Author: Derrick

I am software engineer working in a start-up biotech company in Madison, Wisconsin, USA.

[PHP]Fatal error: Allowed memory size of x bytes exhausted (tried to allocate y bytes)

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A user complained to me that my PHP web applications stopped working today. After I digged into the error log, I found that following message:

PHP Fatal error:  Allowed memory size of 262144 bytes exhausted (tried to allocate 261900 bytes) in Unknown on line 0

Obviously, this is related to the memory error. Therefore I tried to increase the limit of memory_limit in php.ini. Since I have 8G of memory in my box, I think it is okay to set the memory limit of PHP to 4GB.

;memory_limit = 128M
memory_limit = 4096M

When I restart the Apache/PHP, I found another nightmare. My web application stopped working! When the user tries to access http://mywebsite/index.php, instead of rendering the code, the browser kept prompting the user to download the file.

After scratching my head for a while, I found that I missed something, which is very very important. I was running XAMPP (32-bit) on a Fedora 64-bit machine. See the problem? Since XAMPP is running in 32-bit, it does not understand what is 4096 MB. (If you install 4GB of memory in any Windows 32-bit machine, you will notice that Windows can only allocate 3GB of them, and the 1GB left memory is sitting inside your computer and doing nothing…) Therefore, I decrease the memory_limit to 2048MB, and that solved the problem.

Time to move away from XAMPP.

–Derrick

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[Solved]Problem to Update OpenLDAP in FreeBSD

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Recently, I found the following error message when updating my FreeBSD system regarding to the OpenLDAP:

===>  Installing for openldap-client-2.4.31
===>   Generating temporary packing list
===>  Checking if net/openldap24-client already installed
===> Creating users and/or groups.
Using existing group `ldap'.
Creating user `ldap' with uid `389'.
pw: user 'ldap' already exists
*** Error code 74

Stop in /usr/ports/net/openldap24-client.
*** Error code 1

Stop in /usr/ports/net/openldap24-client.

And I don’t use LDAP in particular, however it affects other applications that use LDAP, e.g., PHP

php -v
PHP Warning:  PHP Startup: Unable to load dynamic library '/usr/local/lib/php/20090626/ldap.so' - Shared object "libldap-2.4.so.8" not found, required by "ldap.so" in Unknown on line 0
PHP 5.3.10 with Suhosin-Patch (cli) (built: Feb 14 2012 16:59:15)
Copyright (c) 1997-2012 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2012 Zend Technologies
    with eAccelerator v0.9.6.1, Copyright (c) 2004-2010 eAccelerator, by eAccelerator

It is very simple to solve this problem. All you need is to remove the user ‘ldap’, and install the port again. First, let’s remove the user ‘ldap’ first:

sudo vipw

You will see this line:

ldap:*:389:389::0:0:OpenLDAP Server:/nonexistent:/usr/sbin/nologin

Remove the line by pressing ‘dd’, hit ‘ESC’ button, and then press ‘:wq’ to save the file and quit the editor.

After that, let’s clean the port and run the update again:

cd /usr/ports/net/openldap24-client
sudo make clean
sudo make install clean

That’s it. Your LDAP will be happy and your applications (such as PHP) will not complain.

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–Derrick

[FreeBSD] Samba does not start after updating to 3.5.14

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After I updated my Samba to 3.5.14 on my FreeBSD box today, it stopped working. I couldn’t connect to the Samba server from my Windows clients. Initially, I thought it was the memory cache issues, and I thought the problem would be solved by rebooting both machines. Unfortunately, it didn’t work. Therefore, I accessed to the server and check the cause of the problem.

First, I found that Samba was not evening running.

ps -ax | grep smb

So I started the Samba service manually:

sudo /usr/local/etc/rc.d/samba start

And it returned me the following message:

Cannot 'start' samba. Set winbindd_enable to YES in /etc/rc.conf or use 'onestart' instead of 'start'.

Oh that was easy. All I need to do was to modify my rc.conf:

#Samba service
samba_enable="YES"
winbindd_enable="YES"

And then I started the Samba again:

sudo /usr/local/etc/rc.d/samba start

Yay, Samba is up and running again!

–Derrick

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How to Install a 2.5TB, 3TB drives on Linux

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Recently I got a new hard drive (3TB) for my Linux box at work. I didn’t realize that it is problematic / nightmare to do such a simple work.

First, if you try to use fdisk to add the drive, it won’t work. Or I should say… it works, but it only give you a 2TB usable space. This is a limitation of fdisk, because it can handle up to 2^32 -1 sectors (or 2TB). That’s why fdisk is not a solution here.

It seems that the only solution is using parted.

sudo parted /dev/sdd

It will return something like this:

GNU Parted 2.3
Using /dev/sdd
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted)

First, we want to create a label:

(parted) mklabel gpt
Warning: The existing disk label on /dev/sdd will be destroyed and all data on this disk will be lost. Do you want to continue?
Yes/No? Yes

Then, we want to specify the unit:

(parted) unit TB

And tell parted to use all available space:

(parted) mkpart primary 0 -0

Next, we need to review the summary:

(parted) print
Model: ATA WDC WD30EZRX-00M (scsi)
Disk /dev/sdd: 3.00TB
Sector size (logical/physical): 512B/4096B
Partition Table: gpt

Number  Start   End     Size    File system  Name     Flags
 1      0.00TB  3.00TB  3.00TB  ext2         primary

As you can see, the size is 3TB. Don’t worry about the file system for now (ext2). If it looks good to you, now we need to leave parted.

(parted) quit
Information: You may need to update /etc/fstab.

Next, we need to format the partition:

#CentOS 6
sudo mkfs.ext4 /dev/sdd1

#CentOS 7
sudo mkfs.xfs /dev/sdd1

After few seconds, it will give you some more information about your drive:

mke2fs 1.41.14 (22-Dec-2010)
Filesystem label=
OS type: Linux
Block size=4096 (log=2)
Fragment size=4096 (log=2)
Stride=1 blocks, Stripe width=1 blocks
183148544 inodes, 732566272 blocks
36628313 blocks (5.00%) reserved for the super user
First data block=0
Maximum filesystem blocks=4294967296
22357 block groups
32768 blocks per group, 32768 fragments per group
8192 inodes per group
Superblock backups stored on blocks:
        32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208,
        4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968,
        102400000, 214990848, 512000000, 550731776, 644972544

Writing inode tables: done
Creating journal (32768 blocks): done
Writing superblocks and filesystem accounting information: done

This filesystem will be automatically checked every 35 mounts or
180 days, whichever comes first.  Use tune2fs -c or -i to override.

Now you can use your drive, such as mounting or putting it into /etc/fstab

sudo mount /dev/sdd1 /mnt/
df
/dev/sdd1             2.8T   42G  2.6T   2% /mnt

That’s it! Enjoy your new disk.

–Derrick

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Add-ons for New Version of Firefox 21

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Every time Firefox releases a major upgrade, we love it because it comes with lots of cool features. At the mean time, we hate it because lots of our favorite add-ons are not working with the new Firefox. Sometimes, the owners of the add-ons might be too busy, and it might take a while to release a compatible version. That’s why I put some of my favorite add-ons here. They are 100% compatible with the new Firefox, and I only modified the source codes that by-pass the version compatibly check.

In the other words, the add-on will work the way it was in the old version, and you will receive an upgrade if the owner releases a newer version.

So far I have made the following add-ons available in the latest version of Firefox:

Add-On Download Comment Author’s URL
BandWidthTester 0.5.9 Download Not tested N.A
BlockSite 0.7.1.1 Download Tested Add-on Homepage
Bookmark Duplicate Detector 0.7.5 Download Not tested Add-on Homepage
CopyPlainText 0.3.4 Download Not tested N.A.
del.icio.us 1.2.1 Download Not tested N.A.
FireSheep 0.1.1 Download
Linux (Compiled from Git)		 Not tested Add-on Homepage
Google Calendar Tab 3.8 Download Tested N.A.
Multiproxy Switch 1.33 Download Tested Add-on Homepage
PermaTabs Mod 1.93 Download Not Tested Add-on Homepage
Snap Links Plus 1.08 Download Tested N.A.

If you need any add-on, please post in the comment below. I will try to make it available here.

Enjoy your new Firefox!

–Derrick

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ZFS: Compression VS Deduplication (Dedup) in Simple English

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Last Edited: Jan 17, 2021

Many people are confused between the ZFS compression and ZFS deduplication because they are so similar. Both of them are designed to reduce the size of the data being stored in the storage. Let me explain the difference between them in simple English.

1. This is how your data looks like originally (Assuming only one unique file):

2. This is how your data look like after being stored in a ZFS pool with compression enabled.

3. This is how your data look like after being stored in a ZFS pool with deduplication enabled.

4. Let say we are storing three identical files, i.e.,

5. ZFS: Compression Only

6. ZFS: Deduplication Only

7. ZFS: Compression + Deduplication

The biggest difference between deduplication and compression is the scope. File compression works at the file level. For example, if you have three identical files, ZFS will store the compressed files three times. Deduplication works at the block level. A block is simply the basic unit of the ZFS storage (e.g., 512 bytes, 4k etc). Imagine ZFS needs to store a big file. What it will do is to divide the file into multiple chunks. Each chunk will be stored in a block. What deduplication does is to remember the content of each block (checksum), and avoid storing the same content again. In other words, deduplication works at a narrower level (think of it as a molecule).

One of the reasons why the drug are usually tested on mice because some of mouse genes are 99% identical to human genes. Imagine we need to store the mouse genes into the database. All we need is to store the gene of mouse once. Later on if we need to store the human genes into the database, we can reference the mouse one rather than storing the same copy again.

Of course, enabling both compression and deduplication will save lots of free space. However, it comes with a very high price tag. If you like to enable deduplication, you need to make sure that you have at least 2GB of memory per 1TB of storage. For example, if your ZFS pool is 10TB, you need to have 20GB of memory installed in your system. Otherwise, you will experience a huge performance hit.

Hope this article helps you to understand the difference between compression and deduplication.

–Derrick

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Top Reason Why You Should NOT Use Microsoft Exchange in Your Business

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Today, I sent a message to a company through their contact page on their website. It is a standard contact page, i.e., you need to fill in your contact information and the details of your request, and they will follow up with you later. An hour later, I received a reply from them, saying that they would like more information from me. Therefore, I reply to their email. Few seconds later, I got the following:

Delivery has failed to these recipients or distribution lists:

[email protected]
Your message wasn't delivered because of security policies. Microsoft Exchange will not try to redeliver this message for you. Please provide the following diagnostic text to your system administrator.
Sent by Microsoft Exchange Server 2007


Diagnostic information for administrators:

....

(Another 100 lines of error messages)

Initially, I thought I made a mistake when typing the email address. Therefore, I redid it and verified every single letter in the email address. Unfortunately, I got the same message again. After trying it for 5 times, I gave up, and this company loses a sale.

There are few things we’ve learned here. First, never display very technical error messages to the customers. They are very boring for non-engineers. Second, don’t assume that every customer is patient. Not every one is willing to re-send the same email for 5 times. Third, it takes many years to build a city but it only takes few hours to destroy it. With today’s technology, it is too easy to spread out the bad words.

I think this is not a right way to run a custom request management system (or ticket system). It should never yell to the customer. Instead, it should let the stuffs to evaluate the customer’s reply rather than letting the Microsoft Exchange Server to do it.

I don’t recommend using Microsoft Exchange for your business. It just hurts your business.

–Derrick

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[Solved]Failed to enable the ‘dataready’ Accept Filter

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After I updated the Apache to 2.2.22 for my FreeBSD box today, I got a problem:

#apachectl stop
#apachectl start

[warn] (2)No such file or directory: Failed to enable the 'dataready' Accept Filter

If you search for Failed to enable the ‘dataready’ Accept Filter on Google, you probably will find a lot of posts about this solution, like the following:

#kldload accf_http

Or include the following in the boot loader (/boot/loader.conf):

accf_http_load="YES"

However, even you already done these two things, this problem still exists. 

#kldload accf_http
kldload: can't load accf_http: File exists

Why? That’s because the problem is not coming from accf_http. Instead, the problem is the missing dataready filter, which is accf_data. To solve this problem, simply do the following. First, update the /boot/loader.conf and add the following into the file: 

accf_data_load="YES"

Of course, any changes to the boot loader requires a reboot. If you don’t want to reboot the machine, simple load the module manually and restart the Apache, i.e.,

#kldload accf_data
#apachectl stop
#apachectl start

That’s it! Apache will stop complaining the dataready filter and will work happily.

–Derrick

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[PHP]imagecreatefrompng Error (After upgrading FreeBSD)

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Today, I found that one of my PHP scripts stop working. After some investigations, I found that it was the function, imagecreatefrompng, which caused the problem.

Interestingly, other similar functions such as imagecreatefromgif and imagecreatefromjpeg were completely working fine. The program stopped working when calling imagecreatefrompng only.

Initially, I thought the problem was coming from the PHP side. Therefore, I tried to get the error messages as many as possible, such as PHP error (error_reporting), Apache error (error_log), and even system error (dmesg). Unfortunately, I couldn’t find anything.

The script was working completely fine until I upgraded the system. So I think the problem may come from a missing library. To give you some background, here is how imagecreatefrompng works. First, your program calls imagecreatefrompng, which involves the GD library. GD library calls a PNG function in your system (possibly libpng) to process the PNG file. Since the program comes with from the system library, PHP / Apache will not report anything about it.

Since it will be too complicated to identify which library caused the problem, I decide to reinstall all ports. It sounds a very long process but it wasn’t at all. It only took 20 minutes to finish the whole thing. So here is what I did:

#FreeBSD
#sudo portmaster -fa

After the installation is completed, I rebooted the machine and everything worked again!

Enjoy!

–Derrick

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Say NO to SOPA/PIPA

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Everyday, many people from US and other countries find their solutions here to solve their computer problem through the search engine. If the Stop Online Piracy Act (SOPA) and Protect Intellectual Property Act (PIPA) are passed, it simply allows US government to censor the web. Someday, IceSquare may be blocked from the major search engines. In the other words, you won’t be able to find any solutions of your computer problem here.

Please sign the petition at Google to oppose SOPA and PIPA. If you live in US, please click here to tell your congress not to censor the web. Please visit here if you like to learn more about SOPA and PIPA.

Thank you.

–Derrick

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