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Posted to commits@dlab.apache.org by my...@apache.org on 2020/09/14 10:44:40 UTC
[incubator-dlab] 01/01: [DLAB-2025] - Livy connection for RStudio
availbale, RStudio version updated
This is an automated email from the ASF dual-hosted git repository.
mykolabodnar pushed a commit to branch DLAB-2025
in repository https://gitbox.apache.org/repos/asf/incubator-dlab.git
commit 06b6202155f45c55ebcf704b103f8695b8c2c5a2
Author: bodnarmykola <bo...@gmail.com>
AuthorDate: Mon Sep 14 13:44:08 2020 +0300
[DLAB-2025] - Livy connection for RStudio availbale, RStudio version updated
---
infrastructure-provisioning/src/general/conf/dlab.ini | 2 +-
.../src/general/lib/os/debian/notebook_lib.py | 17 ++++++++++-------
.../src/rstudio/scripts/configure_rstudio_node.py | 2 +-
3 files changed, 12 insertions(+), 9 deletions(-)
diff --git a/infrastructure-provisioning/src/general/conf/dlab.ini b/infrastructure-provisioning/src/general/conf/dlab.ini
index c59d343..830e0b2 100644
--- a/infrastructure-provisioning/src/general/conf/dlab.ini
+++ b/infrastructure-provisioning/src/general/conf/dlab.ini
@@ -243,7 +243,7 @@ tensorflow_version = 2.1.0
### Version of Zeppelin to be installed on notebook
zeppelin_version = 0.8.2
### Version of Rstudio to be installed on notebook
-rstudio_version = 1.2.5033
+rstudio_version = 1.3.1073
### Version of Scala to be installed on notebook
scala_version = 2.12.8
### Version of Livy top be installed on notebook
diff --git a/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py b/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py
index 835656e..819bcd7 100644
--- a/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py
+++ b/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py
@@ -93,6 +93,9 @@ def ensure_r(os_user, r_libs, region, r_mirror):
sudo('apt update')
manage_pkg('-y install', 'remote', 'libcurl4-openssl-dev libssl-dev libreadline-dev')
manage_pkg('-y install', 'remote', 'cmake')
+ #sudo('apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9')
+ #sudo("add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'")
+ #manage_pkg('update', 'remote', '')
manage_pkg('-y install', 'remote', 'r-base r-base-dev')
sudo('R CMD javareconf')
sudo('cd /root; git clone https://github.com/zeromq/zeromq4-x.git; cd zeromq4-x/; mkdir build; cd build; cmake ..; make install; ldconfig')
@@ -116,23 +119,23 @@ def install_rstudio(os_user, local_spark_path, rstudio_pass, rstudio_version):
try:
manage_pkg('-y install', 'remote', 'r-base')
manage_pkg('-y install', 'remote', 'gdebi-core')
- sudo('wget https://download2.rstudio.org/server/trusty/amd64/rstudio-server-{}-amd64.deb'.format(rstudio_version))
+ sudo('wget https://download2.rstudio.org/server/xenial/amd64/rstudio-server-{}-amd64.deb'.format(rstudio_version))
sudo('gdebi -n rstudio-server-{}-amd64.deb'.format(rstudio_version))
sudo('mkdir -p /mnt/var')
sudo('chown {0}:{0} /mnt/var'.format(os_user))
http_proxy = run('echo $http_proxy')
https_proxy = run('echo $https_proxy')
- sudo("sed -i '/Type=forking/a \Environment=USER=dlab-user' /etc/systemd/system/rstudio-server.service")
- sudo("sed -i '/ExecStart/s|=/usr/lib/rstudio-server/bin/rserver|=/bin/bash -c \"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/cudnn/lib64:/usr/local/cuda/lib64; /usr/lib/rstudio-server/bin/rserver --auth-none 1|g' /etc/systemd/system/rstudio-server.service")
- sudo("sed -i '/ExecStart/s|$|\"|g' /etc/systemd/system/rstudio-server.service")
+ sudo("sed -i '/Type=forking/a \Environment=USER=dlab-user' /lib/systemd/system/rstudio-server.service")
+ sudo("sed -i '/ExecStart/s|=/usr/lib/rstudio-server/bin/rserver|=/bin/bash -c \"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/cudnn/lib64:/usr/local/cuda/lib64; /usr/lib/rstudio-server/bin/rserver --auth-none 1|g' /lib/systemd/system/rstudio-server.service")
+ sudo("sed -i '/ExecStart/s|$|\"|g' /lib/systemd/system/rstudio-server.service")
sudo(
- 'sed -i \'/\[Service\]/a Environment=\"HTTP_PROXY={}\"\' /etc/systemd/system/rstudio-server.service'.format(
+ 'sed -i \'/\[Service\]/a Environment=\"HTTP_PROXY={}\"\' /lib/systemd/system/rstudio-server.service'.format(
http_proxy))
sudo(
- 'sed -i \'/\[Service\]/a Environment=\"HTTPS_PROXY={}\"\' /etc/systemd/system/rstudio-server.service'.format(
+ 'sed -i \'/\[Service\]/a Environment=\"HTTPS_PROXY={}\"\' /lib/systemd/system/rstudio-server.service'.format(
https_proxy))
java_home = run("update-alternatives --query java | grep -o \'/.*/java-8.*/jre\'").splitlines()[0]
- sudo('sed -i \'/\[Service\]/ a\Environment=\"JAVA_HOME={}\"\' /etc/systemd/system/rstudio-server.service'.format(
+ sudo('sed -i \'/\[Service\]/ a\Environment=\"JAVA_HOME={}\"\' /lib/systemd/system/rstudio-server.service'.format(
java_home))
sudo("systemctl daemon-reload")
sudo('touch /home/{}/.Renviron'.format(os_user))
diff --git a/infrastructure-provisioning/src/rstudio/scripts/configure_rstudio_node.py b/infrastructure-provisioning/src/rstudio/scripts/configure_rstudio_node.py
index 34fb007..795e555 100644
--- a/infrastructure-provisioning/src/rstudio/scripts/configure_rstudio_node.py
+++ b/infrastructure-provisioning/src/rstudio/scripts/configure_rstudio_node.py
@@ -58,7 +58,7 @@ jars_dir = '/opt/jars/'
templates_dir = '/root/templates/'
files_dir = '/root/files/'
r_libs = ['R6', 'pbdZMQ', 'RCurl', 'devtools', 'reshape2', 'caTools', 'rJava', 'ggplot2', 'evaluate', 'formatR', 'yaml',
- 'Rcpp', 'rmarkdown', 'base64enc', 'tibble']
+ 'Rcpp', 'rmarkdown', 'base64enc', 'tibble', 'sparklyr']
gitlab_certfile = os.environ['conf_gitlab_certfile']
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