vasisht
commented
5 years ago Debian ‘Squeeze' end-of-life was in 2016. I think you’ll have to upgrade the instance to ‘Jessie’. There are some third party StarCluster AMIs with Ubuntu 16.04.4 floating around if that’s helpful for you.
On August 8, 2018 at 9:31:22 AM, kynnjo (notifications@github.com) wrote:
Right after creating a new cluster, I log in to it with starcluster
sshmaster
apt-get update
Get:1 http://archive.cloudera.com squeeze-cdh3u5 Release.gpg [198 B] Get:2 http://archive.cloudera.com squeeze-cdh3u5 Release [2,405 B] Ign http://us-east-1.ec2.archive.ubuntu.com raring Release.gpg Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates Release.gpg Ign http://us-east-1.ec2.archive.ubuntu.com raring Release Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates Release Ign http://us-east-1.ec2.archive.ubuntu.com raring/main Sources/DiffIndex Ign http://us-east-1.ec2.archive.ubuntu.com raring/universe Sources/DiffIndex Ign http://us-east-1.ec2.archive.ubuntu.com raring/main amd64 Packages/DiffIndex Ign http://us-east-1.ec2.archive.ubuntu.com raring/universe amd64 Packages/DiffIndex Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates/main Sources/DiffIndex Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates/universe Sources/DiffIndex Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates/main amd64 Packages/DiffIndex Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates/universe amd64 Packages/DiffIndex Get:3 http://archive.cloudera.com squeeze-cdh3u5/contrib Sources [5,001 B] Ign http://security.ubuntu.com raring-security Release.gpg Get:4 http://archive.cloudera.com squeeze-cdh3u5/contrib amd64 Packages [14.0 kB] Hit http://ppa.launchpad.net raring Release.gpg Ign http://security.ubuntu.com raring-security Release Ign http://us-east-1.ec2.archive.ubuntu.com raring/main Translation-en_US Ign http://us-east-1.ec2.archive.ubuntu.com raring/main Translation-en Ign http://us-east-1.ec2.archive.ubuntu.com raring/universe Translation-en_US Ign http://us-east-1.ec2.archive.ubuntu.com raring/universe Translation-en Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates/main Translation-en_US Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates/main Translation-en Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates/universe Translation-en_US Ign http://us-east-1.ec2.archive.ubuntu.com raring-updates/universe Translation-en Err http://us-east-1.ec2.archive.ubuntu.com raring/main Sources 404 Not Found [IP: 54.152.129.43 80] Err http://us-east-1.ec2.archive.ubuntu.com raring/universe Sources 404 Not Found [IP: 54.152.129.43 80] Err http://us-east-1.ec2.archive.ubuntu.com raring/main amd64 Packages 404 Not Found [IP: 54.152.129.43 80] Err http://us-east-1.ec2.archive.ubuntu.com raring/universe amd64 Packages 404 Not Found [IP: 54.152.129.43 80] Err http://us-east-1.ec2.archive.ubuntu.com raring-updates/main Sources 404 Not Found [IP: 54.152.129.43 80] Ign http://security.ubuntu.com raring-security/main Sources/DiffIndex Err http://us-east-1.ec2.archive.ubuntu.com raring-updates/universe Sources 404 Not Found [IP: 54.152.129.43 80] Err http://us-east-1.ec2.archive.ubuntu.com raring-updates/main amd64 Packages 404 Not Found [IP: 54.152.129.43 80] Err http://us-east-1.ec2.archive.ubuntu.com raring-updates/universe amd64 Packages 404 Not Found [IP: 54.152.129.43 80] Hit http://ppa.launchpad.net raring Release.gpg Ign http://security.ubuntu.com raring-security/universe Sources/DiffIndex Ign http://security.ubuntu.com raring-security/main amd64 Packages/DiffIndex Get:5 http://ppa.launchpad.net raring Release.gpg [316 B] Ign http://security.ubuntu.com raring-security/universe amd64 Packages/DiffIndex Hit http://ppa.launchpad.net raring Release Hit http://ppa.launchpad.net raring Release Get:6 http://ppa.launchpad.net raring Release [9,753 B] Ign http://archive.cloudera.com squeeze-cdh3u5/contrib Translation-en_US Hit http://ppa.launchpad.net raring/main Sources Ign http://archive.cloudera.com squeeze-cdh3u5/contrib Translation-en Hit http://ppa.launchpad.net raring/main amd64 Packages Hit http://ppa.launchpad.net raring/main Sources Hit http://ppa.launchpad.net raring/main amd64 Packages Get:7 http://ppa.launchpad.net raring/main Sources [860 B] Get:8 http://ppa.launchpad.net raring/main amd64 Packages [1,072 B] Ign http://security.ubuntu.com raring-security/main Translation-en_US Ign http://security.ubuntu.com raring-security/main Translation-en Ign http://security.ubuntu.com raring-security/universe Translation-en_US Ign http://security.ubuntu.com raring-security/universe Translation-en Err http://security.ubuntu.com raring-security/main Sources 404 Not Found [IP: 91.189.88.161 80] Err http://security.ubuntu.com raring-security/universe Sources 404 Not Found [IP: 91.189.88.161 80] Err http://security.ubuntu.com raring-security/main amd64 Packages 404 Not Found [IP: 91.189.88.161 80] Err http://security.ubuntu.com raring-security/universe amd64 Packages 404 Not Found [IP: 91.189.88.161 80] Ign http://ppa.launchpad.net raring/main Translation-en_US Ign http://ppa.launchpad.net raring/main Translation-en Ign http://ppa.launchpad.net raring/main Translation-en_US Ign http://ppa.launchpad.net raring/main Translation-en Ign http://ppa.launchpad.net raring/main Translation-en_US Ign http://ppa.launchpad.net raring/main Translation-en Fetched 33.7 kB in 6s (5,163 B/s) W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/raring/main/source/Sources 404 Not Found [IP: 54.152.129.43 80]
W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/raring/universe/source/Sources 404 Not Found [IP: 54.152.129.43 80]
W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/raring/main/binary-amd64/Packages 404 Not Found [IP: 54.152.129.43 80]
W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/raring/universe/binary-amd64/Packages 404 Not Found [IP: 54.152.129.43 80]
W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/raring-updates/main/source/Sources 404 Not Found [IP: 54.152.129.43 80]
W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/raring-updates/universe/source/Sources 404 Not Found [IP: 54.152.129.43 80]
W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/raring-updates/main/binary-amd64/Packages 404 Not Found [IP: 54.152.129.43 80]
W: Failed to fetch http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/raring-updates/universe/binary-amd64/Packages 404 Not Found [IP: 54.152.129.43 80]
W: Failed to fetch http://security.ubuntu.com/ubuntu/dists/raring-security/main/source/Sources 404 Not Found [IP: 91.189.88.161 80]
W: Failed to fetch http://security.ubuntu.com/ubuntu/dists/raring-security/universe/source/Sources 404 Not Found [IP: 91.189.88.161 80]
W: Failed to fetch http://security.ubuntu.com/ubuntu/dists/raring-security/main/binary-amd64/Packages 404 Not Found [IP: 91.189.88.161 80]
W: Failed to fetch http://security.ubuntu.com/ubuntu/dists/raring-security/universe/binary-amd64/Packages 404 Not Found [IP: 91.189.88.161 80]
E: Some index files failed to download. They have been ignored, or old ones used instead.
Indeed, if I then attempt to install fastqc, apt-get complains of not being able to authenticate some packages:
apt-get install fastqc
Reading package lists... Done Building dependency tree Reading state information... Done The following extra packages will be installed: libjbzip2-java libsam-java Suggested packages: picard-tools The following NEW packages will be installed: fastqc libjbzip2-java libsam-java 0 upgraded, 3 newly installed, 0 to remove and 1 not upgraded. Need to get 547 kB of archives. After this operation, 1,115 kB of additional disk space will be used. Do you want to continue [Y/n]? WARNING: The following packages cannot be authenticated! libjbzip2-java libsam-java fastqc Install these packages without verification [y/N]? n E: Some packages could not be authenticated
Maybe StarCluster's default configuration for apt-get is out-of-date?
% starcluster --version StarCluster - (http://star.mit.edu/cluster) (v. 0.95.6) Software Tools for Academics and Researchers (STAR) Please submit bug reports to starcluster@mit.edu
0.95.6
% uname -ar Linux xxx 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2 (2017-04-30) x86_64 GNU/Linux
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kynnjo
Right after creating a new cluster, I log in to it with
starcluster sshmaster <name-of-cluster>, and immediately run the commandapt-get update(as the very first command after login). The output from this command reveals several problems:Indeed, if I then attempt to install
fastqc,apt-getcomplains of not being able to authenticate some packages:Maybe StarCluster's default configuration for
apt-getis out-of-date?On my desktop, my StarCluster version is as follows:
My cluster's distro is:
EDIT: FWIW, the following is the distro for my desktop (not the cluster):