From 349422ddbb2533237c98f50af478594f9898584b Mon Sep 17 00:00:00 2001 From: "John Chodera (MSKCC)" Date: Fri, 5 Feb 2016 19:13:40 -0500 Subject: [PATCH 1/8] Updates for virtualbox plugins --- linux/setup_centos_vm.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/linux/setup_centos_vm.sh b/linux/setup_centos_vm.sh index 5b68983..34e89ab 100644 --- a/linux/setup_centos_vm.sh +++ b/linux/setup_centos_vm.sh @@ -118,3 +118,8 @@ echo "" >> $HOME/.bashrc echo "********** Installing packages via pip..." $HOME/miniconda/bin/pip install --quiet sphinxcontrib-bibtex +# Install things needed to add virtualbox guest plugins. +sudo yum -y --quiet --enablerepo rpmforge install dkms +sudo yum -y --quiet groupinstall "Development Tools" +sudo yum -y --quiet install kernel-devel + From 8266c57d6b2f1d6d9e934899a153b3f15affb09c Mon Sep 17 00:00:00 2001 From: "John Chodera (MSKCC)" Date: Fri, 5 Feb 2016 19:31:51 -0500 Subject: [PATCH 2/8] More testing --- linux/setup_centos_vm.sh | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/linux/setup_centos_vm.sh b/linux/setup_centos_vm.sh index 463f687..750d582 100644 --- a/linux/setup_centos_vm.sh +++ b/linux/setup_centos_vm.sh @@ -11,13 +11,23 @@ sudo rpm -i --quiet epel-release-6-8.noarch.rpm # Install things needed for virtualbox guest additions. echo "********** Removing old kernel package..." #sudo yum remove -y --quiet kernel-2.6.32-431.el6.x86_64 -sudo yum remove -y --quiet kernel +sudo yum remove -y --quiet kernel kernel-headers kernel-devl echo "********** Installing kernel headers and dkms for virtualbox guest additions..." -sudo yum install -y --quiet kernel-devel dkms +#sudo yum install -y --quiet kernel-devel dkms + +# Install things needed to add virtualbox guest plugins. +sudo yum -y --quiet --enablerepo rpmforge install dkms +sudo yum -y --quiet groupinstall "Development Tools" +#sudo yum -y --quiet install kernel-devel +sudo yum -y --quiet install kernel-devel-2.6.32-504.el6.x86_64 echo "********** Updating yum..." sudo yum update -y --quiet + +# DEBUG +exit 0 + # Several of these come from the EPEL repo echo "********** Installing lots of packages via yum..." sudo yum install -y --quiet tar clang cmake graphviz perl flex bison rpm-build texlive texlive-latex ghostscript gcc gcc-c++ git vim emacs swig zip sphinx python-sphinx doxygen screen @@ -120,8 +130,3 @@ echo "" >> $HOME/.bashrc echo "********** Installing packages via pip..." $HOME/miniconda/bin/pip install --quiet sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen -# Install things needed to add virtualbox guest plugins. -sudo yum -y --quiet --enablerepo rpmforge install dkms -sudo yum -y --quiet groupinstall "Development Tools" -sudo yum -y --quiet install kernel-devel - From 4031523ef7aefb1b0c984e9c3a0c3de7d6aec3d8 Mon Sep 17 00:00:00 2001 From: "John Chodera (MSKCC)" Date: Fri, 5 Feb 2016 19:42:37 -0500 Subject: [PATCH 3/8] More testing --- linux/setup_centos_vm.sh | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/linux/setup_centos_vm.sh b/linux/setup_centos_vm.sh index 750d582..c103611 100644 --- a/linux/setup_centos_vm.sh +++ b/linux/setup_centos_vm.sh @@ -11,15 +11,17 @@ sudo rpm -i --quiet epel-release-6-8.noarch.rpm # Install things needed for virtualbox guest additions. echo "********** Removing old kernel package..." #sudo yum remove -y --quiet kernel-2.6.32-431.el6.x86_64 -sudo yum remove -y --quiet kernel kernel-headers kernel-devl +sudo yum remove -y --quiet kernel kernel-headers kernel-devel echo "********** Installing kernel headers and dkms for virtualbox guest additions..." #sudo yum install -y --quiet kernel-devel dkms # Install things needed to add virtualbox guest plugins. -sudo yum -y --quiet --enablerepo rpmforge install dkms -sudo yum -y --quiet groupinstall "Development Tools" +#sudo yum -y --quiet --enablerepo rpmforge install dkms +#sudo yum -y --quiet groupinstall "Development Tools" #sudo yum -y --quiet install kernel-devel -sudo yum -y --quiet install kernel-devel-2.6.32-504.el6.x86_64 +#sudo yum -y --quiet install kernel-devel-2.6.32-504.el6.x86_64 +sudo yum -y --quietinstall dkms +sudo yum -y --quiet --enablerepo centosplus install kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm echo "********** Updating yum..." sudo yum update -y --quiet From 05f28fd860e583482253d989d40d722008de159f Mon Sep 17 00:00:00 2001 From: "John Chodera (MSKCC)" Date: Fri, 5 Feb 2016 19:46:45 -0500 Subject: [PATCH 4/8] More tests --- linux/setup_centos_vm.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/linux/setup_centos_vm.sh b/linux/setup_centos_vm.sh index c103611..ec25fed 100644 --- a/linux/setup_centos_vm.sh +++ b/linux/setup_centos_vm.sh @@ -15,17 +15,17 @@ sudo yum remove -y --quiet kernel kernel-headers kernel-devel echo "********** Installing kernel headers and dkms for virtualbox guest additions..." #sudo yum install -y --quiet kernel-devel dkms +echo "********** Updating yum..." +sudo yum update -y --quiet + # Install things needed to add virtualbox guest plugins. #sudo yum -y --quiet --enablerepo rpmforge install dkms #sudo yum -y --quiet groupinstall "Development Tools" #sudo yum -y --quiet install kernel-devel #sudo yum -y --quiet install kernel-devel-2.6.32-504.el6.x86_64 -sudo yum -y --quietinstall dkms -sudo yum -y --quiet --enablerepo centosplus install kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm - -echo "********** Updating yum..." -sudo yum update -y --quiet - +sudo yum remove -y --quiet kernel kernel-headers kernel-devel +sudo yum -y --quietinstall dkms make gcc kernel-devel kernel-headers +#sudo yum -y --quiet --enablerepo centosplus install kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm # DEBUG exit 0 From e23331b2989d750af20bfa3b0556aaf12aa16298 Mon Sep 17 00:00:00 2001 From: "John Chodera (MSKCC)" Date: Fri, 5 Feb 2016 19:51:33 -0500 Subject: [PATCH 5/8] More tests --- linux/setup_centos_vm.sh | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/linux/setup_centos_vm.sh b/linux/setup_centos_vm.sh index ec25fed..2051648 100644 --- a/linux/setup_centos_vm.sh +++ b/linux/setup_centos_vm.sh @@ -24,7 +24,9 @@ sudo yum update -y --quiet #sudo yum -y --quiet install kernel-devel #sudo yum -y --quiet install kernel-devel-2.6.32-504.el6.x86_64 sudo yum remove -y --quiet kernel kernel-headers kernel-devel -sudo yum -y --quietinstall dkms make gcc kernel-devel kernel-headers +sudo yum -y --quietinstall dkms +wget http://vault.centos.org/6.6/centosplus/x86_64/Packages/kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm +sudo rpm -i --quiet kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm #sudo yum -y --quiet --enablerepo centosplus install kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm # DEBUG From 0f76733b17a31e93e6e50982a501a948b0547dfc Mon Sep 17 00:00:00 2001 From: "John Chodera (MSKCC)" Date: Fri, 5 Feb 2016 20:06:45 -0500 Subject: [PATCH 6/8] More tests --- linux/Vagrantfile | 5 +++-- linux/setup_centos_vm.sh | 7 +++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/linux/Vagrantfile b/linux/Vagrantfile index 536a9d5..b0d170c 100644 --- a/linux/Vagrantfile +++ b/linux/Vagrantfile @@ -10,7 +10,8 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config| # please see the online documentation at vagrantup.com. # Every Vagrant virtual environment requires a box to build off of. - config.vm.box = "chef/centos-6.6" + #config.vm.box = "chef/centos-6.6" + config.vm.box = "bento/centos-6.7" # Disable automatic box update checking. If you disable this, then # boxes will only be checked for updates when the user runs @@ -84,5 +85,5 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config| config.vm.provision "shell", inline: "su -c 'bash -x /vagrant/setup_centos_vm.sh' vagrant" - + end diff --git a/linux/setup_centos_vm.sh b/linux/setup_centos_vm.sh index 2051648..471929b 100644 --- a/linux/setup_centos_vm.sh +++ b/linux/setup_centos_vm.sh @@ -23,10 +23,9 @@ sudo yum update -y --quiet #sudo yum -y --quiet groupinstall "Development Tools" #sudo yum -y --quiet install kernel-devel #sudo yum -y --quiet install kernel-devel-2.6.32-504.el6.x86_64 -sudo yum remove -y --quiet kernel kernel-headers kernel-devel -sudo yum -y --quietinstall dkms -wget http://vault.centos.org/6.6/centosplus/x86_64/Packages/kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm -sudo rpm -i --quiet kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm +sudo yum -y --quiet install dkms kernel-headers +#wget http://vault.centos.org/6.6/centosplus/x86_64/Packages/kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm +#sudo rpm -i --quiet kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm #sudo yum -y --quiet --enablerepo centosplus install kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm # DEBUG From a01f63d0d225ede54ba656afc782233da2773f7e Mon Sep 17 00:00:00 2001 From: "John Chodera (MSKCC)" Date: Fri, 5 Feb 2016 20:45:49 -0500 Subject: [PATCH 7/8] Update provisioning script. --- linux/setup_centos_vm.sh | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/linux/setup_centos_vm.sh b/linux/setup_centos_vm.sh index 471929b..6c859b3 100644 --- a/linux/setup_centos_vm.sh +++ b/linux/setup_centos_vm.sh @@ -9,10 +9,11 @@ wget --quiet http://dl.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch sudo rpm -i --quiet epel-release-6-8.noarch.rpm # Install things needed for virtualbox guest additions. -echo "********** Removing old kernel package..." +sudo yum install -y dkms +#echo "********** Removing old kernel package..." #sudo yum remove -y --quiet kernel-2.6.32-431.el6.x86_64 -sudo yum remove -y --quiet kernel kernel-headers kernel-devel -echo "********** Installing kernel headers and dkms for virtualbox guest additions..." +#sudo yum remove -y --quiet kernel kernel-headers kernel-devel +#echo "********** Installing kernel headers and dkms for virtualbox guest additions..." #sudo yum install -y --quiet kernel-devel dkms echo "********** Updating yum..." @@ -23,14 +24,11 @@ sudo yum update -y --quiet #sudo yum -y --quiet groupinstall "Development Tools" #sudo yum -y --quiet install kernel-devel #sudo yum -y --quiet install kernel-devel-2.6.32-504.el6.x86_64 -sudo yum -y --quiet install dkms kernel-headers +#sudo yum -y --quiet install dkms kernel-headers #wget http://vault.centos.org/6.6/centosplus/x86_64/Packages/kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm #sudo rpm -i --quiet kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm #sudo yum -y --quiet --enablerepo centosplus install kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm -# DEBUG -exit 0 - # Several of these come from the EPEL repo echo "********** Installing lots of packages via yum..." sudo yum install -y --quiet tar clang cmake graphviz perl flex bison rpm-build texlive texlive-latex ghostscript gcc gcc-c++ git vim emacs swig zip sphinx python-sphinx doxygen screen From a16ebf0a5fb831a6b2e189d214ed8e81940e4827 Mon Sep 17 00:00:00 2001 From: jchodera Date: Wed, 10 Feb 2016 19:25:18 -0500 Subject: [PATCH 8/8] Switch to local version of AMD APP SDK --- linux/setup_centos_vm.sh | 36 +++++++++++++++++++----------------- 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/linux/setup_centos_vm.sh b/linux/setup_centos_vm.sh index 6c859b3..462ec99 100644 --- a/linux/setup_centos_vm.sh +++ b/linux/setup_centos_vm.sh @@ -36,6 +36,25 @@ sudo yum install -y --quiet tar clang cmake graphviz perl flex bison rpm-build t # Install GLUT for OpenGL sudo yum install -y --quiet freeglut-devel +# Install AMD APP SDK 3.0 +echo "********** Installing AMD APP SDK 3.0..." +APPSDKFILE="AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2" +mkdir ~/Software/AMD +cd ~/Software/AMD +# Copy the tarball $APPSDKFILE to the directory containing VagrantFile, which will be shared on the guest as /vagrant/ +sudo yum install -y --quiet redhat-lsb +URL="http://jenkins.choderalab.org/userContent/$APPSDKFILE" +#echo "Retrieving AMD APP SDK from $URL..." +#wget --quiet $URL +cp /vagrant/$APPSDKFILE . +echo "Unpacking $APPSDKFILE..." +tar -jxvf $APPSDKFILE +echo "Installing $APPSDKFILE..." +sudo ./AMD-APP-SDK-v3.0.130.135-GA-linux64.sh -- -s -a yes +export OPENCL_HOME=/opt/AMDAPPSDK-3.0 +export OPENCL_LIBPATH=/opt/AMDAPPSDK-3.0/lib/x86_64 + +# Doxygen echo "********** Compiling recent doxygen..." cd ~/Software wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.8.src.tar.gz @@ -104,23 +123,6 @@ export PATH=$HOME/miniconda/bin:$PATH conda config --add channels omnia conda install --yes --quiet fftw3f jinja2 swig sphinx conda-build cmake anaconda-client pip -# Install AMD APP SDK -echo "********** Installing AMD APP SDK 3.0..." -APPSDKFILE="AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2" -mkdir ~/Software/AMD -cd ~/Software/AMD -# Copy the tarball $APPSDKFILE to the directory containing VagrantFile, which will be shared on the guest as /vagrant/ -sudo yum install -y --quiet redhat-lsb -URL="http://jenkins.choderalab.org/userContent/$APPSDKFILE" -echo "Retrieving AMD APP SDK from $URL..." -wget --quiet $URL -echo "Unpacking $APPSDKFILE..." -tar -jxvf $APPSDKFILE -echo "Installing $APPSDKFILE..." -sudo ./AMD-APP-SDK-v3.0.130.135-GA-linux64.sh -- -s -a yes -export OPENCL_HOME=/opt/AMDAPPSDK-3.0 -export OPENCL_LIBPATH=/opt/AMDAPPSDK-3.0/lib/x86_64 - # Add conda to the path. echo "********** Adding paths" cd ~