First learning into pycuda

With last blog which I fail to get a sample working, today I thought of giving pycuda a try. So what is pycuda?

PyCUDA gives you easy, Pythonic access to Nvidia‘s CUDA parallel computation API. 

With that said, I'm gonna give the sample code a try. Let's install python3 pycuda module.

 user@localhost:~/Downloads$ sudo apt-get install python3-pycuda   
 Reading package lists... Done  
 Building dependency tree      
 Reading state information... Done  
 The following packages were automatically installed and are no longer required:  
  libgl1-nvidia-glx:i386 libgl1-nvidia-glx-i386:i386 libllvm3.5v5 libnvidia-glcore:i386 linux-image-4.1.0-2-amd64 linux-image-4.2.0-1-amd64 linux-source-4.3 python3-ecdsa syslinux  
  unetbootin-translations  
 Use 'sudo apt autoremove' to remove them.  
 The following additional packages will be installed:  
  fonts-mathjax libboost-python1.61.0 libboost-system1.61.0 libboost-thread1.61.0 libjs-mathjax python-pycuda-doc python3-appdirs python3-decorator python3-pytools  
 Suggested packages:  
  fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-pycuda python3-pytest python3-opengl python3-pycuda-dbg  
 The following NEW packages will be installed:  
  fonts-mathjax libboost-python1.61.0 libboost-system1.61.0 libboost-thread1.61.0 libjs-mathjax python-pycuda-doc python3-appdirs python3-decorator python3-pycuda python3-pytools  
 0 upgraded, 10 newly installed, 0 to remove and 508 not upgraded.  
 Need to get 7,150 kB of archives.  
 After this operation, 47.8 MB of additional disk space will be used.  
 Do you want to continue? [Y/n] Y  
 Get:1 http://ftp.us.debian.org/debian testing/main amd64 fonts-mathjax all 2.6.1-1 [959 kB]  
 Get:2 http://ftp.us.debian.org/debian testing/main amd64 libboost-python1.61.0 amd64 1.61.0+dfsg-2.1 [137 kB]                                          
 Get:3 http://ftp.us.debian.org/debian testing/main amd64 libboost-system1.61.0 amd64 1.61.0+dfsg-2.1 [32.1 kB]                                          
 Get:4 http://ftp.us.debian.org/debian testing/main amd64 libboost-thread1.61.0 amd64 1.61.0+dfsg-2.1 [71.2 kB]                                          
 Get:5 http://ftp.us.debian.org/debian testing/main amd64 libjs-mathjax all 2.6.1-1 [5,473 kB]                                                  
 Get:6 http://ftp.us.debian.org/debian testing/contrib amd64 python-pycuda-doc all 2016.1-1 [122 kB]                                               
 Get:7 http://ftp.us.debian.org/debian testing/main amd64 python3-appdirs all 1.4.0-2 [11.1 kB]                                                  
 Get:8 http://ftp.us.debian.org/debian testing/main amd64 python3-decorator all 4.0.6-1 [12.8 kB]                                                 
 Get:9 http://ftp.us.debian.org/debian testing/main amd64 python3-pytools all 2016.2.1-1 [33.9 kB]                                                
 Get:10 http://ftp.us.debian.org/debian testing/contrib amd64 python3-pycuda amd64 2016.1-1+b2 [298 kB]                                              
 Fetched 7,150 kB in 1min 23s (85.4 kB/s)                                                                             
 Selecting previously unselected package fonts-mathjax.  
 (Reading database ... 281119 files and directories currently installed.)  
 Preparing to unpack .../fonts-mathjax_2.6.1-1_all.deb ...  
 Unpacking fonts-mathjax (2.6.1-1) ...  
 Selecting previously unselected package libboost-python1.61.0.  
 Preparing to unpack .../libboost-python1.61.0_1.61.0+dfsg-2.1_amd64.deb ...  
 Unpacking libboost-python1.61.0 (1.61.0+dfsg-2.1) ...  
 Selecting previously unselected package libboost-system1.61.0:amd64.  
 Preparing to unpack .../libboost-system1.61.0_1.61.0+dfsg-2.1_amd64.deb ...  
 Unpacking libboost-system1.61.0:amd64 (1.61.0+dfsg-2.1) ...  
 Selecting previously unselected package libboost-thread1.61.0:amd64.  
 Preparing to unpack .../libboost-thread1.61.0_1.61.0+dfsg-2.1_amd64.deb ...  
 Unpacking libboost-thread1.61.0:amd64 (1.61.0+dfsg-2.1) ...  
 Selecting previously unselected package libjs-mathjax.  
 Preparing to unpack .../libjs-mathjax_2.6.1-1_all.deb ...  
 Unpacking libjs-mathjax (2.6.1-1) ...  
 Selecting previously unselected package python-pycuda-doc.  
 Preparing to unpack .../python-pycuda-doc_2016.1-1_all.deb ...  
 Unpacking python-pycuda-doc (2016.1-1) ...  
 Selecting previously unselected package python3-appdirs.  
 Preparing to unpack .../python3-appdirs_1.4.0-2_all.deb ...  
 Unpacking python3-appdirs (1.4.0-2) ...  
 Selecting previously unselected package python3-decorator.  
 Preparing to unpack .../python3-decorator_4.0.6-1_all.deb ...  
 Unpacking python3-decorator (4.0.6-1) ...  
 Selecting previously unselected package python3-pytools.  
 Preparing to unpack .../python3-pytools_2016.2.1-1_all.deb ...  
 Unpacking python3-pytools (2016.2.1-1) ...  
 Selecting previously unselected package python3-pycuda.  
 Preparing to unpack .../python3-pycuda_2016.1-1+b2_amd64.deb ...  
 Unpacking python3-pycuda (2016.1-1+b2) ...  
 Processing triggers for fontconfig (2.11.0-6.5) ...  
 Processing triggers for libc-bin (2.19-22) ...  
 Setting up fonts-mathjax (2.6.1-1) ...  
 Setting up libboost-python1.61.0 (1.61.0+dfsg-2.1) ...  
 Setting up libboost-system1.61.0:amd64 (1.61.0+dfsg-2.1) ...  
 Setting up libboost-thread1.61.0:amd64 (1.61.0+dfsg-2.1) ...  
 Setting up libjs-mathjax (2.6.1-1) ...  
 Setting up python-pycuda-doc (2016.1-1) ...  
 Setting up python3-appdirs (1.4.0-2) ...  
 Setting up python3-decorator (4.0.6-1) ...  
 Setting up python3-pytools (2016.2.1-1) ...  
 Setting up python3-pycuda (2016.1-1+b2) ...  
 Processing triggers for libc-bin (2.19-22) ...  

Okay, we are all good. Let's start python3 interpreter. By the way, I'm using python3.5

 user@localhost:~$ python3  
 Python 3.5.2+ (default, Aug 5 2016, 08:07:14)   
 [GCC 6.1.1 20160724] on linux  
 Type "help", "copyright", "credits" or "license" for more information.  
 >>> import pycuda.autoinit  
 Traceback (most recent call last):  
  File "<stdin>", line 1, in <module>  
  File "/usr/lib/python3/dist-packages/pycuda/autoinit.py", line 5, in <module>  
   cuda.init()  
 pycuda._driver.RuntimeError: cuInit failed: no CUDA-capable device is detected  
   

ah craps, you would think that something is wrong with the lib. It's just that the library did not detect a gpu that is cuda capable. For your information, I have workstation that has two gpu, an intel and nvidia gpu, so it is currently running intel which is not power consumption intensive and I have to explicitly enable nvidia gpu should I need to. With that said, let's try it again.

 user@localhost:~$ optirun python3  
 Python 3.5.2+ (default, Aug 5 2016, 08:07:14)   
 [GCC 6.1.1 20160724] on linux  
 Type "help", "copyright", "credits" or "license" for more information.  
 >>> import pycuda.autoinit  
 >>> import pycuda.driver as drv  
 >>> import numpy  
 >>>   
 >>> from pycuda.compiler import SourceModule  
 >>> mod = SourceModule("""  
 ... __global__ void multiply_them(float *dest, float *a, float *b)  
 ... {  
 ...   const int i = threadIdx.x;  
 ...   dest[i] = a[i] * b[i];  
 ... }  
 ... """)  
 >>> multiple_them = mod.get_function("multiply_them")  
 >>> a = numpy.random.randn(400).astype(numpy.float32)  
 >>> b = numpy.random.randn(400).astype(numpy.float32)  
 >>>   
 >>> dest = numpy.zeros_like(a)  
 >>> multiple_them(drv.Out(dest), drv.In(a), drv.In(b), block=(400,1,1), grid=(1,1))  
 >>> print(dest-a*b)  
 [ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.  
  0. 0. 0. 0.]  

optirun is a command to enable nvidia discreet gpu on debian. So now import library and it works! Brilliant. By the way, I'm using nvidia 960M gpu. That's it for today.

First learning into gpu sort with code compile on gpuqsortlib

Many articles recently showing using gpu to do arithmetic operation and with so many chips on a gpu in comparison with cpu, I thought it is worth while to spend sometime to look into gpu capabilities. Today I'm trying out gpu sort with gpusortlib.

Download the gpusortlib and extract it. Then let's start make command

 user@localhost:~/Desktop/gpuqsortlib$ make   
 nvcc -O3 -I/common/inc -Xcompiler -fPIC -Iinc -c src/gpuqsort.cu -o gpuqsort.o  
 make: nvcc: Command not found  
 Makefile:19: recipe for target 'gpuqsort.o' failed  
 make: *** [gpuqsort.o] Error 127  

nvcc compiler not install, so let's install it. Note that, this required 668MB of disk space!

 user@localhost:~/Desktop/gpuqsortlib$ sudo apt-get install nvidia-cuda-toolkit  
 Reading package lists... Done  
 Building dependency tree      
 Reading state information... Done  
 The following packages were automatically installed and are no longer required:  
  libgl1-nvidia-glx:i386 libgl1-nvidia-glx-i386:i386 libllvm3.5v5 libnvidia-glcore:i386 linux-image-4.1.0-2-amd64 linux-image-4.2.0-1-amd64 linux-source-4.3 python3-ecdsa syslinux  
  unetbootin-translations  
 Use 'sudo apt autoremove' to remove them.  
 The following additional packages will be installed:  
  libcublas7.5 libcuda1 libcuda1:i386 libcuda1-i386:i386 libcudart7.5 libcufft7.5 libcufftw7.5 libcuinj64-7.5 libcurand7.5 libcusolver7.5 libcusparse7.5 libegl1-nvidia libgl1-nvidia-glx  
  libgl1-nvidia-glx:i386 libgles1-nvidia libgles2-nvidia libnppc7.5 libnppi7.5 libnpps7.5 libnvblas7.5 libnvcuvid1 libnvidia-compiler libnvidia-eglcore libnvidia-glcore  
  libnvidia-glcore:i386 libnvidia-ml1 libnvidia-ml1:i386 libnvrtc7.5 libnvtoolsext1 libnvvm3 libthrust-dev libva-x11-1:i386 libvdpau-dev libvdpau-va-gl1:i386 libvdpau1 libvdpau1:i386  
  mesa-vdpau-drivers:i386 nvidia-alternative nvidia-cuda-dev nvidia-cuda-doc nvidia-cuda-gdb nvidia-driver nvidia-driver-bin nvidia-driver-libs nvidia-kernel-support nvidia-opencl-common  
  nvidia-opencl-dev nvidia-opencl-icd nvidia-profiler nvidia-smi:i386 nvidia-vdpau-driver nvidia-visual-profiler opencl-headers vdpau-driver-all:i386 xserver-xorg-video-nvidia  
 Suggested packages:  
  nvidia-cuda-mps nvidia-cuda-mps:i386 libvdpau-doc libcupti-dev nvidia-vdpau-driver:i386 nvidia-legacy-340xx-vdpau-driver:i386  
 Recommended packages:  
  nvidia-smi nvidia-settings nvidia-driver-libs-i386 libnvidia-cfg1  
 The following NEW packages will be installed:  
  libcublas7.5 libcuda1 libcuda1:i386 libcuda1-i386:i386 libcudart7.5 libcufft7.5 libcufftw7.5 libcuinj64-7.5 libcurand7.5 libcusolver7.5 libcusparse7.5 libnppc7.5 libnppi7.5 libnpps7.5  
  libnvblas7.5 libnvcuvid1 libnvidia-compiler libnvidia-glcore libnvidia-glcore:i386 libnvidia-ml1:i386 libnvrtc7.5 libnvtoolsext1 libnvvm3 libthrust-dev libva-x11-1:i386 libvdpau-dev  
  libvdpau-va-gl1:i386 mesa-vdpau-drivers:i386 nvidia-cuda-dev nvidia-cuda-doc nvidia-cuda-gdb nvidia-cuda-toolkit nvidia-driver-libs nvidia-opencl-common nvidia-opencl-dev  
  nvidia-opencl-icd nvidia-profiler nvidia-smi:i386 nvidia-visual-profiler opencl-headers vdpau-driver-all:i386  
 The following packages will be upgraded:  
  libegl1-nvidia libgl1-nvidia-glx libgl1-nvidia-glx:i386 libgles1-nvidia libgles2-nvidia libnvidia-eglcore libnvidia-ml1 libvdpau1 libvdpau1:i386 nvidia-alternative nvidia-driver  
  nvidia-driver-bin nvidia-kernel-support nvidia-vdpau-driver xserver-xorg-video-nvidia  
 15 upgraded, 41 newly installed, 0 to remove and 510 not upgraded.  
 Need to get 668 MB of archives.  
 After this operation, 1,329 MB of additional disk space will be used.  
 Do you want to continue? [Y/n] Y  
 Get:1 http://ftp.us.debian.org/debian testing/non-free amd64 libgles2-nvidia amd64 352.79-10 [170 kB]  
 Get:2 http://ftp.us.debian.org/debian testing/non-free amd64 libgles1-nvidia amd64 352.79-10 [165 kB]  
 Get:3 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-driver amd64 352.79-10 [435 kB]  
 Get:4 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-driver-bin amd64 352.79-10 [230 kB]  
 Get:5 http://ftp.us.debian.org/debian testing/non-free amd64 xserver-xorg-video-nvidia amd64 352.79-10 [3,188 kB]  
 Get:6 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-vdpau-driver amd64 352.79-10 [620 kB]                                            
 Get:7 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-kernel-support amd64 352.79-10 [150 kB]                                           
 Get:8 http://ftp.us.debian.org/debian testing/non-free amd64 libegl1-nvidia amd64 352.79-10 [291 kB]                                               
 Get:9 http://ftp.us.debian.org/debian testing/non-free amd64 libgl1-nvidia-glx amd64 352.79-10 [527 kB]                                             
 Get:10 http://ftp.us.debian.org/debian testing/non-free i386 libgl1-nvidia-glx i386 352.79-10 [518 kB]                                              
 Get:11 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-alternative amd64 352.79-10 [151 kB]                                            
 Get:12 http://ftp.us.debian.org/debian testing/non-free amd64 libnvidia-ml1 amd64 352.79-10 [452 kB]                                               
 Get:13 http://ftp.us.debian.org/debian testing/non-free i386 libnvidia-glcore i386 352.79-10 [6,549 kB]                                             
 Get:14 http://ftp.us.debian.org/debian testing/non-free amd64 libnvidia-glcore amd64 352.79-10 [6,841 kB]                                            
 Get:15 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-driver-libs amd64 352.79-10 [150 kB]                                            
 Get:16 http://ftp.us.debian.org/debian testing/main i386 libvdpau1 i386 1.1.1-3 [39.7 kB]                                                    
 Get:17 http://ftp.us.debian.org/debian testing/main amd64 libvdpau1 amd64 1.1.1-3 [41.1 kB]                                                   
 Get:18 http://ftp.us.debian.org/debian testing/non-free amd64 libnvidia-eglcore amd64 352.79-10 [6,715 kB]                                            
 Get:19 http://ftp.us.debian.org/debian testing/non-free i386 libcuda1 i386 352.79-10 [4,154 kB]                                                 
 Get:20 http://ftp.us.debian.org/debian testing/non-free amd64 libcuda1 amd64 352.79-10 [4,072 kB]                                                
 Get:21 http://ftp.us.debian.org/debian testing/non-free i386 libcuda1-i386 i386 352.79-10 [149 kB]                                                
 Get:22 http://ftp.us.debian.org/debian testing/non-free amd64 libnvcuvid1 amd64 352.79-10 [624 kB]                                                
 Get:23 http://ftp.us.debian.org/debian testing/non-free amd64 libnvidia-compiler amd64 352.79-10 [11.7 MB]                                            
 Get:24 http://ftp.us.debian.org/debian testing/non-free i386 libnvidia-ml1 i386 352.79-10 [426 kB]                                                
 Get:25 http://ftp.us.debian.org/debian testing/main i386 libva-x11-1 i386 1.7.1-2 [19.9 kB]                                                   
 Get:26 http://ftp.us.debian.org/debian testing/main amd64 libvdpau-dev amd64 1.1.1-3 [53.0 kB]                                                  
 Get:27 http://ftp.us.debian.org/debian testing/main i386 libvdpau-va-gl1 i386 0.4.0-2 [73.0 kB]                                                 
 Get:28 http://ftp.us.debian.org/debian testing/main i386 mesa-vdpau-drivers i386 11.2.2-1 [1,669 kB]                                               
 Get:29 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-opencl-common amd64 352.79-10 [150 kB]                                           
 Get:30 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-opencl-icd amd64 352.79-10 [4,141 kB]                                            
 Get:31 http://ftp.us.debian.org/debian testing/non-free i386 nvidia-smi i386 352.79-10 [301 kB]                                                 
 Get:32 http://ftp.us.debian.org/debian testing/main i386 vdpau-driver-all i386 1.1.1-3 [20.2 kB]                                                 
 Get:33 http://ftp.us.debian.org/debian testing/non-free amd64 libcublas7.5 amd64 7.5.18-3 [14.1 MB]                                               
 Get:34 http://ftp.us.debian.org/debian testing/non-free amd64 libcudart7.5 amd64 7.5.18-3 [113 kB]                                                
 Get:35 http://ftp.us.debian.org/debian testing/non-free amd64 libcufft7.5 amd64 7.5.18-3 [66.6 MB]                                                
 Get:36 http://ftp.us.debian.org/debian testing/non-free amd64 libcufftw7.5 amd64 7.5.18-3 [126 kB]                                                
 Get:37 http://ftp.us.debian.org/debian testing/non-free amd64 libcuinj64-7.5 amd64 7.5.18-3 [1,651 kB]                                              
 Get:38 http://ftp.us.debian.org/debian testing/non-free amd64 libcurand7.5 amd64 7.5.18-3 [37.8 MB]                                               
 Get:39 http://ftp.us.debian.org/debian testing/non-free amd64 libcusolver7.5 amd64 7.5.18-3 [16.0 MB]                                              
 Get:40 http://ftp.us.debian.org/debian testing/non-free amd64 libcusparse7.5 amd64 7.5.18-3 [19.2 MB]                                              
 Get:41 http://ftp.us.debian.org/debian testing/non-free amd64 libnppc7.5 amd64 7.5.18-3 [118 kB]                                                 
 Get:42 http://ftp.us.debian.org/debian testing/non-free amd64 libnppi7.5 amd64 7.5.18-3 [30.6 MB]                                                
 Get:43 http://ftp.us.debian.org/debian testing/non-free amd64 libnpps7.5 amd64 7.5.18-3 [2,667 kB]                                                
 Get:44 http://ftp.us.debian.org/debian testing/non-free amd64 libnvblas7.5 amd64 7.5.18-3 [124 kB]                                                
 Get:45 http://ftp.us.debian.org/debian testing/non-free amd64 libnvrtc7.5 amd64 7.5.18-3 [6,254 kB]                                               
 Get:46 http://ftp.us.debian.org/debian testing/non-free amd64 libnvtoolsext1 amd64 7.5.18-3 [41.3 kB]                                              
 Get:47 http://ftp.us.debian.org/debian testing/non-free amd64 libnvvm3 amd64 7.5.18-3 [4,203 kB]                                                 
 Get:48 http://ftp.us.debian.org/debian testing/main amd64 libthrust-dev all 1.8.1-1 [439 kB]                                                   
 Get:49 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-cuda-dev amd64 7.5.18-3 [201 MB]                                              
 Get:50 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-cuda-doc all 7.5.18-3 [73.5 MB]                                               
 Get:51 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-cuda-gdb amd64 7.5.18-3 [2,613 kB]                                             
 Get:52 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-profiler amd64 7.5.18-3 [2,253 kB]                                             
 Get:53 http://ftp.us.debian.org/debian testing/main amd64 opencl-headers all 2.0~svn32091-2 [57.1 kB]                                              
 Get:54 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-opencl-dev amd64 7.5.18-3 [28.2 kB]                                             
 Get:55 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-cuda-toolkit amd64 7.5.18-3 [15.3 MB]                                            
 Get:56 http://ftp.us.debian.org/debian testing/non-free amd64 nvidia-visual-profiler amd64 7.5.18-3 [118 MB]                                           
 Fetched 668 MB in 33min 21s (334 kB/s)                                                                              
 Reading changelogs... Done  
 Extracting templates from packages: 100%  
 (Reading database ... 275391 files and directories currently installed.)  
 Preparing to unpack .../libgles2-nvidia_352.79-10_amd64.deb ...  
 Unpacking libgles2-nvidia:amd64 (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../libgles1-nvidia_352.79-10_amd64.deb ...  
 Unpacking libgles1-nvidia:amd64 (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../nvidia-driver_352.79-10_amd64.deb ...  
 Unpacking nvidia-driver (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../nvidia-driver-bin_352.79-10_amd64.deb ...  
 Unpacking nvidia-driver-bin (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../xserver-xorg-video-nvidia_352.79-10_amd64.deb ...  
 Unpacking xserver-xorg-video-nvidia (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../nvidia-vdpau-driver_352.79-10_amd64.deb ...  
 Unpacking nvidia-vdpau-driver:amd64 (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../nvidia-kernel-support_352.79-10_amd64.deb ...  
 Unpacking nvidia-kernel-support (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../libegl1-nvidia_352.79-10_amd64.deb ...  
 Unpacking libegl1-nvidia:amd64 (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../libgl1-nvidia-glx_352.79-10_i386.deb ...  
 De-configuring libgl1-nvidia-glx:amd64 (352.79-8) ...  
 Unpacking libgl1-nvidia-glx:i386 (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../libgl1-nvidia-glx_352.79-10_amd64.deb ...  
 Unpacking libgl1-nvidia-glx:amd64 (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../nvidia-alternative_352.79-10_amd64.deb ...  
 Unpacking nvidia-alternative (352.79-10) over (352.79-8) ...  
 Preparing to unpack .../libnvidia-ml1_352.79-10_amd64.deb ...  
 Unpacking libnvidia-ml1:amd64 (352.79-10) over (352.79-8) ...  
 Selecting previously unselected package libnvidia-glcore:i386.  
 Preparing to unpack .../libnvidia-glcore_352.79-10_i386.deb ...  
 Unpacking libnvidia-glcore:i386 (352.79-10) ...  
 Selecting previously unselected package libnvidia-glcore:amd64.  
 Preparing to unpack .../libnvidia-glcore_352.79-10_amd64.deb ...  
 Unpacking libnvidia-glcore:amd64 (352.79-10) ...  
 Selecting previously unselected package nvidia-driver-libs:amd64.  
 Preparing to unpack .../nvidia-driver-libs_352.79-10_amd64.deb ...  
 Unpacking nvidia-driver-libs:amd64 (352.79-10) ...  
 Preparing to unpack .../libvdpau1_1.1.1-3_amd64.deb ...  
 De-configuring libvdpau1:i386 (1.1.1-1) ...  
 Unpacking libvdpau1:amd64 (1.1.1-3) over (1.1.1-1) ...  
 Preparing to unpack .../libvdpau1_1.1.1-3_i386.deb ...  
 Unpacking libvdpau1:i386 (1.1.1-3) over (1.1.1-1) ...  
 Preparing to unpack .../libnvidia-eglcore_352.79-10_amd64.deb ...  
 Unpacking libnvidia-eglcore:amd64 (352.79-10) over (352.79-8) ...  
 Selecting previously unselected package libcuda1:amd64.  
 Preparing to unpack .../libcuda1_352.79-10_amd64.deb ...  
 Unpacking libcuda1:amd64 (352.79-10) ...  
 Selecting previously unselected package libcuda1:i386.  
 Preparing to unpack .../libcuda1_352.79-10_i386.deb ...  
 Unpacking libcuda1:i386 (352.79-10) ...  
 Selecting previously unselected package libcuda1-i386:i386.  
 Preparing to unpack .../libcuda1-i386_352.79-10_i386.deb ...  
 Unpacking libcuda1-i386:i386 (352.79-10) ...  
 Selecting previously unselected package libnvcuvid1:amd64.  
 Preparing to unpack .../libnvcuvid1_352.79-10_amd64.deb ...  
 Unpacking libnvcuvid1:amd64 (352.79-10) ...  
 Selecting previously unselected package libnvidia-compiler:amd64.  
 Preparing to unpack .../libnvidia-compiler_352.79-10_amd64.deb ...  
 Unpacking libnvidia-compiler:amd64 (352.79-10) ...  
 Selecting previously unselected package libnvidia-ml1:i386.  
 Preparing to unpack .../libnvidia-ml1_352.79-10_i386.deb ...  
 Unpacking libnvidia-ml1:i386 (352.79-10) ...  
 Selecting previously unselected package libva-x11-1:i386.  
 Preparing to unpack .../libva-x11-1_1.7.1-2_i386.deb ...  
 Unpacking libva-x11-1:i386 (1.7.1-2) ...  
 Selecting previously unselected package libvdpau-dev:amd64.  
 Preparing to unpack .../libvdpau-dev_1.1.1-3_amd64.deb ...  
 Unpacking libvdpau-dev:amd64 (1.1.1-3) ...  
 Selecting previously unselected package libvdpau-va-gl1:i386.  
 Preparing to unpack .../libvdpau-va-gl1_0.4.0-2_i386.deb ...  
 Unpacking libvdpau-va-gl1:i386 (0.4.0-2) ...  
 Selecting previously unselected package mesa-vdpau-drivers:i386.  
 Preparing to unpack .../mesa-vdpau-drivers_11.2.2-1_i386.deb ...  
 Unpacking mesa-vdpau-drivers:i386 (11.2.2-1) ...  
 Selecting previously unselected package nvidia-opencl-common.  
 Preparing to unpack .../nvidia-opencl-common_352.79-10_amd64.deb ...  
 Unpacking nvidia-opencl-common (352.79-10) ...  
 Selecting previously unselected package nvidia-opencl-icd:amd64.  
 Preparing to unpack .../nvidia-opencl-icd_352.79-10_amd64.deb ...  
 Unpacking nvidia-opencl-icd:amd64 (352.79-10) ...  
 Selecting previously unselected package nvidia-smi:i386.  
 Preparing to unpack .../nvidia-smi_352.79-10_i386.deb ...  
 Unpacking nvidia-smi:i386 (352.79-10) ...  
 Selecting previously unselected package vdpau-driver-all:i386.  
 Preparing to unpack .../vdpau-driver-all_1.1.1-3_i386.deb ...  
 Unpacking vdpau-driver-all:i386 (1.1.1-3) ...  
 Selecting previously unselected package libcublas7.5:amd64.  
 Preparing to unpack .../libcublas7.5_7.5.18-3_amd64.deb ...  
 Unpacking libcublas7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libcudart7.5:amd64.  
 Preparing to unpack .../libcudart7.5_7.5.18-3_amd64.deb ...  
 Unpacking libcudart7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libcufft7.5:amd64.  
 Preparing to unpack .../libcufft7.5_7.5.18-3_amd64.deb ...  
 Unpacking libcufft7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libcufftw7.5:amd64.  
 Preparing to unpack .../libcufftw7.5_7.5.18-3_amd64.deb ...  
 Unpacking libcufftw7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libcuinj64-7.5:amd64.  
 Preparing to unpack .../libcuinj64-7.5_7.5.18-3_amd64.deb ...  
 Unpacking libcuinj64-7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libcurand7.5:amd64.  
 Preparing to unpack .../libcurand7.5_7.5.18-3_amd64.deb ...  
 Unpacking libcurand7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libcusolver7.5:amd64.  
 Preparing to unpack .../libcusolver7.5_7.5.18-3_amd64.deb ...  
 Unpacking libcusolver7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libcusparse7.5:amd64.  
 Preparing to unpack .../libcusparse7.5_7.5.18-3_amd64.deb ...  
 Unpacking libcusparse7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libnppc7.5:amd64.  
 Preparing to unpack .../libnppc7.5_7.5.18-3_amd64.deb ...  
 Unpacking libnppc7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libnppi7.5:amd64.  
 Preparing to unpack .../libnppi7.5_7.5.18-3_amd64.deb ...  
 Unpacking libnppi7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libnpps7.5:amd64.  
 Preparing to unpack .../libnpps7.5_7.5.18-3_amd64.deb ...  
 Unpacking libnpps7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libnvblas7.5:amd64.  
 Preparing to unpack .../libnvblas7.5_7.5.18-3_amd64.deb ...  
 Unpacking libnvblas7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libnvrtc7.5:amd64.  
 Preparing to unpack .../libnvrtc7.5_7.5.18-3_amd64.deb ...  
 Unpacking libnvrtc7.5:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libnvtoolsext1:amd64.  
 Preparing to unpack .../libnvtoolsext1_7.5.18-3_amd64.deb ...  
 Unpacking libnvtoolsext1:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libnvvm3:amd64.  
 Preparing to unpack .../libnvvm3_7.5.18-3_amd64.deb ...  
 Unpacking libnvvm3:amd64 (7.5.18-3) ...  
 Selecting previously unselected package libthrust-dev.  
 Preparing to unpack .../libthrust-dev_1.8.1-1_all.deb ...  
 Unpacking libthrust-dev (1.8.1-1) ...  
 Selecting previously unselected package nvidia-cuda-dev.  
 Preparing to unpack .../nvidia-cuda-dev_7.5.18-3_amd64.deb ...  
 Unpacking nvidia-cuda-dev (7.5.18-3) ...  
 Selecting previously unselected package nvidia-cuda-doc.  
 Preparing to unpack .../nvidia-cuda-doc_7.5.18-3_all.deb ...  
 Unpacking nvidia-cuda-doc (7.5.18-3) ...  
 Selecting previously unselected package nvidia-cuda-gdb.  
 Preparing to unpack .../nvidia-cuda-gdb_7.5.18-3_amd64.deb ...  
 Unpacking nvidia-cuda-gdb (7.5.18-3) ...  
 Selecting previously unselected package nvidia-profiler.  
 Preparing to unpack .../nvidia-profiler_7.5.18-3_amd64.deb ...  
 Unpacking nvidia-profiler (7.5.18-3) ...  
 Selecting previously unselected package opencl-headers.  
 Preparing to unpack .../opencl-headers_2.0~svn32091-2_all.deb ...  
 Unpacking opencl-headers (2.0~svn32091-2) ...  
 Selecting previously unselected package nvidia-opencl-dev:amd64.  
 Preparing to unpack .../nvidia-opencl-dev_7.5.18-3_amd64.deb ...  
 Unpacking nvidia-opencl-dev:amd64 (7.5.18-3) ...  
 Selecting previously unselected package nvidia-cuda-toolkit.  
 Preparing to unpack .../nvidia-cuda-toolkit_7.5.18-3_amd64.deb ...  
 Unpacking nvidia-cuda-toolkit (7.5.18-3) ...  
 Selecting previously unselected package nvidia-visual-profiler.  
 Preparing to unpack .../nvidia-visual-profiler_7.5.18-3_amd64.deb ...  
 Unpacking nvidia-visual-profiler (7.5.18-3) ...  
 Processing triggers for libc-bin (2.19-22) ...  
 Processing triggers for glx-alternative-nvidia (0.7.3) ...  
 Processing triggers for desktop-file-utils (0.23-1) ...  
 Processing triggers for gnome-menus (3.13.3-8) ...  
 Processing triggers for mime-support (3.60) ...  
 Processing triggers for man-db (2.7.5-1) ...  
 Processing triggers for update-glx (0.7.3) ...  
 Processing triggers for glx-alternative-nvidia (0.7.3) ...  
 update-alternatives: using /usr/lib/nvidia to provide /usr/lib/glx (glx) in auto mode  
 update-alternatives: warning: skip creation of /usr/lib/x86_64-linux-gnu/libEGL.so.1 because associated file /usr/lib/x86_64-linux-gnu/nvidia/libEGL.so.1 (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/lib/i386-linux-gnu/libGL.so.1 because associated file /usr/lib/i386-linux-gnu/nvidia/libGL.so.1 (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/lib/x86_64-linux-gnu/libGL.so.1 because associated file /usr/lib/x86_64-linux-gnu/nvidia/libGL.so.1 (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/lib/x86_64-linux-gnu/libGLESv1_CM.so.1 because associated file /usr/lib/x86_64-linux-gnu/nvidia/libGLESv1_CM.so.1 (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/lib/x86_64-linux-gnu/libGLESv2.so.2 because associated file /usr/lib/x86_64-linux-gnu/nvidia/libGLESv2.so.2 (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/lib/i386-linux-gnu/libnvidia-cfg.so.1 because associated file /usr/lib/i386-linux-gnu/nvidia/libnvidia-cfg.so.1 (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/lib/x86_64-linux-gnu/libnvidia-cfg.so.1 because associated file /usr/lib/x86_64-linux-gnu/nvidia/libnvidia-cfg.so.1 (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/lib/xorg/modules/linux/libglx.so because associated file /usr/lib/nvidia/libglx.so (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /etc/modprobe.d/nvidia-blacklists-nouveau.conf because associated file /etc/nvidia/nvidia-blacklists-nouveau.conf (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/bin/nvidia-bug-report.sh because associated file /usr/lib/nvidia/nvidia-bug-report.sh (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/share/X11/xorg.conf.d/nvidia-drm-outputclass.conf because associated file /etc/nvidia/nvidia-drm-outputclass.conf (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /etc/modules-load.d/nvidia.conf because associated file /etc/nvidia/nvidia-load.conf (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /etc/modprobe.d/nvidia.conf because associated file /etc/nvidia/nvidia-modprobe.conf (of link group glx) doesn't exist  
 update-alternatives: warning: skip creation of /usr/lib/xorg/modules/drivers/nvidia_drv.so because associated file /usr/lib/nvidia/nvidia_drv.so (of link group glx) doesn't exist  
 update-alternatives: using /usr/lib/mesa-diverted to provide /usr/lib/glx (glx) in auto mode  
 Processing triggers for libc-bin (2.19-22) ...  
 Processing triggers for initramfs-tools (0.120) ...  
 update-initramfs: Generating /boot/initrd.img-4.6.0-1-amd64  
 Processing triggers for bumblebee (3.2.1-13) ...  
 Setting up nvidia-alternative (352.79-10) ...  
 Setting up libnvidia-eglcore:amd64 (352.79-10) ...  
 Setting up libnvidia-glcore:amd64 (352.79-10) ...  
 Setting up libnvidia-glcore:i386 (352.79-10) ...  
 Setting up libvdpau1:amd64 (1.1.1-3) ...  
 Setting up libvdpau1:i386 (1.1.1-3) ...  
 Setting up libnvidia-compiler:amd64 (352.79-10) ...  
 Setting up libva-x11-1:i386 (1.7.1-2) ...  
 Setting up libvdpau-dev:amd64 (1.1.1-3) ...  
 Setting up libvdpau-va-gl1:i386 (0.4.0-2) ...  
 Setting up mesa-vdpau-drivers:i386 (11.2.2-1) ...  
 Setting up nvidia-opencl-common (352.79-10) ...  
 Setting up vdpau-driver-all:i386 (1.1.1-3) ...  
 Setting up libcublas7.5:amd64 (7.5.18-3) ...  
 Setting up libcudart7.5:amd64 (7.5.18-3) ...  
 Setting up libcufft7.5:amd64 (7.5.18-3) ...  
 Setting up libcufftw7.5:amd64 (7.5.18-3) ...  
 Setting up libcurand7.5:amd64 (7.5.18-3) ...  
 Setting up libcusolver7.5:amd64 (7.5.18-3) ...  
 Setting up libcusparse7.5:amd64 (7.5.18-3) ...  
 Setting up libnppc7.5:amd64 (7.5.18-3) ...  
 Setting up libnppi7.5:amd64 (7.5.18-3) ...  
 Setting up libnpps7.5:amd64 (7.5.18-3) ...  
 Setting up libnvblas7.5:amd64 (7.5.18-3) ...  
 Setting up libnvrtc7.5:amd64 (7.5.18-3) ...  
 Setting up libnvtoolsext1:amd64 (7.5.18-3) ...  
 Setting up libnvvm3:amd64 (7.5.18-3) ...  
 Setting up libthrust-dev (1.8.1-1) ...  
 Setting up nvidia-cuda-doc (7.5.18-3) ...  
 Setting up nvidia-cuda-gdb (7.5.18-3) ...  
 Setting up opencl-headers (2.0~svn32091-2) ...  
 Setting up nvidia-opencl-dev:amd64 (7.5.18-3) ...  
 Processing triggers for nvidia-alternative (352.79-10) ...  
 update-alternatives: using /usr/lib/nvidia/current to provide /usr/lib/nvidia/nvidia (nvidia) in auto mode  
 Setting up libgles2-nvidia:amd64 (352.79-10) ...  
 Setting up libgles1-nvidia:amd64 (352.79-10) ...  
 Setting up libgl1-nvidia-glx:amd64 (352.79-10) ...  
 Setting up libgl1-nvidia-glx:i386 (352.79-10) ...  
 Setting up libegl1-nvidia:amd64 (352.79-10) ...  
 Setting up nvidia-driver-libs:amd64 (352.79-10) ...  
 Setting up libnvidia-ml1:amd64 (352.79-10) ...  
 Setting up libnvidia-ml1:i386 (352.79-10) ...  
 Setting up nvidia-driver-bin (352.79-10) ...  
 Setting up xserver-xorg-video-nvidia (352.79-10) ...  
 Setting up nvidia-vdpau-driver:amd64 (352.79-10) ...  
 Setting up nvidia-driver (352.79-10) ...  
 Setting up nvidia-kernel-support (352.79-10) ...  
 Setting up libcuda1:amd64 (352.79-10) ...  
 Setting up libcuda1:i386 (352.79-10) ...  
 Setting up libcuda1-i386:i386 (352.79-10) ...  
 Setting up libnvcuvid1:amd64 (352.79-10) ...  
 Setting up nvidia-opencl-icd:amd64 (352.79-10) ...  
 Setting up nvidia-smi:i386 (352.79-10) ...  
 Setting up libcuinj64-7.5:amd64 (7.5.18-3) ...  
 Setting up nvidia-cuda-dev (7.5.18-3) ...  
 Setting up nvidia-profiler (7.5.18-3) ...  
 Setting up nvidia-cuda-toolkit (7.5.18-3) ...  
 Setting up nvidia-visual-profiler (7.5.18-3) ...  
 Processing triggers for libc-bin (2.19-22) ...  
 Processing triggers for glx-alternative-nvidia (0.7.3) ...  
 Processing triggers for update-glx (0.7.3) ...  
 Processing triggers for glx-alternative-nvidia (0.7.3) ...  
 update-alternatives: using /usr/lib/nvidia to provide /usr/lib/glx (glx) in auto mode  
 update-alternatives: using /usr/lib/nvidia/bumblebee to provide /usr/lib/glx (glx) in auto mode  
 Processing triggers for libc-bin (2.19-22) ...  
 Processing triggers for initramfs-tools (0.120) ...  
 update-initramfs: Generating /boot/initrd.img-4.6.0-1-amd64  
 Processing triggers for bumblebee (3.2.1-13) ...  

Let's run the make command again.

 user@localhost:~/Desktop/gpuqsortlib$ make  
 nvcc -O3 -I/common/inc -Xcompiler -fPIC -Iinc -c src/gpuqsort.cu -o gpuqsort.o  
 src/gpuqsort.cu(429): warning: conversion from a string literal to "char *" is deprecated  
   
 src/gpuqsort.cu(429): warning: conversion from a string literal to "char *" is deprecated  
   
 mkdir -p lib/linux/static  
 mkdir -p lib/linux/shared  
 nvcc -o lib/linux/static/libgpuqsort.a -lib gpuqsort.o  
 nvcc -o lib/linux/shared/libgpuqsort.so -shared gpuqsort.o  
 gcc -O3 -Iinc -c testbench/main.cpp -o main.o  
 testbench/main.cpp:33:21: fatal error: sqlite3.h: No such file or directory  
  #include "sqlite3.h"  
            ^  
 compilation terminated.  
 Makefile:22: recipe for target 'main.o' failed  
 make: *** [main.o] Error 1  

So sqlite3 header is not install, you can comment out define HASSQLITE3 in testbench/defs.h or install it. For me, I have install it

 user@localhost:~/Desktop/gpuqsortlib$ sudo apt-get install libsqlite3-dev  
 Reading package lists... Done  
 Building dependency tree      
 Reading state information... Done  
 The following packages were automatically installed and are no longer required:  
  libgl1-nvidia-glx:i386 libgl1-nvidia-glx-i386:i386 libllvm3.5v5 libnvidia-glcore:i386 linux-image-4.1.0-2-amd64 linux-image-4.2.0-1-amd64 linux-source-4.3 python3-ecdsa syslinux  
  unetbootin-translations  
 Use 'sudo apt autoremove' to remove them.  
 Suggested packages:  
  sqlite3-doc  
 The following NEW packages will be installed:  
  libsqlite3-dev  
 0 upgraded, 1 newly installed, 0 to remove and 510 not upgraded.  
 Need to get 689 kB of archives.  
 After this operation, 2,041 kB of additional disk space will be used.  
 Get:1 http://ftp.us.debian.org/debian testing/main amd64 libsqlite3-dev amd64 3.14.1-1 [689 kB]  
 Fetched 689 kB in 2s (256 kB/s)             
 Selecting previously unselected package libsqlite3-dev:amd64.  
 (Reading database ... 280685 files and directories currently installed.)  
 Preparing to unpack .../libsqlite3-dev_3.14.1-1_amd64.deb ...  
 Unpacking libsqlite3-dev:amd64 (3.14.1-1) ...  
 Setting up libsqlite3-dev:amd64 (3.14.1-1) ...  
   

and try again.

 user@localhost:~/Desktop/gpuqsortlib$ make  
 mkdir -p lib/linux/static  
 mkdir -p lib/linux/shared  
 nvcc -o lib/linux/static/libgpuqsort.a -lib gpuqsort.o  
 nvcc -o lib/linux/shared/libgpuqsort.so -shared gpuqsort.o  
 mkdir -p bin/linux  
 nvcc -o bin/linux/testbench main.o dists.o -lgpuqsort -lglut -L./lib/linux/static -lsqlite3  
 /usr/bin/ld: cannot find -lglut  
 collect2: error: ld returned 1 exit status  
 Makefile:15: recipe for target 'testbench' failed  
 make: *** [testbench] Error 1  
 user@localhost:~/Desktop/gpuqsortlib$ nvcc --version  
 nvcc: NVIDIA (R) Cuda compiler driver  
 Copyright (c) 2005-2015 NVIDIA Corporation  
 Built on Tue_Aug_11_14:27:32_CDT_2015  
 Cuda compilation tools, release 7.5, V7.5.17  

so the library glut (opengl utility toolkit) is not install,

 $ sudo apt-get install freeglut3-dev  
 Reading package lists... Done  
 Building dependency tree      
 Reading state information... Done  
 The following packages were automatically installed and are no longer required:  
  libgl1-nvidia-glx:i386 libgl1-nvidia-glx-i386:i386 libllvm3.5v5 libnvidia-glcore:i386 linux-image-4.1.0-2-amd64 linux-image-4.2.0-1-amd64 linux-source-4.3 python3-ecdsa syslinux  
  unetbootin-translations  
 Use 'sudo apt autoremove' to remove them.  
 The following additional packages will be installed:  
  freeglut3 libice-dev libsm-dev libxt-dev  
 Suggested packages:  
  libice-doc libsm-doc libxt-doc  
 The following NEW packages will be installed:  
  freeglut3 freeglut3-dev libice-dev libsm-dev libxt-dev  
 0 upgraded, 5 newly installed, 0 to remove and 510 not upgraded.  
 Need to get 826 kB of archives.  
 After this operation, 2,941 kB of additional disk space will be used.  
 Do you want to continue? [Y/n] Y  
 Get:1 http://ftp.us.debian.org/debian testing/main amd64 freeglut3 amd64 2.8.1-2 [124 kB]  
 Get:2 http://ftp.us.debian.org/debian testing/main amd64 libice-dev amd64 2:1.0.9-1+b1 [66.3 kB]  
 Get:3 http://ftp.us.debian.org/debian testing/main amd64 libsm-dev amd64 2:1.2.2-1+b1 [35.8 kB]  
 Get:4 http://ftp.us.debian.org/debian testing/main amd64 libxt-dev amd64 1:1.1.5-1 [423 kB]  
 Get:5 http://ftp.us.debian.org/debian testing/main amd64 freeglut3-dev amd64 2.8.1-2 [177 kB]  
 Fetched 826 kB in 2s (373 kB/s)      
 Selecting previously unselected package freeglut3:amd64.  
 (Reading database ... 280696 files and directories currently installed.)  
 Preparing to unpack .../freeglut3_2.8.1-2_amd64.deb ...  
 Unpacking freeglut3:amd64 (2.8.1-2) ...  
 Selecting previously unselected package libice-dev:amd64.  
 Preparing to unpack .../libice-dev_2%3a1.0.9-1+b1_amd64.deb ...  
 Unpacking libice-dev:amd64 (2:1.0.9-1+b1) ...  
 Selecting previously unselected package libsm-dev:amd64.  
 Preparing to unpack .../libsm-dev_2%3a1.2.2-1+b1_amd64.deb ...  
 Unpacking libsm-dev:amd64 (2:1.2.2-1+b1) ...  
 Selecting previously unselected package libxt-dev:amd64.  
 Preparing to unpack .../libxt-dev_1%3a1.1.5-1_amd64.deb ...  
 Unpacking libxt-dev:amd64 (1:1.1.5-1) ...  
 Selecting previously unselected package freeglut3-dev:amd64.  
 Preparing to unpack .../freeglut3-dev_2.8.1-2_amd64.deb ...  
 Unpacking freeglut3-dev:amd64 (2.8.1-2) ...  
 Processing triggers for man-db (2.7.5-1) ...  
 Setting up freeglut3:amd64 (2.8.1-2) ...  
 Setting up libice-dev:amd64 (2:1.0.9-1+b1) ...  
 Setting up libsm-dev:amd64 (2:1.2.2-1+b1) ...  
 Setting up libxt-dev:amd64 (1:1.1.5-1) ...  
 Setting up freeglut3-dev:amd64 (2.8.1-2) ...  
 Processing triggers for libc-bin (2.19-22) ...  

and one more try!

 user@localhost:~/Desktop/gpuqsortlib$ make  
 mkdir -p lib/linux/static  
 mkdir -p lib/linux/shared  
 nvcc -o lib/linux/static/libgpuqsort.a -lib gpuqsort.o  
 nvcc -o lib/linux/shared/libgpuqsort.so -shared gpuqsort.o  
 mkdir -p bin/linux  
 nvcc -o bin/linux/testbench main.o dists.o -lgpuqsort -lglut -L./lib/linux/static -lsqlite3  
 jason@JasonLaptop:~/Desktop/gpuqsortlib$ ./bin/linux/testbench   
   
 Usage:  
    testbench -[m|d|p] uniqueid  
 jason@JasonLaptop:~/Desktop/gpuqsortlib$ ./bin/linux/testbench -m 1  
 Testing 'models'  
 Unable to open file: norm-dragon.dat  

so finally got it compile and run fine.... but looks like there is no input sample file available! If you got beyond this point, leave your comment below and I would like to run on my workstation gpu too!

I have upload source code and compile code here.

investigate into apache cassandra 1.2.19 sstable corrupt

Last, I have investigated in apache cassandra 1.0.8 sstable corruption a fresh node after upgraded to apache cassandra 1.2. Both of the articles can be found here and here. Today, we will take another look at a running apache cassandra 1.2.19 encounter sstable corruption. Below is the stack trace found in cassandra system.log

 org.apache.cassandra.io.sstable.CorruptSSTableException: org.apache.cassandra.io.compress.CorruptBlockException: (/var/lib/cassandra/data/<KEYSPACE>/<COLUMN_FAMILY>/<KEYSPACE>-<CF>-ic-112-Data.db): corruption detected, chunk at 19042661 of length 27265.  
     at org.apache.cassandra.io.compress.CompressedRandomAccessReader.reBuffer(CompressedRandomAccessReader.java:89)  
     at org.apache.cassandra.io.compress.CompressedThrottledReader.reBuffer(CompressedThrottledReader.java:45)  
     at org.apache.cassandra.io.util.RandomAccessReader.read(RandomAccessReader.java:355)  
     at java.io.RandomAccessFile.readFully(RandomAccessFile.java:444)  
     at java.io.RandomAccessFile.readFully(RandomAccessFile.java:424)  
     at org.apache.cassandra.io.util.RandomAccessReader.readBytes(RandomAccessReader.java:380)  
     at org.apache.cassandra.utils.ByteBufferUtil.read(ByteBufferUtil.java:391)  
     at org.apache.cassandra.utils.ByteBufferUtil.readWithShortLength(ByteBufferUtil.java:370)  
     at org.apache.cassandra.io.sstable.SSTableScanner$KeyScanningIterator.next(SSTableScanner.java:175)  
     at org.apache.cassandra.io.sstable.SSTableScanner$KeyScanningIterator.next(SSTableScanner.java:155)  
     at org.apache.cassandra.io.sstable.SSTableScanner.next(SSTableScanner.java:142)  
     at org.apache.cassandra.io.sstable.SSTableScanner.next(SSTableScanner.java:38)  
     at org.apache.cassandra.utils.MergeIterator$Candidate.advance(MergeIterator.java:145)  
     at org.apache.cassandra.utils.MergeIterator$ManyToOne.advance(MergeIterator.java:122)  
     at org.apache.cassandra.utils.MergeIterator$ManyToOne.computeNext(MergeIterator.java:96)  
     at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)  
     at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)  
     at org.apache.cassandra.db.compaction.CompactionTask.runWith(CompactionTask.java:145)  
     at org.apache.cassandra.io.util.DiskAwareRunnable.runMayThrow(DiskAwareRunnable.java:48)  
     at org.apache.cassandra.utils.WrappedRunnable.run(WrappedRunnable.java:28)  
     at org.apache.cassandra.db.compaction.CompactionTask.executeInternal(CompactionTask.java:58)  
     at org.apache.cassandra.db.compaction.AbstractCompactionTask.execute(AbstractCompactionTask.java:60)  
     at org.apache.cassandra.db.compaction.CompactionManager$BackgroundCompactionTask.run(CompactionManager.java:208)  
     at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)  
     at java.util.concurrent.FutureTask.run(FutureTask.java:262)  
     at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)  
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)  
     at java.lang.Thread.run(Thread.java:745)  
 Caused by: org.apache.cassandra.io.compress.CorruptBlockException: (/var/lib/cassandra/data/<KEYSPACE>/<COLUMN_FAMILY>/<KEYSPACE>-<CF>-ic-112-Data.db): corruption detected, chunk at 19042661 of length 27265.  
     at org.apache.cassandra.io.compress.CompressedRandomAccessReader.decompressChunk(CompressedRandomAccessReader.java:128)  
     at org.apache.cassandra.io.compress.CompressedRandomAccessReader.reBuffer(CompressedRandomAccessReader.java:85)  
     ... 27 more  

Okay, let's trace into the stacktrace and study what actually cause this and what is sstable corruption means.

     at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)  
     at java.util.concurrent.FutureTask.run(FutureTask.java:262)  
     at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)  
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)  
     at java.lang.Thread.run(Thread.java:745)      

Simple, a thread is run by the executor.

     at org.apache.cassandra.db.compaction.CompactionTask.runWith(CompactionTask.java:145)  
     at org.apache.cassandra.io.util.DiskAwareRunnable.runMayThrow(DiskAwareRunnable.java:48)  
     at org.apache.cassandra.utils.WrappedRunnable.run(WrappedRunnable.java:28)  
     at org.apache.cassandra.db.compaction.CompactionTask.executeInternal(CompactionTask.java:58)  
     at org.apache.cassandra.db.compaction.AbstractCompactionTask.execute(AbstractCompactionTask.java:60)  
     at org.apache.cassandra.db.compaction.CompactionManager$BackgroundCompactionTask.run(CompactionManager.java:208)  

We see that a background compaction task is started. Code below.

   // the actual sstables to compact are not determined until we run the BCT; that way, if new sstables  
   // are created between task submission and execution, we execute against the most up-to-date information  
   class BackgroundCompactionTask implements Runnable  
   {  
     private final ColumnFamilyStore cfs;  
   
     BackgroundCompactionTask(ColumnFamilyStore cfs)  
     {  
       this.cfs = cfs;  
     }  
   
     public void run()  
     {  
       compactionLock.readLock().lock();  
       try  
       {  
         logger.debug("Checking {}.{}", cfs.table.name, cfs.columnFamily); // log after we get the lock so we can see delays from that if any  
         if (!cfs.isValid())  
         {  
           logger.debug("Aborting compaction for dropped CF");  
           return;  
         }  
   
         AbstractCompactionStrategy strategy = cfs.getCompactionStrategy();  
         AbstractCompactionTask task = strategy.getNextBackgroundTask(getDefaultGcBefore(cfs));  
         if (task == null)  
         {  
           logger.debug("No tasks available");  
           return;  
         }  
         task.execute(metrics);  
       }  
       finally  
       {  
         compactingCF.remove(cfs);  
         compactionLock.readLock().unlock();  
       }  
       submitBackground(cfs);  
     }  
   }  

     at org.apache.cassandra.utils.MergeIterator$Candidate.advance(MergeIterator.java:145)  
     at org.apache.cassandra.utils.MergeIterator$ManyToOne.advance(MergeIterator.java:122)  
     at org.apache.cassandra.utils.MergeIterator$ManyToOne.computeNext(MergeIterator.java:96)  
     at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)  
     at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)  

Here we see an iterator going over the sstables for compaction.

     at org.apache.cassandra.io.sstable.SSTableScanner$KeyScanningIterator.next(SSTableScanner.java:175)  
     at org.apache.cassandra.io.sstable.SSTableScanner$KeyScanningIterator.next(SSTableScanner.java:155)  
     at org.apache.cassandra.io.sstable.SSTableScanner.next(SSTableScanner.java:142)  
     at org.apache.cassandra.io.sstable.SSTableScanner.next(SSTableScanner.java:38)  

DecoratedKey key = sstable.decodeKey(ByteBufferUtil.readWithShortLength(dfile));

     
Here we see that what actually get iterated is the sstable and particular on the key.

     at org.apache.cassandra.io.compress.CompressedRandomAccessReader.reBuffer(CompressedRandomAccessReader.java:89)  
     at org.apache.cassandra.io.compress.CompressedThrottledReader.reBuffer(CompressedThrottledReader.java:45)  
     at org.apache.cassandra.io.util.RandomAccessReader.read(RandomAccessReader.java:355)  
     at java.io.RandomAccessFile.readFully(RandomAccessFile.java:444)  
     at java.io.RandomAccessFile.readFully(RandomAccessFile.java:424)  
     at org.apache.cassandra.io.util.RandomAccessReader.readBytes(RandomAccessReader.java:380)  
     at org.apache.cassandra.utils.ByteBufferUtil.read(ByteBufferUtil.java:391)  
     at org.apache.cassandra.utils.ByteBufferUtil.readWithShortLength(ByteBufferUtil.java:370)  

Here, there is code reference has change in a few files due to method override, nonetheless, the important part on method reBuffer.

   @Override  
   protected void reBuffer()  
   {  
     try  
     {  
       decompressChunk(metadata.chunkFor(current));  
     }  
     catch (CorruptBlockException e)  
     {  
       throw new CorruptSSTableException(e, getPath());  
     }  
     catch (IOException e)  
     {  
       throw new FSReadError(e, getPath());  
     }  
   }  
     
   private void decompressChunk(CompressionMetadata.Chunk chunk) throws IOException  
   {  
     if (channel.position() != chunk.offset)  
       channel.position(chunk.offset);  
   
     if (compressed.capacity() < chunk.length)  
       compressed = ByteBuffer.wrap(new byte[chunk.length]);  
     else  
       compressed.clear();  
     compressed.limit(chunk.length);  
   
     if (channel.read(compressed) != chunk.length)  
       throw new CorruptBlockException(getPath(), chunk);  
   
     // technically flip() is unnecessary since all the remaining work uses the raw array, but if that changes  
     // in the future this will save a lot of hair-pulling  
     compressed.flip();  
     try  
     {  
       validBufferBytes = metadata.compressor().uncompress(compressed.array(), 0, chunk.length, buffer, 0);  
     }  
     catch (IOException e)  
     {  
       throw new CorruptBlockException(getPath(), chunk);  
     }  
   
     if (metadata.parameters.getCrcCheckChance() > FBUtilities.threadLocalRandom().nextDouble())  
     {  
       checksum.update(buffer, 0, validBufferBytes);  
   
       if (checksum(chunk) != (int) checksum.getValue())  
         throw new CorruptBlockException(getPath(), chunk);  
   
       // reset checksum object back to the original (blank) state  
       checksum.reset();  
     }  
   
     // buffer offset is always aligned  
     bufferOffset = current & ~(buffer.length - 1);  
   }  

we read that if chunk checksum is not the same as the updated crc32 checksum, this is consider sstable corruption.

For this type of exception, I remember I did many things such as below.

1. try online nodetool scrub, does not work
2. try offline sstablescrub, does not work.
3. wipeout the node and rebuild again, does not work.

we had to change the hardware altogether. Then we don't see the problem anymore.

Brief go through fuglu a mail scanner daemon

This is way long overdue that I promised to write a blog for a good dear friend on his python mail scanner daemon. And today, finally got my spare time to review Fuglu. First, what is Fuglu?

Fuglu is a mail scanner daemon written in Python. Installed as a postfix before-queue or after-queue filter fuglu can be used to filter spam, viruses, unwanted attachments etc.

As I'm not a mail admin, so this article will skip some mail related features. Let's install fuglu by cloning from the github repository.

 $ git clone https://github.com/gryphius/fuglu.git  
 $ cd fuglu/fuglu  
 $ sudo python setup.py install  

If the installation is successful, then we go to the basic configuration. Running fuglu --lint

 root@localhost:/etc/fuglu# fuglu --lint  
 Could not drop privileges to nobody/nobody : Can not drop privileges, user nobody or group nobody does not exist  
 Fuglu 0.6.6-2-ge18e56b  
 ---------- LINT MODE ----------  
 Checking dependencies...  
 sqlalchemy: not installed Optional dependency, required if you want to enable any database lookups  
 BeautifulSoup: V4 installed  
 magic: not installed Optional dependency, without python-file or python-magic the attachment plugin's automatic file type detection will easily be fooled  
 Loading extensions...  
 fuglu.extensions.sql: disabled (sqlalchemy not installed)  
 Loading plugins...  
 Plugin loading complete  
 Linting main configuration  
 OK  
   
 Linting Plugin Archive Config section: ArchivePlugin  
 SuspectFilter file not found: /etc/fuglu/archive.regex  
 ERROR  
   
 Linting Plugin Attachment Blocker Config section: FiletypePlugin  
 python libmagic bindings (python-file or python-magic) not available. Will only do content-type checks, no real file analysis  
 ERROR  
   
 Linting Plugin Debugger Config section: debug  
 OK  
   
 Linting Plugin Plugin Skipper Config section: PluginSkipper  
 SuspectFilter file not found: /etc/fuglu/skipplugins.regex  
 ERROR  
 3 plugins reported errors.  
   
 WARNING:  
 Skipping logging configuration check because I could not switch to user 'nobody' earlier.  
 please re-run fuglu --lint as privileged user  
 (problems in the logging configuration could prevent the fuglu daemon from starting up)  
 root@localhost:/etc/fuglu#  

You should really fix the above lint error before continue to get a good setup for the incoming features. The solution is different for each lint error output above but for mine, I did the following.

 root@localhost:/etc/fuglu# cp archive.regex.dist archive.regex  
 root@localhost:/etc/fuglu# cp fuglu_mrtg.cfg.dist fuglu_mrtg.cfg  
 root@localhost:/etc/fuglu# cp logging.conf.dist logging.conf  
 root@localhost:/etc/fuglu# cp skipplugins.regex.dist skipplugins.regex  
 root@localhost:/etc/fuglu# apt-get install python-sqlalchemy python-magic   
 root@localhost:/etc/fuglu# groupadd nobody  

Run again the fuglu lint command

 root@localhost:/etc/fuglu# fuglu --lint  
 Fuglu 0.6.6-2-ge18e56b  
 ---------- LINT MODE ----------  
 Checking dependencies...  
 sqlalchemy: installed  
 BeautifulSoup: V4 installed  
 magic: found python-file/libmagic bindings (http://www.darwinsys.com/file/)  
 Loading extensions...  
 fuglu.extensions.sql: enabled (available)  
 Loading plugins...  
 Plugin loading complete  
 Linting main configuration  
 OK  
   
 Linting Plugin Archive Config section: ArchivePlugin  
 OK  
   
 Linting Plugin Attachment Blocker Config section: FiletypePlugin  
 Found python-file/libmagic bindings (http://www.darwinsys.com/file/)  
 No database configured. Using per user/domain file configuration from /etc/fuglu/rules  
 rarfile library not found, RAR support disabled  
 Archive scan, available file extensions: ['z', 'zip']  
 OK  
   
 Linting Plugin Debugger Config section: debug  
 OK  
   
 Linting Plugin Plugin Skipper Config section: PluginSkipper  
 OK  
 0 plugins reported errors.  
   
 Checking logging configuration....  
 OK  

Perfect! Everything is OK. We are ready to move on. As for fuglu postfix configuration, you can refer here.This I will skip for the aforementioned reason. To start fuglu, just run the command fuglu and fuglu will run in the background. Give -f if you want to quickly test it.

 root@localhost:~# fuglu  
 root@localhost:~#   
 root@localhost:~# tail -F /var/log/fuglu/fuglu.log  
 2016-06-23 20:44:15,178 root    : INFO FuGLU Version 0.6.6-2-ge18e56b starting up  
 2016-06-23 20:44:15,289 fuglu.MainController: INFO Init Stat Engine  
 2016-06-23 20:44:15,290 fuglu.MainController: INFO Init Threadpool  
 2016-06-23 20:44:15,290 fuglu.MainController: INFO Starting interface sockets...  
 2016-06-23 20:44:15,291 fuglu.MainController: INFO starting connector smtp/10025  
 2016-06-23 20:44:15,291 fuglu.incoming.10025: INFO SMTP (After Queue) Server running on port 10025  
 2016-06-23 20:44:15,291 fuglu.MainController: INFO starting connector smtp/10099  
 2016-06-23 20:44:15,292 fuglu.incoming.10099: INFO SMTP (After Queue) Server running on port 10099  
 2016-06-23 20:44:15,292 fuglu.MainController: INFO starting connector smtp/10888  
 2016-06-23 20:44:15,292 fuglu.incoming.10888: INFO SMTP (After Queue) Server running on port 10888  
 2016-06-23 20:44:15,293 fuglu.control.fuglu_control.sock: INFO Control/Info Server running on port /tmp/fuglu_control.sock  
 2016-06-23 20:44:15,293 fuglu.MainController: INFO Startup complete  

Started okay. Now let us print out some fuglu status.

 $ sudo fuglu_control stats  
 Fuglu statistics  
 ---------------  
 Uptime:          0:00:20.218391  
 Avg scan time:     0  
 Total msgs:     0  
 Ham:          0  
 Spam:          0  
 Virus:          0  
   
   
 $ sudo fuglu_control workerlist  
 Total 2 Threads  
   
 [1]: waiting for task  
 *******  
 [2]: waiting for task  

The response is fast and yet the statistics are simple to understand. If you are a mail admin, I suggest you also setup fuglu so that statistics can be plotted into mrtg. Fuglu comes support with mrtg natively, you can find out how here.

To take a step further, mail admin should really read on the plugin page. It contains all various goodies you will required and if you want more, you can actually write your plugin and integrate to fuglu. You can read it here as the example given on how to write the plugin.

Last but not least, if you have question, you can reach the author in many different medium. You can find it here.

If you are mail admin, consider fuglu your mail scanner daemon!

Sharing thoughts on article 'Agile Vs. Lean: Yeah Yeah, What’s the Difference?'

In this article, I took a bit different writing than the usual coverage on software technology. Today, as I read an article about the different between lean and agile, some points really need extra explanation. I felt compel and need to complement the original article as some non I.T. staff may not really understand.

2. Build Quality In
4. Defer Commitment
5. Deliver Fast

Many especially the management and sales department has NO idea about these three points (other than just we want it now or yesterday). Well yea, in this article, it came with priority listed as 2, 4 and then 5. But really in actual software house, how to achieve this whilst make the non I.T. staff in company understand. In my opinion, there is no immediate unless the software is ready. Development software is a iteration process and hence, that takes time. A software that without quality, that is without going through testing (manual or auto) is something that cannot be profitable. IMO, during scrum stand up meeting, there could be a lot of things discussed and to deliver on the spot is something extremely impractical. I think to defer such commitment to a later date and time will give positive result. That is, individual has the time to think, work and prepare rather than just bullshit just to answer that point 'deliver fast'. In order to achieve quality in software and to deliver fast, an automated tests is the only path to choose. Because of that, a quality end product can be achievable. If you are in software company, you should know this need time to accomplish.

6. Respect People

In a house, we have elder and youngster, in a company, we have different charts of ranking and in a country, we have different society in various lifestyle. But in a company, there are some companies really practice ranking habit and worst some promised flat organization but in actual day to day working style, show sign of ranking practice. IMO, in order to respect people, and to actually do it in line with what promised, ranking/position MUST be abolished. In order to respect people, there should not be ranking in principal or in practical. By respecting people and by removed ranking, only then a team can formed. If you have never feel what's a team like, please contact me.

Eliminating waste means eliminating useless meetings, tasks and documentation. 

Countless this I have heard before during my past working life or from word of mouth from friends. I'm sure you have heard something like, "oh i have meeting from 9 to 11 and afternoon 2 to 4. Although I never discount the importance of a meeting, don't get me wrong, I have no ill wrong concept toward meeting, but a meeting should be concise and agenda oriented. A meeting should be a place where people discuss on a predefined topic and some questions which cannot solve over other communication channel.

It also means eliminating inefficient ways of working – like multitasking (!) – so we can deliver fast.

Seriously, to adapt computer multitask into human imho is just stupid. Rather than a staff that produced many things without quality, I choose a staff which is focused on the work and produced the work on time with quality. But really, look at Malaysia companies, how many really understand the actual multitasking definition and how they adapt the change necessary when things does not work in actual practical working life?

For example, many managers want to “optimize” individual developers by ensuring they’re always at 100% – but most of the time, this is actually counter-productive. Let’s not have people coding something that isn’t needed (or fully defined yet) just for the sake of coding, because that actually creates more work for us in the future 

Generally I agree to this statement but should be a spare time, either this spare time can be used privately by the team to do something fun (games/hobby) or better yet, code something that can keep their mind sharp. There are many sites that provide this facilities such as hackerrank and StackOverflow when you can answer questions which really beneficial to the company and the individual itself. It's a win win situation really.

Along those lines, Lean says to respect that the people doing the work are the ones that best know how to do it. Give them what they need to be effective and then trust them to do it. Software development is about learning, so structure the work to ensure we’re continuously learning. 

Countless times I see before how the manager and/or senior interrupt coder/programmer when they are actively solving problem. There are many problems come to this. First, when a programmer actively solving problem, an interrupt even 5 minutes will take away something programmer might forget later. Second, continuous interruptions means programmer cannot concentrate fully on their work and thus damage the company as a whole. It become worst if only programmer know how to code but not the manager or the management staff. There are numerous more to justify but enough to say that, to empower and to trust a staff to do what they are supposed to do, can produce many positive outcome. Even when a feature/bug fix screw up, it should be a journey of learning experience and the staff should inform accordingly and the manager/management should protect as a whole. This is one classic yet typical example you can hardly find. Remember, a trust is earn and build over time, it will collapse immediate if it is not fix.

3. Frequent delivery of software

continuous delivery of software in actually means, coder added feature or fix a problem where the changes get commit into a software repository, sufficient coverage are done, build is okay and deliver to customer right after. But for a small company house, if any parts of the aforementioned did not do it properly, it only bring disaster. Trust me, I have seen this shit. It's better to understand self and adapt adequately than to pursue whatever out technology out there.

6. Face-to-face conversation is best

Not necessary, I have been in voice communication for years and I think voice communication work best. Why? because software progress normally require reference on work that they do. Text communication is even more vital than voice communication but they do serve complement to each other. Think of it, you don't need to look at your partner face to discuss things. However, you both require to look at the codes and discussed problem. We need to read the code at display and listen to understand problem at hand but not looking at each other. ;)

12. Regular reflection & adaptation

I agree regular reflection and changes are important. This also served a time when everyone can sit (or stand?) to listen and learn from each other. This is something seldom companies practice. This is another recipe to form toward a great team too. In essence, reflection and adaptation is something that should not be miss.


Last but not least, all these software development methodologies might work in company A or company B fully but that does not mean company like you should blindly follow. But if you are startup and have no clue, it is best to learn from this, to serve as a guide and improve and self reflect along the way. Most importantly, to form a team is more important than anything else.

angelhack kuala lumpur 2016

Coding is something I have passion about and if you have been following me in my blog, you should know most of the article are big data technologies related. Two weeks ago as of this write up, a professor from MMU Malaysia asking me if I would like to join on his team on a hackathon event which held at the city centre in a mall, times square.

I took a look at the events which can be found here and here. To my astonishment it is a paid coding event which the currency operated at united state dollar even though we are in Malaysia. As this is something that I have never done before, that is, go to physical location and start to code for a project to compete against each other is one of my decisive factors and of cause, to know who are in the local development community, get to know more developers as well as have some fun!

There are mainly three challenges this year which are
* big data analytics
* o2o commerce
* smart living

and a grand prize which is an exclusive invite to a hackcelerator program and a chance to fly to silicon valley to compete further! Of cause, each categories come with prize pool!

Having practical background in big data technology and startup before, the professor think by inviting could form a team of five to compete on the big data analytics category. With that, I just give it a try and see how it goes. This event held on 4 and 5th June 2016 and of cause, on the weekend where just fit nicely with working professional schedule.

For my part, I have bring in big data technology and this time I selected elasticsearch as the nosql keystore which match with the challenge category we are aiming for. It was an unfortunate that since much of my time have been devoted to mid and backend development, my user interface development skill has been reduced tremendously. (Note to self, start to code GUI back!) But fortunately, to fix that gap, there was a good combination of software that came with elasticsearch, which is known as kibana fix what I have not bring to the table. Combination elasticsearch and kibana, we are not able to ingest the 65m of iproperty data into the machine, we are able to query and represent it nicely in colour graphs form.

As for the remaining of the team, which bring in skillsets like deep learning and predictive analysis which these two skillsets answer on 'predictive' and 'prescriptive' part. The idea of our product is that, user able to upload a picture of a property through a web interface (through a phone camera) and the system will learn that image and output the result using iproperty dataset that was store in elasticsearch and display in another page.

Below are some interesting pictures taken during the events.

the stage

panorama view

and the developers

As you can see from the above pictures, there are plenty of coders! Each skillful at what they are good at. There are estimated around 370 participants and that's including female coders too! Overall I think the organizer done really good job for this two days events. The participants actually got power, cool air, water, food, network devices and cable, junk food, tshirt, cup, writing notebook and the staffs are very helpful.

One of them actually came to me and asking what do I like, and actually handed me a paper cup with coffee as I requested. I could not express more gratitude since I got there around 8am and that's early for weekend. ;-) But I would like to point out there are definite areas to improve for next year.

* warm air on day one, it was not continuous but you feel the warm air.
* some of the schedule planned (the judging and present) written in paper is way too far off from the actual events flow.
* power and internet connection drop from time to time for two days.
* less junk food and perhaps replaced with fruits.
* the table arrangement too small for computer devices as well as personal comfortable.

But all in all, a good job to complete this two days event in a safe and sounds manner. If you know me, and the moto of this website striving for contribution and mutual benefits, I found out that there are still some and if not many of the developers who are very selfish in term of code sharing and/or code learning. For instance, all my codes and infrastructure are available online which can be found here.But in return, there are many excuses of them not share in between and something really go against my principle. I know that event such as this is compete against other team, I think what's more valuable above all these monetary values is the innovation and to cultivate coding passion. Something still I do not see this year and I don't believe we can thrive in closing environment and innovation definitely does not grow under such shallow person attitude.

hackathon ending in 5 minutes

pitching schedule

the team during pitching session.

Many coder actually slept on the mall but for me, home sweet home. I had a self reflection with the team and professor actually gave valuable insight on the night in slack and on the next days. Something that I have never experience since left academic. The coding session stop at 12pm on day 2 and then participant are free for lunch whilst the organizer and judges are preparing themselves for participant's pitching session. There were two rounds of pitching and each team just got about 2-3 minutes explanation their product and 1-2 minutes for question and answer.

It's a sad but reality that, during shortlisted team who pitch again on the stage, many judges keep using the word such as intellectual property, monetization, how you sell your products or how you make money out of your product. Honestly, these types of questions should be the responsible of the business segment professional. Event such as this should have been focus on the coding spirit and to actually value on the product that actually meet the set criterias. Yes, no doubt money is the topic of a company but that should have been an trivial issue for company, what's matter above is companies should be the main catalyst to drive the country to a better quality country. Not just project monetary society. Remember, the participant are as young as 15.

team effort

solo view

By the time the big data category announcement was made, I was dead tired.It's interesting to learn from other teams on the user interface design as well as the idea to transformed into the mockup prototype in just two days or less. To my surprise, we actually got the second prize for the challenge we compete for! That's worth 3000MYR and what's more valuable is a chance to be invited to Big App Challenge 3.0 Semi Finals. Hehe, whilst I fully acknowledge this reward rightfully belong to a team but a solo picture taken to acknowledge my contribution is not too much to ask for too.

Till then, keep coding and if you are interested to code, please feel free to contact me for any possibility to work together.

Initial learning into apache cassandra paxos

Recently I have been reading into apache lightweight transaction in cassandra 2.0 and interested into how it implemented in code level. From end user perspective, when you manupulating data either insert and update with if not exists, then internally, paxos operation willl be used.

An example of lightweight transaction.

 INSERT INTO USERS (login, email, name, login_count) values ('jbellis', 'jbellis@datastax.com', 'Jonathan Ellis', 1) IF NOT EXISTS  
   
 UPDATE users SET reset_token = null, password = ‘newpassword’ WHERE login = ‘jbellis’ IF reset_token = ‘some-generated-reset-token’  

Essentially the paxos how operation concerntrated in class StorageProxy.We read that from the code documentation,

There are three phases to Paxos:
1. Prepare: the coordinator generates a ballot (timeUUID in our case) and asks replicas to (a) promise
   not to accept updates from older ballots and (b) tell us about the most recent update it has already
   accepted.
2. Accept: if a majority of replicas reply, the coordinator asks replicas to accept the value of the
   highest proposal ballot it heard about, or a new value if no in-progress proposals were reported.
3. Commit (Learn): if a majority of replicas acknowledge the accept request, we can commit the new
   value.

So it involve a few operation before an insert and update can be perform and this is not something you want to replace in bulk operation call with. We see that in class StorageService, several paxos verbs are registered. You can find them mostly in the paxos packages. Following are some useful paxos classes.

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/PaxosState.java

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/Commit.java

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/PrepareVerbHandler.java

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/ProposeVerbHandler.java

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/CommitVerbHandler.java

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/AbstractPaxosCallback.java

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/ProposeCallback.java

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/PrepareCallback.java

https://github.com/apache/cassandra/blob/cassandra-2.0.7/src/java/org/apache/cassandra/service/paxos/PrepareResponse.java

Interesting in the class PaxosState, noticed the following

locks - an array of length 1024

call system keyspace class to load and save paxos state.

When you check into cassandra using cqlsh, you will find the following.

 cqlsh:jw_schema1> use system;  
 cqlsh:system> desc tables;  
   
 available_ranges     peers        paxos      range_xfers  
 batches          compaction_history batchlog    local     
 "IndexInfo"        sstable_activity  size_estimates hints     
 views_builds_in_progress peer_events     built_views    
   
 cqlsh:system> select * from paxos;  
   
  row_key | cf_id | in_progress_ballot | most_recent_commit | most_recent_commit_at | most_recent_commit_version | proposal | proposal_ballot | proposal_version  
 ---------+-------+--------------------+--------------------+-----------------------+----------------------------+----------+-----------------+------------------  
   
 (0 rows)  

You can also read the unit test for paxos in cassandra 2.0.17 as can be read here.

This compare and set (cas) operation looks interesting if you want to ensure the value only be created if it not exists, a nifty feature found in apache cassandra 2.0 onward. Feel free to explore further!