Installing Theano and CUDA on Mac OS X

I started trying Theano today and wanted to use the GPU (NVIDIA GeForce GT 750M 2048 MB) on my Mac. Here’s a brief instruction on how to use the GPU on Mac, largely following the instructions from http://deeplearning.net/software/theano/install.html#mac-os.

Install Theano:

Download and install CUDA: https://developer.nvidia.com/cuda-downloads

Put the following lines into your ~/.bash_profile:

Note that the PATH line is necessary. Otherwise you may see the following message:

ERROR (theano.sandbox.cuda): nvcc compiler not found on $PATH. Check your nvcc installation and try again.

Configure Theano:

Test if GPU is used:

A more realistic example:

So it seems this GPU does not outperform the CPU. Well,GT 750M may not be the best GPU you can get… Someone else here has a similar experience.

 

OSX Yosemite cannot boot when TRIM is enabled on third-party SSD

After upgrading my MBP to OSX Yosemite and enabling TRIM, the computer cannot boot into the system after restart. It stuck with a no-entry sign.

You can solve this issue by following instructions from http://www.cindori.org/trim-in-os-x-yosemite/

Boot your Mac in Recovery Mode by holding Cmd-R during boot

Open the Terminal from the menu bar

Run these commands, replacing YourDisk with the name of your Mac disk

rm -rf /Volumes/YourDisk/System/Library/Extensions/IOAHCIFamily.kext
cp -r /System/Library/Extensions/IOAHCIFamily.kext /Volumes/YourDisk/System/Library/Extensions/IOAHCIFamily.kext
touch /Volumes/YourDisk/System/Library/Extensions
kextcache -u /Volumes/YourDisk

For me, I have to first use the disk utility to unlock my SSD first since I have Filevault enabled, otherwise the first command above will complain about “readonly” files.

Since TRIM is very helpful for SSDs, it’s encouraged to have it enabled for better performance. You can use Trim Enabler v3.2.5 and above without issues. But note that it disables kext signing on your mac, “it still leaves you with the same amount of security as in OS X Mavericks, where the kext signing requirement didn’t exist”. (http://www.cindori.org/update-on-trim-in-yosemite/)

Debugging Apache configuration files on Mac OS X

Sometimes I make some modification to my site’s apache config and apache stops functioning, but I cannot get enough information from /var/log/apache2/error.log. Here’s a command that will tell you where the problem is:

It starts apache for debugging and prints out the messages on screen, so that hopefully you can find something useful.

mod_wsgi and mod_xsendfile on OS X 10.9 Mavericks

Updated on Nov 4, 2013: The following tricks may still work, however I have found a much easier solution. Simply install Xcode command line developer tools and you should be able to compile source code without issues:

After upgrading my Mac from 10.8 to 10.9 Mavericks my apache stopped working, so I have to reinstall mod_wsgi and mod_xsendfile. However, tricks are needed to compile and install these mods successfully.

Upgrade Xcode

Upgrade Xcode in App Store. As mentioned by Valerie:

I had to manually upgrade Xcode (after Mavericks upgrade) from the App Store & agree to its license because ./configure hung forever until I did that.

mod_wsgi

For mod_wsgi installation, create a soft link to OSX10.9.xctoolchain:

Then run configure under mod_wsgi source code directory:

It will generate a Makefile similar as follows:

However, this Makefile is not correct and running ‘make’ the compiler will complain something like:

Prepend the following line to CPPFLAGS value:

Save the Makefile and it will look something like:

Then make && install:

Modify /etc/apache2/httpd.conf to enable mod_wsgi:

mod_xsendfile

Use the following command to compile and install mod_xsendfile:

Enabling HTTPS/SSL

After upgrading OS X the apache configuration was reset, but your original config is save to /etc/apache2/httpd.conf.pre-update. I need to enable SSL in httpd.conf again by uncommenting the following line:

Restart Apache and everything should work fine

Solution: dd too slow on Mac OS X

When I was cloning SD cards on Mac OS X using dd', it takes ages to get things done. I was using the following command:

It takes much less time when using /dev/rdisk2 instead of /dev/disk2:

The reason is that rdisks are "raw" thus resulting in a higher R/W speed, according to man hdiutil` [1]:

/dev/rdisk nodes are character-special devices, but are “raw” in the BSD sense and force block-aligned I/O. They are closer to the physical disk than the buffer cache. /dev/disk nodes, on the other hand, are buffered block-special devices and are used primarily by the kernel’s filesystem code.

[1] http://superuser.com/questions/631592/mac-osx-why-is-dev-rdisk-20-times-faster-than-dev-disk

A “normal” sed on Mac

The sed program on Mac is not a standard (GNU) one. To get the normal one, use brew:

After this, alter PATH. For example, add the following line to your ~/.bash_profile:

And now you have a normal sed!

 

A faster key repeat rate for Mac OS X

The fastest one can get via System Preferences is 2. You can set it to either 0 or 1, depending on your preferences.

To check your current repeat rate, issue the following command in Terminal:

See: http://hints.macworld.com/article.php?story=20090823193018149

Installing mod_xsendfile on OS X Lion

First download mod_xsendfile.c from https://tn123.org/mod_xsendfile/

Then compile and install it:

Add the following line to /etc/apache2/httpd.conf at the end of the first block of “Load” statements:

At last, restart the apache server

Hi, the company I’m working for (yabroad.com) is hiring Website Backend and Frontend Developers to our platform team. We are building an open platform for youngsters to travel beyond boarders and we offer youngsters internship, language study, travel and volunteer opportunities. Please contact me if you are interested.

XBMC and OS X firewall permission popups

I installed XBMC on my Mac OS X Lion and every time I open up the program, a firewall permission dialog pops up. It didn’t help even if I added the XBMC in my firewall configurations. Popups still show up. This link solves the problem neatly — You can generate a certificate and sign the program by yourself. After that the frustrating dialog should appear only once (at most). In case the link becomes invalid, here’s a screenshot of the instructions. Click to see the large picture.

Block unauthorized ssh login attempts (attacks)

My friends and I am working on a hobby project and  we need a Git server, so I set up one on my MacBook Pro. We access the repository via SSH. However when I checked the ssh log I found someone trying to get ssh access to my machine by guessing usernames. The log looks as follows:

I first tried to use DenyHosts, however, there are still attempts from other IP addresses. Since there are three of us accessing the repository, I configured the hosts.allow and hosts.deny manually: deny all hosts other than the IP addresses I trust.

hosts.deny:

hosts.allow:

Now the log file should be quite…

GitHub couples

I’m feeling good today because of theses things:

  1. My mobile phone ran out of battery and the alarm clock didn’t ring this morning, but I still managed to get up just in time and caught the bus at the last minute — and arrived at the company at my usual time.
  2. My manager told me it looks positive to renew my contract and hopefully it will be one and half years. He also says he tries to get it done before the summer vacation, which makes my life a lot easier. Also he says it’s possible to save my holidays till winter. So I’ll be back in China for some time in winter this year.
  3. A very old lady managed to stop and got on the bus even though she waved her hand a bit late to the bus driver. The bus driver was polite and that what I like about Finland: people generally don’t get angry.
  4. Here’s one very funny and geeky picture I saw from xda-developers. In case the link gets invalidated later, the picture reads: “So, where did you two meet?” “Windows users: at the office” “Mac users: at Starbucks” “Linux users: GitHub”.

 

Downgrade Preview in OS X Lion

I’ve had enough with the slow Preview application in Lion. After some digging I found this tutorial to downgrade the Preview in Lion to the Snow Leopard version. Basically you need to have a copy of both the Preview.app and /System/Library/PrivateFrameworks/MeshKit.framework from Snow Leopard. If you need to associate the default app to open pdf/png with the downgraded Preview, you have to delete the original Preview.app.

Update: after installing OS X updates you need to remove the Preview.app again and put the SL Preview.app to /Applications/ directory.

i386-jos-elf toolchain on OS X Lion

Yesterday friend and I decided to follow the MIT Operating System Engineering course together in order to get a deep understanding of OS’s. And today I started setting up the cross compling environment for the labs. At first I wanted to get the toolchain from macports, but unluckily it didn’t successfully build binutils on my Mac. As a result, I started building the toolchain from the source code, following the instructions at http://pdos.csail.mit.edu/6.828/2011/tools.html.

The programs you need for the toolchain include binutils, gcc, and gdb. For compiling gcc you also need GMP, MPFR, and MPC. The source codes are available at:

Unzip them in a directory and build binutils, gcc, and gdb one by one.

In order to build gcc, GMP, MPFR and MPC needs to be built first.

Note that it’s essential to build gcc in a directory different from the source code directory to avoid compiling errors.

Then make gdb:

QEMU is available in macports:

Port already in use issue of Arduino for Eclipse plugin

When uploading with avrdude the plugin give a error prompt saying “Port already in use” (while no other application is using the port). After clicking OK it actually uploads the program to Arduino board.

port_in_use

After reading issue #6 I check the librxtxSerial.jnilib in eclipse:

While in my Arduino application the librxtxSerial.jnilib output is:

So I just copied the Arduino.app//Contents/Resources/Java/librxtxSerial.jnilib file to eclipse/configuration/org.eclipse.osgi/bundles/419/1/.cp/librxtxSerial.jnilib It works after restarting eclipse. No error prompts are shown.

iCal crashes with iCal Reply Checker uninstalled

My iCal crashes everytime when someone sends me an invitation and I try either to accapt or decline it. After some investigation I found out it is the problem with iCal Reply Checker” at http://www.nhoj.co.uk/icalreplychecker

After unstalled this app, it resets the Mail.scpt file to an empty file. To solve the problem: get another copy of Mail.scpt from another Mac, preferably from the same OS X version; and put it inside the folder: /Applications/iCal.app/Contents/Resources/Scripts

Lesson learnt: take care when trying amature software.