Archive for November, 2007

How to repaire MySQL corrupted table

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If you get an error message like this:

Table './labsupply/db_cache' is marked as crashed and should be repaired.
You can repair the table using the following steps:
1, Login to mysql

# mysql uroot -p

2, change database

mysql> use labsupply
Database changed

3, check table

mysql> check table db_cache;
+——————–+——-+———-+————————————————— ——-+
| Table | Op | Msg_type | Msg_text |
+——————–+——-+———-+————————————————— ——-+
| labsupply.db_cache | check | warning | Table is marked as crashed |
| labsupply.db_cache | check | warning | 3 clients are using or haven’t closed the table pr operly |
| labsupply.db_cache | check | status | OK |
+——————–+——-+———-+————————————————— ——-+
3 rows in set (0.03 sec)

4, repair table.

mysql> repair table db_cache;
+——————–+——–+———-+———-+
| Table | Op | Msg_type | Msg_text |
+——————–+——–+———-+———-+
| labsupply.db_cache | repair | status | OK |
+——————–+——–+———-+———-+
1 row in set (0.00 sec)


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Culture of hyperthermophilic archaebacterium Pyrococcus furiosus

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1, Method 1

Pyrococcus furiosus cells can be grown at 90 oC in a 100 l enamel-coated fermenter (Braun-Biotech) in a slightly modified medium used for cultivation of Thermococcales containing 1.0 g/l yeast extract (Difco), 5.0 g/l peptone (Difco), 5.0 g/l soluble starch (Merck), 18.4 g/l NaCl, 12.6 g/l MgCl 2 ·6H 2 O,0.16 g/l NaHCO 3, 3.24 g/l Na 2SO4 , 2.38 g/l CaCl 2 ·2H2O, 0.56 g/lKCl, 0.5 g/l L -cysteine and 0.0001% resazurine. Trace minerals (80 mg/l KBr, 57 mg/l SrCl2 ·6H 2 O, 22 mg/l H 3 BO 4, 10 mg/l Na 2 HPO 4 , 4 mg/l sodium metasilicate·5H 2 O, 2.4 mg/l NaF and 1.6 mg/l KNO 3 ) were added from a stock solution. The pH was adjusted to 6.0 with sulphuric acid. The fermenter was gassed with N 2 /CO 2 at a ratio of 80:20 (2 l/min) to remove hydrogen formed during growth of Pyrococcus . The agitation rate was 200 r.p.m. Cells were rapidly cooled before harvesting, collected by centrifugation and stored at -70 C.

2, Method 2

The following describes how the hyperthermophilic archaebacterium, P. furiosus, is routinely grown in a 500 liter fermentor for the purpose of obtaining cell mass in sufficient quantities for large scale protein purification. It is a modified version (Bryant et al., J. Biol. Chem., 264:5070-5079 (1989)) of the original protocol of Fiala et al., Arch. Microbiol., 145:56-61 (1986).

For culture maintenance, P. furiosus (DSM 3638) is routinely grown at 85°-88° C. as a closed static culture in 100 ml of the medium described in Table 2.

                  TABLE 2
    ______________________________________
    Maltose              5       g/l
    NH4 Cl          1.25    g/l
    Elemental Sulfur     5       g/l
    Na2 S           0.5     g/l
    Synthetic Sea Water1
    Vitamin mixture2
                         1       ml/l
    FeCl3           25      µM
    Na2 WO4    10      µM
    Yeast Extract        0.01%
    ______________________________________
     1 Synthetic Sea Water:
     NaCl, 13.8 g/l
     MgSO4, 3.5 g/l
     MgCl2, 2.7 g/l
     KCl, 0.3 g/l
     CaCl2, 0.75 g/l
     KH2 PO4, 0.5 g/l
     NaBr, 0.0-5 g/l
     KI, 0.05 g/l
     H3 BO3, 0.015 g/l
     Sodium citrate, 0.005 g/l
     2. Vitamin mixture (Balch et al., Microbiol. Rev., 43:260-296 (1979)):
     Biotin, 2 mg/l
     Folic acid, 2 mg/l
     Pyridoxine hydrochloride, 10 mg/l
     Thiamine hydrochloride, 5 mg/l
     Riboflavin, 5 mg/l
     Nicotinic acid, 5 mg/l
     DLCalcium pantothenate, 5 mg/l
     Vitamin B12, 0.1 mg/l
     pAminobenzoic acid, 5 mg/l
     Lipoic acid, 5 mg/l

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MySQL InnoDB database recovery from crash due to disk-full

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Cause of crash: Disk full.

when you try to start MySQL using this command:

/etc/rc.d/init.d/mysqld start

it failed to start.

So you check log file:

tail -100 /var/log/mysqld.log

and you see:

071120 18:36:06 mysqld started
InnoDB: The log sequence number in ibdata files does not match
InnoDB: the log sequence number in the ib_logfiles!
071120 18:36:06 InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files…
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer…
InnoDB: Last MySQL binlog file position 0 110344596, file name ./mysql-bin.000082
071120 18:36:06 InnoDB: Started; log sequence number 0 3039427084
/usr/libexec/mysqld: File ‘./mysql-bin.000082′ not found (Errcode: 2)
071120 18:36:06 [ERROR] Failed to open log (file ‘./mysql-bin.000082′, errno 2)
071120 18:36:06 [ERROR] Could not open log file
071120 18:36:06 [ERROR] Can’t init tc log
071120 18:36:06 [ERROR] Aborting

071120 18:36:06 InnoDB: Starting shutdown...
071120 18:36:09 InnoDB: Shutdown completed; log sequence number 0 3039427084
071120 18:36:09 [Note] /usr/libexec/mysqld: Shutdown complete

071120 18:36:09 mysqld ended

Easy fix: open mysql-bin.index, delete all content in the file and restart MySQL again.

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