1:BUILD_BY[name] student4
1:BUILD_ENVIRONMENT[operating system 32 vs 64]

1:END_BUILD_ENVIRONMENT
1:DEPENDENCIES[list of dependencies with where to get them]
Get CUDA installers: https://developer.nvidia.com/cuda-downloads
1:END_DEPENDENCIES
1:NOTES[notes on attempted build]
Got Cuda 5.5, perhaps it isn't compatible
 - release mentions 3.1
 
When I run hmmingbird it gives me an error:
CUDA compilation failure.
Makefile:57: /home/student/NVIDIA_GPU_Computing_SDK/C/common/common.mk: No such file or directory
make: *** No rule to make target `/home/student/NVIDIA_GPU_Computing_SDK/C/common/common.mk'.  Stop.

this directory doesn't exist
1:END_NOTES



2:BUILD_BY[name] student8
2:BUILD_ENVIRONMENT[operating system 32 vs 64] Ubuntu 12.04 64-bit

$ lspci | grep -E "VGA|3D"
01:00.0 VGA compatible controller: NVIDIA Corporation G96 [GeForce 9400 GT] (rev a1)

2:END_BUILD_ENVIRONMENT
2:DEPENDENCIES[list of dependencies with where to get them]

DIA CUDA Toolkit (http://developer.download.nvidia.com/compute/cuda/4_0/toolkit/cudatoolkit_4.0.17_linux_64_ubuntu10.10.run)
NVIDIA CUDA SDK (http://developer.download.nvidia.com/compute/cuda/4_0/sdk/gpucomputingsdk_4.0.17_linux.run)
I downloaded version 4.0 to match to time frame of pldi12.
Both found at https://developer.nvidia.com/cuda-toolkit-40
sudo apt-get install gcc-4.4
sudo apt-get install g++-4.4
sudo apt-get install nvidia-current

2:END_DEPENDENCIES
2:NOTES[notes on attempted build]

To install the toolkit and SDK:
1. chmod +x cudatoolkit_4.0.17_linux_64_ubuntu10.10.run
2. sudo ./cudatoolkit_4.0.17_linux_64_ubuntu10.10.run

* Please make sure your PATH includes /usr/local/cuda/bin
* Please make sure your LD_LIBRARY_PATH
*   for 32-bit Linux distributions includes /usr/local/cuda/lib
*   for 64-bit Linux distributions includes /usr/local/cuda/lib64:/usr/local/cuda/lib
* OR
*   for 32-bit Linux distributions add /usr/local/cuda/lib
*   for 64-bit Linux distributions add /usr/local/cuda/lib64 and /usr/local/cuda/lib
* to /etc/ld.so.conf and run ldconfig as root

* Please read the release notes in /usr/local/cuda/doc/

* To uninstall CUDA, delete /usr/local/cuda
* Installation Complete

3. chmod +x gpucomputingsdk_4.0.17_linux.run
4. sudo ./gpucomputingsdk_4.0.17_linux.run

* Please make sure your PATH includes /usr/local/cuda/bin
* Please make sure your LD_LIBRARY_PATH includes /usr/local/cuda/lib

* To uninstall the NVIDIA GPU Computing SDK, please delete /lhome/student/NVIDIA_GPU_Computing_SDK
* Installation Complete

To make libcutil_x86_64:
cd /lhome/student/NVIDIA_GPU_Computing_SDK/C/common/
sudo make

To make libshrutil_x86_64:
cd /lhome/student/NVIDIA_GPU_Computing_SDK/shared/
sudo make

To install gcc 4.4.7 and g++ 4.4.7, I did:
sudo apt-get install gcc-4.4
sudo apt-get install g++-4.4

To make gcc 4.4.7 and g++ 4.4.7 my default gcc, I did:
sudo cp /usr/bin/gcc-4.4 /usr/bin/gcc
sudo cp /usr/bin/g++-4.4 /usr/bin/g++

To run hmmingbird:
$ ./hmmingbird examples/casino.hmm

I found the compiled casino in the subdirectory release.

I tried to run that:
$ ./casino
./casino: error while loading shared libraries: libcudart.so.4: cannot open shared object file: No such file or directory

Then I did:
sudo ln -s /usr/local/cuda/lib64/libcudart.so /usr/lib/x86_64-linux-gnu/libcudart.so.4

Ran again:
$ ./casino
usage: ./casino filename

Again:
$ ./casino ../examples/proteins-13355.fa 
/lhome/student/NVIDIA_GPU_Computing_SDK/C/src/../common/inc/cutil_inline_runtime.h(366) : cudaSafeCallNoSync() Runtime API error 35 : CUDA driver version is insufficient for CUDA runtime version.

I updated my NVIDIA driver:
sudo apt-get install nvidia-current

$ ./casino ../examples/proteins-13355.fa 
/lhome/student/NVIDIA_GPU_Computing_SDK/C/src/../common/inc/cutil_inline_runtime.h(366) : cudaSafeCallNoSync() Runtime API error 38 : no CUDA-capable device is detected.

Tried to install CUDA 6 but still no luck:
$ ./hmmingbird examples/casino.hmm 
CUDA compilation failure.
Makefile:57: /lhome/student/NVIDIA_GPU_Computing_SDK/C/common/common.mk: No such file or directory
make: *** No rule to make target `/lhome/student/NVIDIA_GPU_Computing_SDK/C/common/common.mk'.  Stop.

So, the work itself, which is a compiler, could be built and run. But the output
program from the compiler could not be run.

In summary, it works with an older version of CUDA. But that version of CUDA
may not work with Ubuntu 12.04 (It was intended for 10.10 as described on the
website). Using version 6 of CUDA (which is compatible with 12.04 according to
the website) does not work.

2:END_NOTES