[ale] Mysql troubles. Updates are very slow

[Jim Lynch]

Here's a strange one.  I'm running a database update:  The code looks like:

     try {
         $sth = $dbh->prepare("update  child set class_rank=:rank where 
child_id=:child");
         foreach($childRanks as $kidId=>$rank) {
             $sth->bindParam(':rank',$rank,PDO::PARAM_INT);
             $sth->bindParam(':child',$kidId,PDO::PARAM_INT);
             $sth->execute();
     //        prof_flag("update child set rank $kidId");
             file_put_contents("/tmp/kids","$kidId $rank\n",FILE_APPEND);

         }
There is an index on child_id.  It takes 19 seconds to execute on 506 
updates.

Number of ranks = 506 Start
    0.011958
Start at try
    0.044773
Get child data next
    0.025755
loop through familys
    0.005682
update child set rank
    19.035966
Done
That's output from a custom profiling app.  time php xxx.php gives 
similar results without the profiling.    It seems like a lot, so I've 
run it on another machine, a VPS in the cloud.

506 Start
    0.000419
Start at try
    0.050433
Get child data next
    0.048817
loop through familys
    0.003815
update child set rank
    0.116944
Done
This is a mysql database.  The slow one is on a 4 processor AMD machine 
with a single 1 TB Seagate SATA drive. (3 mb/s).  Nothing else is 
running except apache, chrome and mysql.  Memory usage is 3GB out of 
4GB.  Cpu usage is around 5% average on each of the 4 processors.  Very 
little swap is used.  CPU bogomips 6443.  Running on a ext4 FS.  
Smartctl says nothing is amiss.  No errors in logs.

The VPS shows a 2 processor  Intel running 6800 bogomips.  Can't tell 
anything about I/O.  Main memory is 512 MB with 100 MB used. Most of 
swap is also used.

Version on tower:
mysqld  Ver 5.5.44-0ubuntu0.14.04.1 for debian-linux-gnu on x86_64 
((Ubuntu))
version on VPS:
mysqld  Ver 5.5.46-0ubuntu0.14.04.2 for debian-linux-gnu on x86_64 
((Ubuntu))

No special configurations done to either mysql.  Running it as it was 
installed via apt-get.  No tuning.

I verified that both runs actually did update the table.  The indexes 
are identical.  I exported the tables on the tower and imported them 
into the VPS.  I verified they were the same.

Tower is running Mint 17.2 while the VPS is running Ubuntu 14.04.1.

I don't see anything other than updates that are running slow. Selects 
and inserts are OK.

Any ideas?

Thanks,
Jim.