Category: Everyday Computer Problem

install: /usr/ports/…/doc/: Inappropriate file type or format

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While I tried to upgrade both of my FreeBSD server (9 & 10) today, I got the following error:

install: /usr/ports/…/doc/: Inappropriate file type or format

Actually, here is the complete error message:

===>  Staging for memcached-1.4.17_1
===>   memcached-1.4.17_1 depends on shared library: libevent-2.0.so - found
===>   Generating temporary packing list
/usr/bin/make  install-recursive
Making install in doc
/usr/bin/make  install-am
test -z "/usr/local/man/man1" || /bin/mkdir -p "/usr/ports/databases/memcached/work/stage/usr/local/man/man1"
 install  -o root -g wheel -m 444 memcached.1 '/usr/ports/databases/memcached/work/stage/usr/local/man/man1'
test -z "/usr/local/bin" || /bin/mkdir -p "/usr/ports/databases/memcached/work/stage/usr/local/bin"
  install  -s -o root -g wheel -m 555 memcached '/usr/ports/databases/memcached/work/stage/usr/local/bin'
test -z "/usr/local/include/memcached" || /bin/mkdir -p "/usr/ports/databases/memcached/work/stage/usr/local/include/memcached"
 install  -o root -g wheel -m 444 protocol_binary.h '/usr/ports/databases/memcached/work/stage/usr/local/include/memcached'
install  -o root -g wheel -m 555 /usr/ports/databases/memcached/work/memcached-1.4.17/scripts/memcached-tool /usr/ports/databases/memcached/work/stage/usr/local/bin
install  -o root -g wheel -m 444 /usr/ports/databases/memcached/work/memcached-1.4.17/doc/ /usr/ports/databases/memcached/work/stage/usr/local/man/man1
install: /usr/ports/databases/memcached/work/memcached-1.4.17/doc/: Inappropriate file type or format
*** [post-install] Error code 71

Stop in /usr/ports/databases/memcached.
*** [install] Error code 1

Stop in /usr/ports/databases/memcached.

Initially, I thought the problem was caused by the syntax error of the code, therefore, I tried to do the following:

#Shut down the server
sudo /usr/local/etc/rc.d/memcached stop

#Remove Memcached from the system
sudo make deinstall

#Clean up the package
sudo make clean

#Compile the package
sudo make

#Install the package
sudo make install

Unfortunately, it still gave the same error message. I noticed that the error message has something to do with the documentation, so I decide to remove the documentation option in the installation page, i.e.,

#Enter the package setup
sudo make config

#Remove the "doc" option.

Unfortunately, it still gave the same response. I then tried to investigate the cause of the error. So I tried to copy the error command and re-ran it:

install  -o root -g wheel -m 444 /usr/ports/databases/memcached/work/memcached-1.4.17/doc/ /usr/ports/databases/memcached/work/stage/usr/local/man/man1

Which return the exact the same error message:

install: /usr/ports/databases/memcached/work/memcached-1.4.17/doc/: No such file or directory

So I came up an idea. Since I don’t really need the documentation, why not I disable the document option?

cd /usr/ports/databases/memcached

sudo nano Makefile

Change the following from:

post-install:
        ${INSTALL_SCRIPT} ${WRKSRC}/scripts/memcached-tool ${STAGEDIR}${PREFIX}/bin
        ${INSTALL_MAN} ${WRKSRC}/doc/${MAN1} ${STAGEDIR}${MAN1PREFIX}/man/man1
        @${MKDIR} ${STAGEDIR}${DOCSDIR}

To:

post-install:
        ${INSTALL_SCRIPT} ${WRKSRC}/scripts/memcached-tool ${STAGEDIR}${PREFIX}/bin
#        ${INSTALL_MAN} ${WRKSRC}/doc/${MAN1} ${STAGEDIR}${MAN1PREFIX}/man/man1
        @${MKDIR} ${STAGEDIR}${DOCSDIR}

That’s right, I just want to comment out the installation of the man/documentation part. Now, let’s try to reinstall the package again.

#sudo make install

Guess what, it works! Have fun!

–Derrick

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The easiest way to improve the performance of MySQL server on FreeBSD

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There are many different ways to improve the MySQL performance. In general, it breaks down into two different categories: Server side and client side.

On the server side, we can optimize the database and table structure, such as indexing the columns etc. On the client side, we can optimize the queue to minimize the workload, or we can cache and share the result such that the traffic to the server will be minimized. However, these methods are doable if you have access to the source code, or you understand the logic of the software. If you are a system administrator, you may not want to touch the source code, because you never know what will happen after the modifications. Plus your modification may be overwritten in the next update.

I am going to show you a quick and easy way to solve this problem. First, I am assuming that you build the MySQL from source. In the other words, this article will not work if you install the MySQL through pkg_add, yum, apt-get etc.

My solution is very simple: Compiling the MySQL server with static option enabled

By default, we will compile the software from source, it is not built in static. According to MySQL documentation, building the binary using static will result a 13% improvement comparing to building the binary using dynamic. Here is an example how to build MySQL with static option enabled:

cd /usr/ports/databases/mysql56-server
make BUILD_OPTIMIZED=yes BUILD_STATIC=yes
make install clean

This method will work for the first time. It may be a problem in the long run. For example, I use portsnap to update the port tree, and I use portmaster to upgrade the application. By default, portmaster will use the default options to rebuild the port. In the other words, the MySQL will not be built using static.

To solve this problem, I will need to make the build static option as a default settings. First of all, try to include the following in /etc/make.conf

sudo nano /etc/make.conf

WITH_CHARSET=utf8
WITH_COLLATION=utf8_general_ci
BUILD_OPTIMIZED=yes
BUILD_STATIC=yes

We can update the port tree and ports again. This will make the system to use the new settings.

sudo portsnap fetch update
sudo portmaster -Day

#Don't forget to restart the MySQL server.
sudo /usr/local/etc/rc.d/mysql-server start

Now your MySQL server and other applications are built using static.

Please click here to learn more about building static versus building dynamics.

–Derrick

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ZFS Compression: lz4 VS lzjb

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ZFS offers a new compression method in the latest version: lz4. It claims to be better than lzjb. Since lzjb is pretty good already, I am curious to find out how good will lz4 be comparing to lzjb. According to my tests, lz4 is performing better than lzjb in terms of spacing saving and I/O, but not too much.

lz4 VS lzjb: Space Saving

Long story short, here is what I did. I set up two servers with brand new ZFS settings. One server is set to lzjb, and the other server is set to lz4. Both servers have exact the same hardware, software, operating system etc. Both of them are loaded with the same set of data (10TB) via rsync and rsyncd. These data are real data that I use everyday, which includes office documents (PDF, Word, Excel), photos(Raw and JPEG), music(mp3), video(mpeg), zip, source codes, binary applications, database (MySQL, Redis), webserver files (PHP, HTML, CSS), etc. Notice that some of these files are already compressed (such as jpeg, zip etc), and the file types are not evenly distributed (e.g., 40% of the files are jpeg, 25% are docs, 10% are zip, 5% are something else). I want to make a test in a more realistic scenario.

Also, all ZFS settings are set BEFORE loading the data. This will ensure that all data on the same server share the same compression settings. Below is the summary of the used space. Keep in mind that the space saving test is independent to the hardware, such as CPU type, memory, speed of the disks, etc. Just like running the same command to compress the same set of files in two systems. We expect the result will have the same size. The only difference will be the time spent on compressing the data.

#ZFS with lzjb
df
Filesystem    512-blocks        Used     Avail Capacity  Mounted on
storage/data 23007987368 22996620466  11366902   100%    /storage/data

#Used space: 22996620466 blocks = 10965.6 GB

#ZFS with lz4
df
Filesystem    512-blocks        Used      Avail Capacity  Mounted on
storage/data 31527470077 22942284913 8585185164    73%    /storage/data

#Used space: 22942284913 blocks = 10939 GB

I found that for 10TB of data, the server with lzjb uses 26GB more space than lz4, which translate to 0.23% (26GB out of 10TB). The difference is quite small and not too significant. However, when your ZFS is nearly full or you are too busy to upgrade your system, the extra saving may matter a lot.

lz4 VS lzjb: Time Saving

I am also curious to know how much time I will save by switching from lzjb to lz4. Therefore I did another simple test. First, I generated a 1GB of random data and wrote to the lzjb system. After that, I destroyed the zpool and rebuilt the zpool with lz4. This will eliminate other factors such as hardware, network traffic etc, because both tests were done within the same system. 

#ZFS with lzjb
time dd if=/dev/random of=/storage/data/file.out bs=1M count=1000
1000+0 records in
1000+0 records out
1048576000 bytes transferred in 23.725955 secs (44195313 bytes/sec)

real    0m24.144s
user    0m0.024s
sys     0m18.326s

#ZFS with lz4
time dd if=/dev/random of=/storage/data/file.out bs=1M count=1000
1000+0 records in
1000+0 records out
1048576000 bytes transferred in 22.589257 secs (46419234 bytes/sec)

real    0m22.802s
user    0m0.016s
sys     0m18.273s

P.S. The /dev/random in FreeBSD is nothing like the one in Linux. It is very fast.

By just upgrading from lzjb to lz4, the time is reduced from 24.144 to 22.802 seconds, which translate to 5.5% (1.342s out of 24.144s) improvement.

This result also agrees with my overall experience: The improvement is small and not noticeable. In fact, I barely notice any performance improvement after switching from lzjb to lz4, which primarily includes transferring the files between Windows and FreeBSD-based ZFS system via Samba on a gigabit network. The I/O speed are about the same. However, if you are talking about a busy server with lots of traffic, a 5% improvement will be something.

Anyway, this is what I recommend. If lz4 is available in your ZFS version, use it. It can’t be wrong.

sudo zfs set compression=lz4 myzpool

–Derrick

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ZFS Performance Boost/Improvement: How I push the I/O speed to 126MBps

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This article is part of my main ZFS tutorial: How to improve ZFS performance. That article covers everything you need. If you already have the basic knowledge, or you just want to know how I push the I/O speed to 120+ MBps, you can skip that article and read this one.

Long story short, here is the result of my iostat:

sudo zpool iostat -v

               capacity     operations    bandwidth
pool        alloc   free   read  write   read  write
----------  -----  -----  -----  -----  -----  -----
storage     7.85T  12.1T      1  1.08K  2.60K   126M < ---126 MBps!
  raidz2    5.51T  8.99T      1    753  2.20K  86.9M
    ada0        -      -      0    142    102  14.5M
    ada1        -      -      0    143    102  14.5M
    ada3        -      -      0    146    307  14.5M
    ada4        -      -      0    145    409  14.5M
    ada5        -      -      0    144    204  14.5M
    ada6        -      -      0    143    204  14.5M
    ada7        -      -      0    172    409  14.5M
    ada8        -      -      0    171    511  14.5M
  raidz1    2.34T  3.10T      0    349    409  39.5M
    da0         -      -      0    169    204  13.2M
    da1         -      -      0    176      0  13.2M
    da2         -      -      0    168    102  13.2M
    da3         -      -      0    173    102  13.2M
----------  -----  -----  -----  -----  -----  -----

I measured the speed while I was transferring 10TB of data from one FreeBSD-based ZFS server to another FreeBSD-based ZFS server, over a consumer-level gigabit network. Basically, every components I used are consumer-level. The hard drives I used are standard PATA and SATA hard drives (i.e., not even the light speed SSD hard drive). The data I transferred are real data (rather than all zeros or ones generated through dd).

First of all, here are the settings I used. Both server and client have similar configurations.

sudo zpool history
History for 'storage':
2014-01-22.20:28:59 zpool create -f storage raidz2 /dev/ada0 /dev/ada1 /dev/ada3 /dev/ada4 /dev/ada5 /dev/ada6 /dev/ada7 /dev/ada8 raidz /dev/da0 /dev/da1 /dev/da2 /dev/da3
2014-01-22.20:29:07 zfs create storage/data
2014-01-22.20:29:15 zfs set compression=lz4 storage
2014-01-22.20:29:19 zfs set compression=lz4 storage/data
2014-01-22.20:30:19 zfs set atime=off storage

#where the ad* and da* are nothing more than standard SATA drives:
#ZFS Drives
#8 x 2TB standard SATA hard drives connected to the motherboard
#4 x 1.5TB standard SATA hard drives connected to a PCI-e RAID card

da0: 1430799MB (2930277168 512 byte sectors: 255H 63S/T 182401C)
da1: 1430799MB (2930277168 512 byte sectors: 255H 63S/T 182401C)
da2: 1430799MB (2930277168 512 byte sectors: 255H 63S/T 182401C)
da3: 1430799MB (2930277168 512 byte sectors: 255H 63S/T 182401C)
ada0: 300.000MB/s transfers (SATA 2.x, UDMA6, PIO 512bytes)
ada0: 1907729MB (3907029168 512 byte sectors: 16H 63S/T 16383C)
ada1: 300.000MB/s transfers (SATA 2.x, UDMA6, PIO 8192bytes)
ada1: 1907729MB (3907029168 512 byte sectors: 16H 63S/T 16383C)
ada3: 300.000MB/s transfers (SATA 2.x, UDMA5, PIO 8192bytes)
ada3: 1907729MB (3907029168 512 byte sectors: 16H 63S/T 16383C)
ada4: 300.000MB/s transfers (SATA 2.x, UDMA5, PIO 8192bytes)
ada4: 1907729MB (3907029168 512 byte sectors: 16H 63S/T 16383C)
ada5: 300.000MB/s transfers (SATA 2.x, UDMA5, PIO 8192bytes)
ada5: 1907729MB (3907029168 512 byte sectors: 16H 63S/T 16383C)
ada6: 300.000MB/s transfers (SATA 2.x, UDMA5, PIO 8192bytes)
ada6: 1907729MB (3907029168 512 byte sectors: 16H 63S/T 16383C)
ada7: 300.000MB/s transfers (SATA 2.x, UDMA5, PIO 8192bytes)
ada7: 1907729MB (3907029168 512 byte sectors: 16H 63S/T 16383C)
ada8: 300.000MB/s transfers (SATA 2.x, UDMA5, PIO 8192bytes)
ada8: 1907729MB (3907029168 512 byte sectors: 16H 63S/T 16383C)


#System Drive
#A PATA 200MB drive from 2005
ada2: maxtor STM3200820A 3.AAE ATA-7 device
ada2: 100.000MB/s transfers (UDMA5, PIO 8192bytes)
ada2: 190782MB (390721968 512 byte sectors: 16H 63S/T 16383C)

Here are the corresponding hardware components:

#CPU
hw.machine: amd64
hw.model: Intel(R) Core(TM) i7 CPU         920  @ 2.67GHz
hw.ncpu: 8
hw.machine_arch: amd64


#Memory - 3 x 2GB
real memory  = 6442450944 (6144 MB)
avail memory = 6144352256 (5859 MB)

#Network - Gigabit network on the motherboard / PCI-e
#If your gigabit network card is PCI, that will be your bottleneck.
re0: realtek 8168/8111 B/C/CP/D/DP/E/F PCIe Gigabit Ethernet

Other than that, I didn’t really specify any special settings in my OS. Everything else are default:

#uname -a
FreeBSD 9.2-RELEASE-p3 FreeBSD 9.2-RELEASE-p3 #0: Sat Jan 11 03:25:02 UTC 2014     [email protected]:/usr/obj/usr/src/sys/GENERIC  amd64

The way how to transfer 10TB of data is through rsync and rsyncd. First of all, I set up a rsync as daemon on the server. Keep in mind that rsync as a daemon (service) is not the same as rsync. If you want to know how I set up the rsyncd, please visit How to Improve rsync Performance.

After you have set up the rsyncd on the server, I run the following on the client.

rsync -av server_ip::rsync_share_name /my_directory/

#Example
rsync -av 192.168.1.101::storage /mydata/

Notice that I didn’t enable the compression option. That’s because my files are pretty much compressed (jpeg, zip, tar, 7z etc). If your file types are different, you may want to enable the compression, i.e.,

rsync -avz server_name::rsync_share_name /my_directory/

Give it a try and see whether it improves the I/O speed.

Here are few things I have learned to improve the ZFS performance.

Keep the ZFS structure small and simple. For example, keep the number of disks in your vdev small. Previously, I set up a giant big pool with 14 disks RAIDZ in one single vdev. This is a bad idea. There is a maximum number of disks for RAIDZ. That’s why I split my disks into two groups:

#Group 1 - RAIDZ2
#8 x 2TB standard SATA hard drives connected to the motherboard

#Group2 - RAIDZ
#4 x 1.5TB standard SATA hard drives connected to a PCI-e RAID card

zpool create -f storage myzpool group1 raidz group2

Keep the ZFS settings clean. Enable the only thing you need, and disable the junk settings. In my case, I enable the best compression (lz4) and disable the access time:

2014-01-22.20:29:15 zfs set compression=lz4 storage
2014-01-22.20:30:19 zfs set atime=off storage

Keep the ZFS clean. I see the performance gain on a brand new ZFS than a few years old ZFS, even both of them contain the same data. Unfortunately, there is no easy way to clean the ZFS. The only way is to destroy the current ZFS first, create a new one and bring the data back. Typically, it takes about 2 days to transfer 10TB of data over a gigabit LAN. So it is really not too bad to spend about 5 days to rebuild your ZFS.

That’s it. Again, if you want to learn about tricks, please visit How to improve ZFS performance for more information.

–Derrick

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How to Remote Desktop To Linux From Windows Using XRDP

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If you are looking for ways to remote desktop to Linux from Windows, and you are sick of VNC, you are in the right place.

I have been looking for a solution to do something very simple. I want to remotely access the desktop of my Linux servers from Windows machine. Of course, it must be at a usable level.

I’ve tried different applications before, incluing XMing, XManager (X11 forwarding), VNC, 2X, NoMachine, ranging from open-source to commercial. Unfortunately, they offer nothing close to the Windows to Windows Remote Desktop experience.

Why XMing is bad?

XMing allows you to run a remote application (e.g., Firefox) on your desktop. It works great as long as you keep the session available. Once you close your session, there is no way to go back to the previous session. For example, suppose I am browsing a website using the Firefox on the remote server via XMing. If I decide to close the XMing (without closing the browser), there is no way for me to go back to the page I left off later. Of course, in reality, it doesn’t make too much sense to use a Firefox on a remote server. I was referring to some software that takes days to run, such as R, Matlab etc.

By the way, it is an application level, meaning that it does not work with the desktop level.

Why VNC is bad?

VNC is nearly perfect. It offers something similar to Windows Remote Desktop, i.e., I can access to the desktop level. If I work on something, I can get my previous session back even my session is closed. There are only two disadvantages: Slow, and not for multiple users.

VNC uses a stone-age protocol to delivery the remote desktop experience: Screen capture. When there is a change on the remote server, it takes a screen shot and send it to the client. You can imagine how slow it will be over the Internet. Although they released a better algorithm, which works directly at the graphic card level, i.e., only send the modified area to the client instead of everything. However the new protocol is still far from usable. The Microsoft Remote Desktop just blows VNC far far away.

Another thing I don’t like VNC is that it is at the machine/server level, not the user level. VNC uses its own user authorization. When you set up a VNC service, you define your own password. That’s it. In the other words, if I open a desktop on the server as derrick. Everybody will be able to see my desktop content via VNC as long as they enter the correct password. Unless I go to the server physically and switch to a different user, otherwise there is no way to protect the content of my desktop.

The good thing about VNC is that it is cross-platform. It works on OS X, Windows, Linux etc. Wait a minute. Java is cross-platform too. Do you want to use it?

Why XManager is bad?

XManager is better than VNC. It uses some special protocol such that the speed is not an issue. However, it is suffered in the session problem like XMing. If I remote desktop to the server using XManager, and I close my session later, there is no way for me to go back to my previous sessions. In the other words, I will lose all opened applications and contents.

And no, the session is still running silently on the server. They are just orphans. XManager doesn’t allow you to connect to the old session when you try to establish a new connection.

Solution: xrdp

I am so happy that I finally found something useful and usable. That’s xrdp. Here is a step-by-step tutorial on how to install it on Fedora/CentOS Linux. The instruction will be similar to Debian/Ubuntu Linux. The set up time should take no more than 5 minutes.

#Install xrdp
sudo yum install -y xrdp

If your Linux is too old, or your default repository does not have xrdp available, you may want to run the following:

#Don't forget to use the right (i686 or x86_64) architecture.

sudo rpm -Uvh  http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
sudo rpm -Uvh  http://rpms.famillecollet.com/enterprise/remi-release-6.rpm
sudo yum update -y

sudo yum install -y xrdp

Next, we want to start the xrdp service

sudo /etc/rc.d/init.d/xrdp start

You may want to enable this service during the boot up:

sudo chkconfig  xrdp on

Don’t forget to open the port 3389 in your firewall:

sudo nano /etc/sysconfig/iptables

-A INPUT -m state --state NEW -m tcp -p tcp --dport 3389 -j ACCEPT

Don’t forget to restart the firewall:

sudo service iptables stop
sudo service iptables start

Now, run the remote desktop on Windows, and enter the IP address of the server to see what happen.

–Derrick

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[FreeBSD]mount: /dev/da0p2: R/W mount of / denied. Filesystem is not clean – run fsck. Forced mount will invalidate journal contents: Operation not permitted

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When I tried to mount a hard drive on FreeBSD today, I got the following error message.

sudo mount -t ufs /dev/da0p2 /mnt/
mount: /dev/da0p2: R/W mount of / denied. Filesystem is not clean - run fsck. Forced mount will invalidate journal contents: Operation not permitted

Here is how to fix it:

sudo mount -r -t ufs /dev/da0p2 /mnt/

where ufs refers to the file system of FreeBSD.

That’s it.

–Derrick

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[FreeBSD] ZFS FAULTED / kernel: (ada0:ahcich4:0:0:0): lost device

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I am so happy that I finally solved a problem today. This problem had existed in my server farms for few months already. In the past few months, I had absolutely no idea what was causing the issues. Here is my story:

I built a file server using FreeBSD and ZFS. The hardware components are consumer grade hardware. Basically, it is a desktop computer with multiple hard drives. The hard drives are connected to the SATA ports on the motherboard. It is a very simple setup.

After I set up a ZFS pool, I started to load the data and stress tested the system. I noticed that the ZFS pool turned into a fault state after 15 mins, e.g., 

#sudo zpool status -v
  pool: storage
 state: FAULTED
status: One or more devices could not be opened.  There are insufficient
        replicas for the pool to continue functioning.
action: Attach the missing device and online it using 'zpool online'.
config:

        NAME        STATE     READ WRITE CKSUM
        storage     ONLINE       0     0     0
          raidz1-0  ONLINE       0     0     0
            ada4    ONLINE       0     0     0
            ada0    REMOVED      0     0     0 
            ada2    ONLINE       0     0     0
            ada5    ONLINE       0     0     0
            ada3    ONLINE       0     0     0

errors: Permanent errors have been detected in the following files:

In short, a drive is missing. So I tried to run dmesg 

Oct 17 20:24:00 kernel: (ada0:ahcich4:0:0:0): lost device
Oct 17 20:24:00 kernel: (ada0:ahcich4:0:0:0): removing device entry
Oct 19 20:42:14 kernel: (ada0:ahcich3:0:0:0): lost device
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): lost device
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): removing device entry
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): lost device
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): removing device entry
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): lost device
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): removing device entry
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): lost device
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): removing device entry
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): lost device
Oct 19 23:19:18 kernel: (ada0:ahcich4:0:0:0): removing device entry
Oct 19 23:33:02 kernel: (ada0:ahcich4:0:0:0): Synchronize cache failed
Oct 20 22:53:40 kernel: (ada0:ahcich4:0:0:0): WRITE_FPDMA_QUEUED. ACB: 61 40 30 af 4e 40 7a 00 00 00 00 00
Oct 20 22:53:40 kernel: (ada0:ahcich4:0:0:0): CAM status: ATA Status Error
Oct 20 22:53:40 kernel: (ada0:ahcich4:0:0:0): ATA status: 61 (DRDY DF ERR), error: 04 (ABRT )
Oct 20 22:53:40 kernel: (ada0:ahcich4:0:0:0): RES: 61 04 00 00 00 40 00 00 00 00 00
Oct 20 22:53:40 kernel: (ada0:ahcich4:0:0:0): Retrying command

I also verified the content in /dev/, e.g.,

#ls /dev/ad0

crw-r-----  1 root  operator   0x6f Oct 18 22:10 /dev/ada0

Interestingly, the device is still available. This is very confusing because the system sees the hardware (with some error), but the application could not see the hardware. So I decided to perform the following tests:

  • Reboot
  • Shutdown and reboot
  • Replacing the SATA cables
  • Connecting the hard drive to a different SATA port
  • Replacing the hard drive with a new one that is certified by the manufacturer
  • Replacing the motherboard
  • Replacing the hard drive power cable
  • Replacing the power supply
  • Updating the firmware of the motherboard

Unfortunately, none of these fixed the problem. I also checked the S.M.A.R.T. status of the hard drives but I didn’t see any issues. One thing I noticed is that the error is not consistent. It happens randomly on different SATA port and hard drive. That doesn’t make any sense to me because I saw the same thing on 3 different motherboards. Finally, I decided to try one last thing: I connected the hard drives through an USB port. Guess what, my FreeBSD box stopped complaining.

So I decided to a different approach. I used the same hardware setup (the hard drives were connected using SATA instead of USB) and loaded a Windows. The system worked perfectly fine and stable. I didn’t experience any issue at all. So I believed the problem had nothing to do with the hardware. It must be the software settings issue.

Finally, I decided to try one last thing, something I hadn’t paid attention before: BIOS Settings

AHCI/IDE

Typically there is a setting to control how the motherboard interacts with the hard drives: IDE or AHCI. I usually stick with the default settings. In my case, the default value of my motherboard is IDE. After I changed the settings to AHCI, I found that the problem is gone. Yes, it’s gone and my headache is gone too.

That was easy!

–Derrick

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FreeBSD.org Was Compromised. What Should You Do Next?

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In case you are not aware this bad news. FreeBSD.org was compromised on September 17, 2012. Good news is that the compromise was caused by a human error (a stupid developer leaked a SSH private key somewhere), which has nothing to do with the code quality of the FreeBSD. 🙂 Bad news is that this may affect you if you use port. 🙁

The compromise is believed to have occurred due to the leak of an SSH key from a developer who legitimately had access to the machines in question, and was not due to any vulnerability or code exploit within FreeBSD.

We unfortunately cannot guarantee the integrity of any packages available for installation between 19th September 2012 and 11th November 2012, or of any ports compiled from trees obtained via any means other than through svn.freebsd.org or one of its mirrors. Although we have no evidence to suggest any tampering took place and believe such interference is unlikely, we have to recommend you consider reinstalling any machine from scratch, using trusted sources.

In short, the port tree was affected from September 19, 2012 to November 11, 2012. If you downloaded the ports in between this period, you are likely a victim of this incident. 🙁 Here is how to clean up the mess:

Stop using cvsup/csup to update your port. Use portsnap instead.

If you already used portsnap, do the following:

sudo portsnap fetch extract
sudo portsnap upgrade

If you have no idea what is portsnap, here is a quick tutorial:

First, install the portmaster and portupgrade. Port-Upgrade downloads the new ports to your server and Port-Master updates your applications based on the downloaded ports.

sudo pkg_add -r portupgrade portmaster

Download all ports. Notice that this is one-time work.

sudo portsnap fetch extract

If you decide to update your port tree, run the following:

sudo portsnap fetch update

Or if you like to run it in a cron job, run the following instead:

sudo nano /etc/crontab

#Run every three hours
0       */3     *       *       *       root    portsnap -I cron update && pkg_version -vIL= >/dev/null 2>&1

Now you have an updated port tree. Next you will need to update your applications based on your local port tree:

sudo portmaster -Dai

That’s it.

And remember, NEVER put your SSH private key in a public area.

–Derrick

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[Adobe Lightroom / Photomatix]Lightroom rendition failed

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Yesterday, I was processing some of the pictures in Adobe Lightroom. I liked to export few of them to Photomatix for HDR processing. Then, the system complained with this error message:

Lightroom rendition failed

After searching this error message on Google, I found that this message was generated by the Photomatix plug-in. According to Photomatix’s FAQ, it seems that the original picture is missing.

So, I ran a quick test (Find Missing Photos) in Adobe Lightroom, and of course it didn’t find anything. After some investigations, I found that the problem was caused by low free space in harddrive.

It is very easy to solve this problem. Simply change the Windows temporary drive to somewhere else and you are done.

So what cause this problem? When you export the pictures to other applications, Lightroom will first convert them in some common format first (usually TIFF), such that the other applications will be able to read the files. During this process, Lightroom will store these pictures in the temporary directory provided by Windows, and this settings cannot be changed within Lightroom.

By default, the temporary directory is in the system drive (e.g., C:). If you are using SSD harddrive, you may have very limited amount of free space left. Therefore, it is a good idea to assign the temporary directory to another drive with more space.

Here are the step by step tutorial:

  1. Start
  2. Control Panel
  3. System
  4. Advanced system settings
  5. Environment Variables

Now we are ready to change the location of temporary directory. Let’s edit the TEMP and TMP, and change them to something else. In my case, I have more space in d:, so I set them to D:\Temp.

Click OK and save. Now, restart your Lightroom and the error message will be gone.

–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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