Porting CUDA program from ArchLinux to Ubuntu 16.04

Today I ported a CUDA project from Arch Linux to Ubuntu 16.04, and this post records the pitfalls.

(0) Update cmake to newest version (follow this);

(1) Specify nvcc path in CMakeLists.txt:

SET(CMAKE_CUDA_COMPILER /usr/local/cuda-9.0/bin/nvcc)

otherwise, following error may generate:

......
No CMAKE_CUDA_COMPILER could be found.
......

(2) Since Ubuntu 16.04‘s default compiler is still gcc-5, install gcc-6 first, then pass gcc-6 as default compiler for nvcc:

......
SET(CMAKE_CXX_STANDARD 11)
SET(CMAKE_CUDA_FLAGS "-std=c++11 -ccbin gcc-6")
......

(3) Execute cmake command:

cmake -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 -DCMAKE_BUILD_TYPE=Release ..

References:
Not Locating CUDA Compiler;
CMake: How to pass mode dependent compile flags to nvcc in visual studio environment;
Tensorflow crashes on build on Ubuntu 16.04 when building for skylake (avx512).

 

Notice the linking library position on Ubuntu

This week, I ported tcpbench from OpenBSD to Linux. The idiomatic method of OpenBSD is putting the linking library in front of generating final target:

cc -g -O2 -Wall -levent -o tcpbench tcpbench.c

However this doesn’t work in Ubuntu since its the linker uses --as-needed option. So I change the Makefile to put the library at the end:

cc -g -O2 -Wall -o tcpbench tcpbench.c -levent

Please refer this discussion if you are interested.

Build the newest Docker environment

This tutorial explains how to build the newest Docker environment. My host is Ubuntu 16.04.1, and it is already shipped withDocker 1.12.0:

# systemctl status docker
● docker.service - Docker Application Container Engine
   Loaded: loaded (/lib/systemd/system/docker.service; enabled; vendor preset: enabled)
  Drop-In: /etc/systemd/system/docker.service.d
   └─http-proxy.conf
   Active: active (running) since Tue 2016-08-09 03:49:08 EDT; 3min 24s ago
 Docs: https://docs.docker.com
 Main PID: 30465 (dockerd)
Tasks: 26
   Memory: 36.5M
  CPU: 2.394s
   CGroup: /system.slice/docker.service
   ├─30465 /usr/bin/dockerd -H fd://
   └─30473 docker-containerd -l unix:///var/run/docker/libcontainerd/docker-containerd.sock --shim docker-containerd-shim --metrics

Aug 09 03:49:08 ubuntu dockerd[30465]: time="2016-08-09T03:49:08.114671045-04:00" level=info msg="Graph migration to content-addressability
......
# docker version
Client:
 Version:  1.12.0
 API version:  1.24
 Go version:   go1.6.3
 Git commit:   8eab29e
 Built:Thu Jul 28 22:11:10 2016
 OS/Arch:  linux/amd64

Server:
 Version:  1.12.0
 API version:  1.24
 Go version:   go1.6.3
 Git commit:   8eab29e
 Built:Thu Jul 28 22:11:10 2016
 OS/Arch:  linux/amd64

(1) The prerequisite is the Go environment is ready on your host, and GOPATH environment variable is also set. If not, please follow thisdocument to setup.

(2) Download the newest Docker code:

# go get -d -u github.com/docker/docker
package github.com/docker/docker: no buildable Go source files in /go/src/github.com/docker/docker

Build the Docker:

# cd $GOPATH/src/github.com/docker/docker/
# make DOCKER_BUILD_ARGS="--build-arg http_proxy=http://web-proxy.corp.xxxxxx.com:8080/ --build-arg https_proxy=https://web-proxy.corp.xxxxxx.com:8080/" DOCKER_DEBUG=1

Because my host works behind proxy, I need to specify proxy address in command line. Whether adding DOCKER_DEBUG or not depends on your personal flavor.

(3) After above building process succeeds, backup old Docker files:

# systemctl stop docker
# cd /usr/bin
# mkdir backup_docker
# mv docker* backup_docker

(4) Change back to $GOPATH/src/github.com/docker/docker/, and copy new Docker binaries:

# cd $GOPATH/src/github.com/docker/docker/
# cd bundles/latest/
# ls
binary-client  binary-daemon

binary-client contains Docker executable file:

# cd binary-client/
# ls
docker  docker-1.13.0-dev  docker-1.13.0-dev.md5  docker-1.13.0-dev.sha256
# cp docker /usr/bin/

Then copy Docker daemon related files:

# cd ../binary-daemon/
# ls
docker-containerd             docker-containerd.sha256       dockerd-1.13.0-dev         docker-proxy-1.13.0-dev.md5
docker-containerd-ctr         docker-containerd-shim         dockerd-1.13.0-dev.md5     docker-proxy-1.13.0-dev.sha256
docker-containerd-ctr.md5     docker-containerd-shim.md5     dockerd-1.13.0-dev.sha256  docker-runc
docker-containerd-ctr.sha256  docker-containerd-shim.sha256  docker-proxy               docker-runc.md5
docker-containerd.md5         dockerd                        docker-proxy-1.13.0-dev    docker-runc.sha256
# cp docker-containerd docker-containerd-ctr docker-containerd-shim docker-runc dockerd docker-proxy /usr/bin/

(5) Restart Docker and check it:

# systemctl start docker
# systemctl status docker
● docker.service - Docker Application Container Engine
   Loaded: loaded (/lib/systemd/system/docker.service; enabled; vendor preset: enabled)
  Drop-In: /etc/systemd/system/docker.service.d
           └─http-proxy.conf
   Active: active (running) since Tue 2016-08-09 04:26:16 EDT; 9s ago
     Docs: https://docs.docker.com
 Main PID: 4961 (dockerd)
    Tasks: 24
   Memory: 13.6M
      CPU: 367ms
   CGroup: /system.slice/docker.service
           ├─4961 /usr/bin/dockerd -H fd://
           └─4968 docker-containerd -l unix:///var/run/docker/libcontainerd/docker-containerd.sock --shim docker-containerd-shim --metrics-

Aug 09 04:26:15 ubuntu dockerd[4961]: time="2016-08-09T04:26:15.795281048-04:00" level=info msg="Graph migration to content-addressability
......
# docker version
Client:
 Version:      1.13.0-dev
 API version:  1.25
 Go version:   go1.6.3
 Git commit:   b2b41b2
 Built:        Tue Aug  9 07:49:54 2016
 OS/Arch:      linux/amd64

Server:
 Version:      1.13.0-dev
 API version:  1.25
 Go version:   go1.6.3
 Git commit:   b2b41b2
 Built:        Tue Aug  9 07:49:54 2016
 OS/Arch:      linux/amd64

Now you are playing the freshest Docker! Enjoy it!

 

Wget only recognizes http_proxy, not https_proxy

My Ubuntu 16.04 LTS works behind proxy. I have set HTTP_PROXY and HTTPS_PROXY environmental variables:

HTTP_PROXY=http://web-proxy.corp.xxxxxx.com:8080/
HTTPS_PROXY=https://web-proxy.corp.xxxxx.com:8080/

But wget can’t work:

# wget -P /tmp https://github.com/NVIDIA/nvidia-docker/releases/download/v1.0.0-rc.3/nvidia-docker_1.0.0.rc.3-1_amd64.deb
--2016-07-14 22:51:12--  https://github.com/NVIDIA/nvidia-docker/releases/download/v1.0.0-rc.3/nvidia-docker_1.0.0.rc.3-1_amd64.deb
Resolving github.com (github.com)... 192.30.253.112
Connecting to github.com (github.com)|192.30.253.112|:443... connected.
ERROR: cannot verify github.com's certificate, issued by ‘O=Fortinet Ltd.,CN=FG3K6C3A15800021’:
  Self-signed certificate encountered.
    ERROR: certificate common name ‘FG3K6C3A15800021’ doesn't match requested host name ‘github.com’.
To connect to github.com insecurely, use `--no-check-certificate'.
[email protected]:~# wget --no-check-certificate -P /tmp https://github.com/NVIDIA/nvidia-docker/releases/download/v1.0.0-rc.3/nvidia-docker_1.0.0.rc.3-1_amd64.deb

After setting http_proxy and https_proxy:

http_proxy=http://web-proxy.corp.xxxxxx.com:8080/
https_proxy=https://web-proxy.corp.xxxxx.com:8080/
HTTP_PROXY=http://web-proxy.corp.xxxxxx.com:8080/
HTTPS_PROXY=https://web-proxy.corp.xxxxx.com:8080/

Now wget works:

# wget -P /tmp https://github.com/NVIDIA/nvidia-docker/releases/download/v1.0.0-rc.3/nvidia-docker_1.0.0.rc.3-1_amd64.deb     --2016-07-14 22:57:30--  https://github.com/NVIDIA/nvidia-docker/releases/download/v1.0.0-rc.3/nvidia-docker_1.0.0.rc.3-1_amd64.deb
Resolving web-proxy.xxxxxx.hp.com (web-proxy.xxxxxx.hp.com)... xxx.xxx.xxx.xxx
Connecting to web-proxy.xxxxxx.hp.com (web-proxy.xxxxxx.hp.com)|xxx.xxx.xxx.xxx|:8080... connected.
Proxy request sent, awaiting response... 302 Found
......

So we can conclude that wget is picky about uppercase and lowercase words.

 

Install docker on Ubuntu 14.04

If you want to play docker on Ubuntu 14.04, please pay attention to the installation instruction: it is “apt-get install docker.io“, not “apt-get install docker“. You can find the difference between them by following command:

# apt-cache search docker
......
docker - System tray for KDE3/GNOME2 docklet applications
......
docker.io - Linux container runtime
......

OK! Since you have set up docker successfully, you can check its process now:

# ps -ef | grep docker
root       4715      1  0 13:22 ?        00:00:00 /usr/bin/docker -d
root       4857   4691  0 13:50 pts/0    00:00:00 grep --color=auto docker
# pstree -ps 4715
init(1)───docker(4715)─┬─{docker}(4717)
                       ├─{docker}(4722)
                       ├─{docker}(4723)
                       ├─{docker}(4724)
                       ├─{docker}(4734)
                       ├─{docker}(4754)
                       ├─{docker}(4762)
                       ├─{docker}(4769)
                       └─{docker}(4793)

You can use “service start docker” and “service stop docker” to start and stop docker daemon.

If your host runs behind proxy, you may meet problems when pulling image:

# docker run hell-world
Unable to find image 'hell-world:latest' locally
Pulling repository hell-world
FATA[0005] Get https://index.docker.io/v1/repositories/library/hell-world/images: x509: certificate is valid for FG3K6C3A15800021, not index.docker.io

The solution is add proxy configurations in /etc/default/docker:

......
# If you need Docker to use an HTTP proxy, it can also be specified here.
export http_proxy="http://web-proxy.corp.xxxxxx.com:8080/"
export https_proxy="https://web-proxy.corp.xxxxxx.com:8080/"
......

Then you can download images successfully:

# docker run hello-world
Unable to find image 'hello-world:latest' locally
latest: Pulling from hello-world
d59cd4c39e50: Pull complete
f1d956dc5945: Pull complete
Digest: sha256:4f32210e234b4ad5cac92efacc0a3d602b02476c754f13d517e1ada048e5a8ba
Status: Downloaded newer image for hello-world:latest

Hello from Docker.
This message shows that your installation appears to be working correctly.
......

Now that all the preparations are ready, please enjoy playing docker!