license
Server version 3.23.41-log
Maybe we should check in application for the warning?
How can I see the warning? -Not on terminal, not in server logfile ...
--
Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs
MIPS / Institute for Bioinformatics http://mips.gsf.de
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
-
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Re: myisampack dumps core on some tables
On Fri, 31 Aug 2001, Michael Widenius wrote: mmokrejs == mmokrejs iso-8859-2 writes: mmokrejs On Thu, 30 Aug 2001, Michael Widenius wrote: mmokrejs Hi, mmokrejs yes this patch *fixes* all of my problems, except one table which is/was mmokrejs probably too big? I haven't found any options that would make myisamchk to mmokrejs ask for less memory. mmokrejs /usr/local/mysql/bin/myisamchk: Out of memory (Needed 4294922813 bytes) mmokrejs /usr/local/mysql/bin/myisamchk: error: 12 when opening MyISAM-table '/data/mysql/Celegans/rep.MYI' mmokrejs /usr/local/mysql/bin/myisamchk: Out of memory (Needed 4294922813 bytes) mmokrejs /usr/local/mysql/bin/myisamchk: error: 12 when opening MyISAM-table '/data/mysql/Celegans/rep.MYI' No tables should ever be too big for myisamchk. What options did you use with myisamchk ? /usr/local/mysql/bin/myisamchk -f -d /data/mysql/$db/$table.MYI But even /usr/local/mysql/bin/myisamchk /data/mysql/$db/$table.MYI or with only -S or only -a. Just everything sensible. mmokrejs Well, the other rep tables are fine. I'm a bit angry about myself, mmokrejs because I dropped the Celegans.rep tables:!!! :( Well, intentionally. :( mmokrejs I managed successfully to run myisamchk -rq on it, myisampack and again mmokrejs myisamchk -rq. So now I can only tell you that broken datafile can cause mmokrejs myisamchk to ask for too much memory. :( As you can guess, this doesn't help me to find out where the problem is :( I know. mmokrejs So unfortunately, I don't have the broken table anymore, only the mmokrejs screen dumps (size od .MYD and .MYI differed). It seems the mmokrejs broken datafile had 6 bytes more, broken index was much smaller. mmokrejs That's all I can tell you. ;) mmokrejs Maybe it helps. Unfortunately this doesn't help me to solve this. If you ever get this problem again, save the tables so that we can repeat it and fix the problem! Sure! Thanks. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
ERROR 1054 at line 52: Unknown column 'nan' in 'field list'
Hi again, I have the following problem: mysqldump -# --socket=/tmp/mysql.sock --add-drop-table -f --extended-insert --quick Cmuridarum rep | mysql -f --host=pednew -C Cmuridarum ERROR 1054 at line 52: Unknown column 'nan' in 'field list' I have even tried OPTIMIZE TABLE REP; REPAIR TABLE REP;, no luck. SHOW COLUMNS FROM REP; does NOT show any column name `nan'. Even when I use SELECT * FROM REP; and search for nan , I have no match. see pub/mysql/secret/rep.tgz Thanks for any reply! PS.: Tested still on linux with 3.23.41 binaries from your website, as seen in my previous postings. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: ERROR 1054 at line 52: Unknown column 'nan' in 'field list'
And should say that update rep set low='0.00' where id=148; solved my problem for command: mysqldump -f --socket=/tmp/mysql.sock --add-drop-table --extended-insert --quick --databases Cmuridarum rep | mysql -f --host=pednew -C Cmuridarum ... to be complete. ;) -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: ERROR 1054 at line 52: Unknown column 'nan' in 'field list'
On Fri, 31 Aug 2001, Sinisa Milivojevic wrote:
May be you used some special chars in column names. In that case you
should use instruct mysqldump to use backticks for table and column
names.
Ehh, now I know what you meant: - to use -Q option to mysqldump , ok
but it anyway did not help.
CREATE TABLE `rep` (
`id` mediumint(8) unsigned NOT NULL default '0',
`prot_data_id` mediumint(8) unsigned NOT NULL default '0',
`contig_data_id` mediumint(8) unsigned NOT NULL default '0',
`contig_data_code` varchar(100) NOT NULL default '',
`code` varchar(100) NOT NULL default '',
`length` int(11) NOT NULL default '0',
`mw` float(10,2) NOT NULL default '0.00',
`pI` float(10,2) NOT NULL default '0.00',
`class` varchar(255) NOT NULL default '',
`mem` int(11) NOT NULL default '0',
`low` float(10,2) NOT NULL default '0.00',
`nonglob` float(10,2) NOT NULL default '0.00',
`coil` float(10,2) NOT NULL default '0.00',
`sigp` int(11) NOT NULL default '0',
`loc` varchar(255) NOT NULL default '',
`summary` text,
`geneid` varchar(255) NOT NULL default '',
`classification` varchar(255) NOT NULL default '',
`pubmed` varchar(255) NOT NULL default '',
`comments` text,
`remarks` text,
`descr` varchar(255) NOT NULL default '',
`manual` enum('yes','no') default NULL,
PRIMARY KEY (`id`),
KEY `class` (`class`),
KEY `loc` (`loc`),
KEY `geneid` (`geneid`),
KEY `classification` (`classification`),
KEY `pubmed` (`pubmed`),
KEY `descr` (`descr`),
KEY `code` (`code`),
KEY `prot_data_id` (`prot_data_id`),
KEY `contig_data_id` (`contig_data_id`)
) TYPE=MyISAM PACK_KEYS=1;
I'm pretty sure the problem is with text nan being in place of a float
number.
--
Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs
MIPS / Institute for Bioinformatics http://mips.gsf.de
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
-
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Re: myisampack dumps core on some tables
On Wed, 29 Aug 2001, Sasha Pachev wrote: On Wednesday 29 August 2001 15:14, Martin MOKREJ? wrote: Description: I have on Linux running 3.23.41 the following problem: $ /usr/local/mysql/bin/myisampack -v -v -f --tmpdir=/tmp /data/mysql/Aactinomycetemcomitans/blimps.MYI Compressing /data/mysql/Aactinomycetemcomitans/blimps.MYD: (1443 records) - Calculating statistics normal: 7 empty-space: 0 empty-zero: 0 empty-fill: 7 pre-space: 0 end-space: 3 intervall-fields: 0 zero: 1 Original trees: 16 After join: 9 - Compressing file Segmentation fault (core dumped) $ gdb /usr/local/mysql/bin/myisampack ./core [...] Core was generated by `/usr/local/mysql/bin/myisampack -v -v -f --tmpdir=/tmp /data/mysql/Aactinomycet'. Program terminated with signal 11, Segmentation fault. #0 0x400f00d5 in ?? () (gdb) where #0 0x400f00d5 in ?? () #1 0x8050557 in compress_isam_file () #2 0x804e18c in compress () #3 0x804d4b4 in main () #4 0x400b3a42 in ?? () (gdb) quit $ The calling perl script reports as an error value in $! Illegal seek. It happens to me with 3 table-types: Packing blast Aactinomycetemcomitans failed: Illegal seek Packing blimps Aactinomycetemcomitans failed: Illegal seek Packing rep Aactinomycetemcomitans failed: Illegal seek Packing rep Aeropyrum_pernix_K1 failed: Illegal seek Packing rep Anabaena failed: Illegal seek Packing rep Aquifex_aeolicus_VF5 failed: Illegal seek Packing rep Archaeoglobus_fulgidus failed: Illegal seek Packing rep Athaliana_I failed: Illegal seek May I upload you some tables? ;-) Go ahead. For future refrence, if you can type How-to-repeat with good instructions after that, write directly to [EMAIL PROTECTED] Look in pub/mysql/secret for myisampack_failing.tgz . It contains I hope representative sample of our failing tables, i.e. not all of them, but all table-types are included. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs MIPS / Institute for Bioinformatics http://mips.gsf.de GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: myisampack dumps core on some tables
On Thu, 30 Aug 2001, Michael Widenius wrote:
Hi,
yes this patch *fixes* all of my problems, except one table which is/was
probably too big? I haven't found any options that would make myisamchk to
ask for less memory.
/usr/local/mysql/bin/myisamchk: Out of memory (Needed 4294922813 bytes)
/usr/local/mysql/bin/myisamchk: error: 12 when opening MyISAM-table
'/data/mysql/Celegans/rep.MYI'
/usr/local/mysql/bin/myisamchk: Out of memory (Needed 4294922813 bytes)
/usr/local/mysql/bin/myisamchk: error: 12 when opening MyISAM-table
'/data/mysql/Celegans/rep.MYI'
-rwxrwx---1 mysqlmysql21108759 Aug 28 20:31 /data/mysql/Celegans/rep.MYD
-rwxrwx---1 mysqlmysql1024 Aug 29 21:55 /data/mysql/Celegans/rep.MYI
-rwxrwx---1 mysqlmysql9247 Aug 28 20:30 /data/mysql/Celegans/rep.frm
Well, the other rep tables are fine. I'm a bit angry about myself,
because I dropped the Celegans.rep tables:!!!
mysql drop table rep;
Query OK, 0 rows affected (0.05 sec)
and dumped them again via network from master site, so I got:
-rw-rw1 mysqlmysql44130688 Aug 30 21:39 /data/mysql/Celegans/rep.MYD
-rw-rw1 mysqlmysql 2411520 Aug 30 21:39 /data/mysql/Celegans/rep.MYI
-rw-rw1 mysqlmysql9247 Aug 30 21:38 /data/mysql/Celegans/rep.frm
I managed successfully to run myisamchk -rq on it, myisampack and again
myisamchk -rq. So now I can only tell you that broken datafile can cause
myisamchk to ask for too much memory. :(
This is on master site:
-rw-rw1 pedant users44130688 Jul 11 13:41 /home/mysql/Celegans/rep.MYD
-rw-rw1 pedant users 1645568 Jul 11 13:41 /home/mysql/Celegans/rep.MYI
-rw-rw1 pedant users9247 Jul 11 13:40 /home/mysql/Celegans/rep.frm
mysql select count(id) from rep;
+---+
| count(id) |
+---+
| 19223 |
+---+
1 row in set (0.02 sec)
mysql
and this is on backup site after compression and rebuilding index:
-rw-rw1 mysqlmysql21108573 Aug 30 21:41 /data/mysql/Celegans/rep.MYD
-rw-rw1 mysqlmysql 1644544 Aug 30 21:41 /data/mysql/Celegans/rep.MYI
-rw-rw1 mysqlmysql9247 Aug 30 21:38 /data/mysql/Celegans/rep.frm
and also 19223 lines.
So unfortunately, I don't have the broken table anymore, only the
screen dumps (size od .MYD and .MYI differed). It seems the
broken datafile had 6 bytes more, broken index was much smaller.
That's all I can tell you. ;)
Maybe it helps.
Hi!
Sasha == Sasha Pachev [EMAIL PROTECTED] writes:
Sasha On Wednesday 29 August 2001 15:14, Martin MOKREJ? wrote:
Description:
I have on Linux running 3.23.41 the following problem:
$ /usr/local/mysql/bin/myisampack -v -v -f --tmpdir=/tmp
Sasha /data/mysql/Aactinomycetemcomitans/blimps.MYI
Compressing /data/mysql/Aactinomycetemcomitans/blimps.MYD: (1443 records)
- Calculating statistics
normal: 7 empty-space: 0 empty-zero: 0 empty-fill: 7
pre-space: 0 end-space: 3 intervall-fields: 0 zero: 1
Original trees: 16 After join: 9
- Compressing file
Segmentation fault (core dumped)
cut
Thanks Martin for the test case; It enabled me to quickly find the
bug.
Here is a patch for this (This will be in 3.23.42)
= myisam/myisampack.c 1.9 vs edited =
*** /tmp/myisampack.c-1.9-8558Wed Aug 22 01:45:03 2001
--- edited/myisam/myisampack.cThu Aug 30 14:09:40 2001
***
*** 251,257
static void print_version(void)
{
! printf(%s Ver 1.9 for %s on %s\n,my_progname,SYSTEM_TYPE,MACHINE_TYPE);
}
static void usage(void)
--- 251,257
static void print_version(void)
{
! printf(%s Ver 1.10 for %s on %s\n,my_progname,SYSTEM_TYPE,MACHINE_TYPE);
}
static void usage(void)
***
*** 1670,1676
max_calc_length+=huff_counts[i].tree-height;
else if (huff_counts[i].field_type == FIELD_BLOB ||
huff_counts[i].field_type == FIELD_VARCHAR)
! max_calc_length=huff_counts[i].tree-height*huff_counts[i].max_length +
huff_counts[i].length_bits +1;
else
max_calc_length+=
(huff_counts[i].field_length - huff_counts[i].max_zero_fill)*
--- 1670,1676
max_calc_length+=huff_counts[i].tree-height;
else if (huff_counts[i].field_type == FIELD_BLOB ||
huff_counts[i].field_type == FIELD_VARCHAR)
! max_calc_length+=huff_counts[i].tree-height*huff_counts[i].max_length +
huff_counts[i].length_bits +1;
else
max_calc_length+=
(huff_counts[i].field_length - huff_counts[i].max_zero_fill)*
Regards,
Monty
--
Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs
MIPS / Institute for Bioinformatics http://mips.gsf.de
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany
myisampack dumps core on some tables
Description: I have on Linux running 3.23.41 the following problem: $ /usr/local/mysql/bin/myisampack -v -v -f --tmpdir=/tmp /data/mysql/Aactinomycetemcomitans/blimps.MYI Compressing /data/mysql/Aactinomycetemcomitans/blimps.MYD: (1443 records) - Calculating statistics normal: 7 empty-space: 0 empty-zero: 0 empty-fill: 7 pre-space: 0 end-space: 3 intervall-fields: 0 zero: 1 Original trees: 16 After join: 9 - Compressing file Segmentation fault (core dumped) $ gdb /usr/local/mysql/bin/myisampack ./core [...] Core was generated by `/usr/local/mysql/bin/myisampack -v -v -f --tmpdir=/tmp /data/mysql/Aactinomycet'. Program terminated with signal 11, Segmentation fault. #0 0x400f00d5 in ?? () (gdb) where #0 0x400f00d5 in ?? () #1 0x8050557 in compress_isam_file () #2 0x804e18c in compress () #3 0x804d4b4 in main () #4 0x400b3a42 in ?? () (gdb) quit $ The calling perl script reports as an error value in $! Illegal seek. It happens to me with 3 table-types: Packing blast Aactinomycetemcomitans failed: Illegal seek Packing blimps Aactinomycetemcomitans failed: Illegal seek Packing rep Aactinomycetemcomitans failed: Illegal seek Packing rep Aeropyrum_pernix_K1 failed: Illegal seek Packing rep Anabaena failed: Illegal seek Packing rep Aquifex_aeolicus_VF5 failed: Illegal seek Packing rep Archaeoglobus_fulgidus failed: Illegal seek Packing rep Athaliana_I failed: Illegal seek May I upload you some tables? ;-) How-To-Repeat: See above. Fix: Submitter-Id: submitter ID Originator: Organization: organization of PR author (multiple lines) MySQL support: [none | licence | email support | extended email support ] Synopsis: synopsis of the problem (one line) Severity: [ non-critical | serious | critical ] (one line) Priority: [ low | medium | high ] (one line) Category: mysql Class: [ sw-bug | doc-bug | change-request | support ] (one line) Release: mysql-3.23.41 (Source distribution) Environment: machine, os, target, libraries (multiple lines) System: Linux pednew 2.4.9 #1 SMP Tue Aug 28 09:58:52 CEST 2001 i686 unknown Architecture: i686 Some paths: /usr/local/bin/perl /usr/bin/make /usr/bin/gcc /usr/bin/cc GCC: Reading specs from /usr/lib/gcc-lib/i386-linux/2.95.2/specs gcc version 2.95.2 2220 (Debian GNU/Linux) Compilation info: CC='gcc' CFLAGS='-O3 -mpentiumpro -felide-constructors -fno-exceptions -fno-rtti' CXX='gcc' CXXFLAGS='-O3 -mpentiumpro -felide-constructors -fno-exceptions -fno-rtti' LDFLAGS='' LIBC: lrwxrwxrwx1 root root 14 Aug 24 19:20 /lib/libc.so.5 - libc.so.5.4.46 -rw-r--r--1 root root 586720 Feb 9 1999 /lib/libc.so.5.4.46 lrwxrwxrwx1 root root 13 Jul 24 15:43 /lib/libc.so.6 - libc-2.1.3.so -rwxr-xr-x1 root root 887712 Jul 24 15:43 /lib/libc-2.1.3.so -rw-r--r--1 root root 2089576 Mar 26 00:36 /usr/lib/libc.a -rw-r--r--1 root root 178 Mar 26 00:36 /usr/lib/libc.so Configure command: ./configure --prefix=/usr/local/mysql --enable-assembler --with-mysqld-ldflags=-all-static -with-libwrap -with-named-z-lib --with-charset=latin1 --enable-thread-safe-client --with-named-curses-libs=/usr/lib/libncurses.a --with-pthread Perl: This is perl, version 5.005_03 built for i386-linux - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: repairing MyISAM table kills mysqld with SIG11
On Mon, 27 Aug 2001, Sinisa Milivojevic wrote: Hi! Try to repair the same table with 3.23.41. If it fails, please let us know, so that we can give you upload instructions. kulan$ ls -la /home/mysql/Mbovis/cogs_data* -rw-rw1 pedant users54195408 Jul 4 03:52 /home/mysql/Mbovis/cogs_data.MYD -rw-rw1 pedant users 72704 Aug 27 18:44 /home/mysql/Mbovis/cogs_data.MYI -rw-rw1 pedant users8714 Jul 4 03:52 /home/mysql/Mbovis/cogs_data.frm 3.23.41 also fails: mysql use Mbovis; Database changed mysql check table cogs_data; +--+---+--+-+ | Table| Op| Msg_type | Msg_text | | +--+---+--+-+ | Mbovis.cogs_data | check | warning | Table is marked as crashed and last repair |failed | | Mbovis.cogs_data | check | warning | Size of indexfile is: 72704 Should be: |25600 | | Mbovis.cogs_data | check | warning | Size of datafile is: 54195408 Should be: |54195388 | | Mbovis.cogs_data | check | error| Found 3277 keys of 257 | | | Mbovis.cogs_data | check | error| Corrupt | | +--+---+--+-+ 5 rows in set (0.05 sec) mysql repair table cogs_data; ERROR 2013: Lost connection to MySQL server during query mysql quit 0x8079ab8 handle_segfault__Fi + 380 0x8128eba pthread_sighandler + 150 0x814f0b6 chunk_free + 222 0x8151203 free + 155 0x8111cdc my_no_flags_free + 16 0x8106684 mi_repair + 2220 0x80c28e8 repair__9ha_myisamP3THDR17st_mi_check_paramb + 624 0x80c25ee repair__9ha_myisamP3THDP15st_ha_check_opt + 286 0x80c9430 mysql_admin_table__FP3THDP13st_table_listP15st_ha_check_optPCc13thr_lock_typebT5UiPM7handlerFP7handlerP3THDP15st_ha_check_opt_i + 1432 0x80cc173 mysql_repair_table__FP3THDP13st_table_listP15st_ha_check_opt + 67 0x8080fb1 mysql_execute_command__Fv + 4117 0x8083fa2 mysql_parse__FP3THDPcUi + 210 0x807f6bd do_command__FP3THD + 1269 0x807ebbb handle_one_connection__FPv + 551 Binaries produced on the problematic machine (Redhat 6.2), 2.2.19: CFLAGS=-O3 -mpentiumpro -felide-constructors -fno-exceptions -fno-rtti CXX=gcc CXXFLAGS=-O3 -mpentiumpro -feli de-constructors -fno-exceptions -fno-rtti ./configure --prefix=/usr/local/mysql --enable-assembler --with-mysqld -ldflags=-all-static -with-libwrap -with-named-z-lib --with-charset=latin1 --enable-thread-safe-client --with-nam ed-curses-libs=/usr/local/lib/libncurses.a --with-pthread If I should try also your binary distribution, please let me know. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs [EMAIL PROTECTED] Faculty of Science, The Charles University - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: repairing MyISAM table kills mysqld with SIG11 (fwd)
Hi, sorry I did not send the last e-mail to the whole list, so here it is. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs [EMAIL PROTECTED] Faculty of Science, The Charles University -- Forwarded message -- Date: Mon, 27 Aug 2001 17:39:07 +0200 (MET DST) From: Martin MOKREJ [EMAIL PROTECTED] To: Sinisa Milivojevic [EMAIL PROTECTED] Subject: Re: repairing MyISAM table kills mysqld with SIG11 On Mon, 27 Aug 2001, Sinisa Milivojevic wrote: Please try out our binary distro. I guess that you would not like either that we spend our time on fixing something that should not be fixed. OK, so this is from mysql-3.23.41-pc-linux-gnu-i686/bin/mysqld.sym.gz et al.: mysql check table cogs_data; +--+---+--+-+ | Table| Op| Msg_type | Msg_text | | +--+---+--+-+ | Mbovis.cogs_data | check | warning | Table is marked as crashed and last repair |failed | | Mbovis.cogs_data | check | warning | Size of indexfile is: 72704 Should be: |25600 | | Mbovis.cogs_data | check | warning | Size of datafile is: 54195408 Should be: |54195388 | | Mbovis.cogs_data | check | error| Found 3277 keys of 257 | | | Mbovis.cogs_data | check | error| Corrupt | | +--+---+--+-+ 5 rows in set (0.55 sec) mysql repair table cogs_data; ERROR 2013: Lost connection to MySQL server during query mysql quit 0x807b1b8 handle_segfault__Fi + 380 0x812af8a pthread_sighandler + 154 0x81517df free + 39 0x8114a6c my_no_flags_free + 16 0x8109304 mi_repair + 2236 0x80c4768 repair__9ha_myisamP3THDR17st_mi_check_paramb + 624 0x80c446e repair__9ha_myisamP3THDP15st_ha_check_opt + 286 0x80cb320 mysql_admin_table__FP3THDP13st_table_listP15st_ha_check_optPCc13thr_lock_typebT5UiPM7handlerFP7handlerP3THDP15st_ha_check_opt_i + 1432 0x80ce076 mysql_repair_table__FP3THDP13st_table_listP15st_ha_check_opt + 70 0x8082641 mysql_execute_command__Fv + 4133 0x80856a6 mysql_parse__FP3THDPcUi + 210 0x8080d2d do_command__FP3THD + 1261 0x808022c handle_one_connection__FPv + 548 If that repair crashes our latest binary, make a tar.gz out of your table and upload it to: ftp://support.mysql.com/pub/mysql/secret kulan$ ftp support.mysql.com Connected to support.mysql.com. 220 www.mysql.com FTP server ready. Name (support.mysql.com:pedant): ftp 331 Guest login ok, send your complete e-mail address as password. Password: 530 Can't set guest privileges. Login failed. ftp user anonymous 331 Guest login ok, send your complete e-mail address as password. Password: 530 Can't set guest privileges. Login failed. ftp And send me a direct mail with a name of your tarball. http://pednew.gsf.de/cogs_data.tgz Please let me know that I can remove the file. ;) Thanks! -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs [EMAIL PROTECTED] Faculty of Science, The Charles University - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: repairing MyISAM table kills mysqld with SIG11 (fwd)
On Mon, 27 Aug 2001, Martin MOKREJ wrote: ftp://support.mysql.com/pub/mysql/secret Hmm, I can already login as ftp, but can only chdir to /pub/mysql, there's no secret directory. ;( http://pednew.gsf.de/cogs_data.tgz Hmm, try out http://kulan.gsf.de/cogs_data.tgz , but I'm sure the previous worked for me. ;-) Do you have it? -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs [EMAIL PROTECTED] Faculty of Science, The Charles University - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: repairing MyISAM table kills mysqld with SIG11 (fwd)
Sorry about that - we have now fixed the problems with our anonymous FTP upload, and it should be working. lokk in pub/mysql/secret/ for: 15593452(size) cogs_data.tgz But same file should be accessible already via the 2 web links I've sent to you via personal e-mail. Thanks. -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs [EMAIL PROTECTED] Faculty of Science, The Charles University - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Got a packet bigger than 'max_allowed_packet'
Hi, I have a problem with one machine running Debian kernels 2.4.7 (2.4.9) on Intel EtherExperssPro100 and mysql-3.23.39. When I try to upload data into database, I get the error in %Subj%. The command used is: bioadmin@caribou$ cat apernix.contig.sql | mysql --host=pednew ApernixK1 ERROR 2006 at line 30: MySQL server has gone away bioadmin@caribou$ ls -la apernix.contig.sql -rw-r--r-- 1 bioadmin users1670573 Aug 21 13:13 apernix.contig.sql bioadmin@caribou$ From the size of file imported it's clean, that we shouldn't exceed 16MB limit of mysql. (Yes, I have set max_allowed_packet=16M in my.conf). As far as I understand we can't set max_allowed_packet to higher value. Anyway, in this case the file has 1.6MB, so it should fit into 16MB. When I upgraded on this EtherExperssPro100 machine mysql to 3.23.41, the mysql client gives me again back the 200^ error, BUT in mysqld-logfile is not anymore the error message pointing to max_allowed_packet! Even worse, no new lines appended relating to this test case. --- In real, we have another machine running Redhat with 2.2.19 kernel, same mysql version, same config file and 3Com905B. And, the shell command above successfully imports the 1.6MB file into database. From reading Changelog at mysql.com I see that to avoid some network problems net_buffer_length is being kept small. Does it mean that broken packets do enter mysql? I thought they get assembled at the TCP/IP layer. Although, I read that net_buffer_length should be smaller than max_allowed_packet, i.e. under 16MB, right? On the machine with 3Com card I have successfully tested even max_allowed_packet=96M with no problems. Although I'm trying to believe it could be a kernel-network problem, it might mysql. Does anyone have some suggestions? TIA -- Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs [EMAIL PROTECTED] Faculty of Science, The Charles University - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Cannot start 3.23.39 - system limits?
Description: While starting mysqld, mysqld stops with default values from support-files/my-medium.cnf. I'm not sure if it's really a bug or just inadequate buffer settings. Anyway, you asked in the $hostname.err to make a bug report. ;-) My compile time flags you have in my previous posts to bugs@ list under the thread make test fails' - to be onest, I removed two site-specific options like -I/software/@sys/usr/local/include and same for libs. How-To-Repeat: root# ulimit -a; /usr/local/mysql/bin/safe_mysqld --user=mysql core file size (blocks) unlimited data seg size (kbytes) 1048576 file size (blocks) unlimited max memory size (kbytes)152220 open files 200 pipe size (512 bytes) 20 stack size (kbytes) 65536 cpu time (seconds) unlimited max user processes 170 virtual memory (kbytes) 1048576 [2] 253026 root# Starting mysqld daemon with databases from /usr/local/mysql/var 010622 09:21:20 mysqld ended [2]- Done/usr/local/mysql/bin/safe_mysqld --user=mysql root# root# cat $hostname.err 010622 09:21:19 mysqld started mysqld got signal 11; This could be because you hit a bug. It is also possible that this binary or one of the libraries it was linked agaist is corrupt, improperly built, or misconfigured. This error can also be caused by malfunctioning hardware. We will try our best to scrape up some info that will hopefully help diagnose the problem, but since we have already crashed, something is definitely wrong and this may fail key_buffer_size=16773120 record_buffer=131072 sort_buffer=524280 max_used_connections=0 max_connections=100 threads_connected=0 It is possible that mysqld could use up to key_buffer_size + (record_buffer + sort_buffer)*max_connections = 80379 K bytes of memory Hope that's ok, if not, decrease some variables in the equation 010622 09:21:20 mysqld ended Fix: how to correct or work around the problem, if known (multiple lines) Submitter-Id: submitter ID Originator:Super-User Organization: organization of PR author (multiple lines) MySQL support: [none | licence | email support | extended email support ] Synopsis: mysqld doesn't start Severity: [ non-critical | serious | critical ] (one line) Priority: [ low | medium | high ] (one line) Category: mysql Class: sw-bug Release: mysql-3.23.39 (Source distribution) Environment: machine, os, target, libraries (multiple lines) System: IRIX nmrindy 6.5 01101244 IP22 Some paths: /usr/sbin/perl /software/@sys/usr/local/bin/make /software/@sys/usr/local/bin/gcc /usr/bin/cc GCC: Reading specs from /usr/local/lib/gcc-lib/mips-sgi-irix6.5/2.95.3/specs gcc version 2.95.3 20010315 (release) Compilation info: CC='cc' CFLAGS='-O3 -n32 -TARG:platform=IP22' CXX='CC' CXXFLAGS='-O3 -n32 -TARG:platform=IP22' LDFLAGS='' LIBC: -r-xr-xr-t 1 root sys 2362688 Mar 13 14:40 /lib/libc.so.1 lrwxr-xr-x 1 root sys19 Jan 1 2000 /usr/lib/libc.so - ../../lib/libc.so.1 lrwxr-xr-x 1 root sys19 Jan 1 2000 /usr/lib/libc.so.1 - ../../lib/libc.so.1 Configure command: ./configure --prefix=/usr/local/mysql --with-berkeley-db --with-innodb --with-charset=czech --with-extra-charsets=latin1 --with-libwrap --with-named-curses-libs=/software/@sys/usr/local/lib/libncurses.a Perl: This is perl, version 5.004_04 built for irix-n32 - Before posting, please check: http://www.mysql.com/manual.php (the manual) http://lists.mysql.com/ (the list archive) To request this thread, e-mail [EMAIL PROTECTED] To unsubscribe, e-mail [EMAIL PROTECTED] Trouble unsubscribing? Try: http://lists.mysql.com/php/unsubscribe.php
Re: Cannot start 3.23.39 - system limits?
Hi,
some more notes:
when using strace to trace the startup, I see some strange errors:
read(198, test -z \$defaults\\n then\n..., 1024) = 1024
xstat(2, /usr/local/mysql/var/data/mysql, 0xe0a31d0) = -1 ENOENT (No such file or
directory)
xstat(2, ./share/mysql/english/errmsg.sys, 0xe0a31d0) = -1 ENOENT (No such file or
directory)
xstat(2, ./bin/mysqld, 0xe0a31d0) = -1 ENOENT (No such file or directory)
xstat(2, ./var/mysql/db.frm, 0xe0a31d0) = -1 ENOENT (No such file or directory)
xstat(2, ./share/mysql/english/errmsg.sys, 0xe0a31d0) = -1 ENOENT (No such file or
directory)
xstat(2, ./libexec/mysqld, 0xe0a31d0) = -1 ENOENT (No such file or directory)
xstat(2, /usr/local/mysql/libexec/mysqld-max, 0xe0a31d0) = -1 ENOENT (No such file
or directory)
read(198, print_defaults=\./bin/my_print..., 1024) = 1024
xstat(2, ./bin/my_print_defaults, 0xe0a31d0) = -1 ENOENT (No such file or directory)
xstat(2, /usr/local/mysql/bin/my_print_defaults, {st_mode=01750311, st_size=0, ...})
= 0
I configured mysql with default-charrset=czech and additional-charset=latin1, so maybe
it's correct that
those files which are missing shouldn't be really there...:
xstat(2, /usr/local/mysql/share/mysql/charsets/big5.conf, 0x7fff28b0) = -1 ENOENT
(No such file or directory)
xstat(2, /usr/local/mysql/share/mysql/charsets/ujis.conf, 0x7fff28b0) = -1 ENOENT
(No such file or directory)
xstat(2, /usr/local/mysql/share/mysql/charsets/sjis.conf, 0x7fff28b0) = -1 ENOENT
(No such file or directory)
xstat(2, /usr/local/mysql/share/mysql/charsets/tis620.conf, 0x7fff28b0) = -1 ENOENT
(No such file or directory)
xstat(2, /usr/local/mysql/share/mysql/charsets/euc_kr.conf, 0x7fff28b0) = -1 ENOENT
(No such file or directory)
xstat(2, /usr/local/mysql/share/mysql/charsets/gb2312.conf, 0x7fff28b0) = -1 ENOENT
(No such file or directory)
xstat(2, /usr/local/mysql/share/mysql/charsets/gbk.conf, 0x7fff28b0) = -1 ENOENT (No
such file or directory)
SIGSEGV:
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] getmountid(0x7fff1911, 0x7fff1cf8) = 0
[pid 253453] lxstat(2, ../../../../../software, {st_mode=0200, st_size=0, ...}) = 0
[pid 253453] close(5) = 0
[pid 253453] open(../../../../../.., O_RDONLY|O_NONBLOCK) = 5
[pid 253453] fcntl(5, F_SETFD, FD_CLOEXEC) = 0
[pid 253453] fxstat(2, 5, {st_mode=0200, st_size=0, ...}) = 0
[pid 253453] fxstat(2, 5, {st_mode=0200, st_size=0, ...}) = 0
[pid 253453] close(5) = 0
[pid 253453] readlink(/software/usr/local/mysql/var/master.info, 0x7fff1de0, 1025) =
-1 ENOENT (No such file or directory)
[pid 253453] xstat(2, ./master.info, 0x7fff2c28) = -1 ENOENT (No such file or
directory)
[pid 253453] open(./, O_RDONLY|O_NONBLOCK) = 5
[pid 253453] fcntl(5, F_SETFD, FD_CLOEXEC) = 0
[pid 253453] fxstat(2, 5, {st_mode=S_IFSOCK|S_ISUID|020400507, st_size=0, ...}) = 0
[pid 253453] ngetdents(0x5, 0x104607f0, 0x4000, 0x7fff1c70) = 648
[pid 253453] close(5) = 0
[pid 253453] xstat(2, ./nmrindy-bin.013, 0x7fff2340) = -1 ENOENT (No such file or
directory)
[pid 253453] open(./nmrindy-bin.013, O_WRONLY|O_APPEND|O_CREAT, 0660) = 5
[pid 253453] lseek(5, 0, SEEK_CUR) = 0
[pid 253453] open(./nmrindy-bin.index, O_RDWR|O_APPEND|O_CREAT, 0660) = 6
[pid 253453] time() = 993203999
[pid 253453] lseek(5, 0, SEEK_SET) = 0
[pid 253453] write(5, \376bin\37\0273;\1\1\0\0\0E\0\0\0..., 73) = 73
[pid 253453] write(6, ./nmrindy-bin.013, 17) = 17
[pid 253453] write(6, \n, 1) = 1
[pid 253453] --- SIGSEGV (Segmentation fault) ---
[pid 253453] write(2, mysqld got signal , 18) = 18
[pid 253453] write(2, 11;\nThis, 8) = 8
[pid 253453] write(2, could be because you hit a bug, 221) = 221
--
Martin Mokrejs - PGP5.0i key is at http://www.natur.cuni.cz/~mmokrejs
[EMAIL PROTECTED] Faculty of Science, The Charles University
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