Base software kit - Revision history

Craigje at 16:43, 14 January 2021

2021-01-14T16:43:54Z

← Older revision		Revision as of 16:43, 14 January 2021
Line 1:		Line 1:
	These software packages should be installed on every machine we provision, regardless of their purpose. A script [https://gitlab.cluster.earlham.edu/sysadmin/server-scripts/tree/master on GitLab] has a dirt-simple script to do this, though it should be improved and/or developed (including making an Ansible playbook for easy install on a bunch of cluster nodes).		These software packages should be installed on every machine we provision, regardless of their purpose. A script [https://gitlab.cluster.earlham.edu/sysadmin/server-scripts/tree/master on GitLab] has a dirt-simple script to do this, though it should be improved and/or developed (including making an Ansible playbook for easy install on a bunch of cluster nodes).

			These are done in a playbook now, see the sysadmin/Ansible-Playbooks project in GitLab:
	* nano - text editor		* nano - text editor
	* vim - text editor		* vim - text editor
Line 9:		Line 11:
	* gcc - most recent C compiler (modules can support as many versions as we'd like but we need at least one)		* gcc - most recent C compiler (modules can support as many versions as we'd like but we need at least one)
	* ntp - get a time server		* ntp - get a time server
	* ~~modules~~		* mlocate
	* rsync		* rsync
			* strace
			* zsh
			* curl
	* rclone		* rclone
	* openldap		* openldap
	* openldap-clients		* openldap-clients
	* openssh-ldap		* openssh-ldap
	* pam_ldap		* pam_ldap or libpam-ldap
	* nss-pam-ldapd		* nss-pam-ldapd
	* unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)		* unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)

			Do these manually (or expand the playbook):
			* Install Nagios
			* modules
			* LDAP client

	On a high-performance computing server or cluster, add these:		On a high-performance computing server or cluster, add these:

Craigje at 14:59, 21 May 2020

2020-05-21T14:59:52Z

← Older revision		Revision as of 14:59, 21 May 2020
Line 24:		Line 24:
	* OpenMPI (latest version)		* OpenMPI (latest version)

	If ~~your~~ server will be used for bioinformatics, add these:		If the server will be used for bioinformatics, add these:
	* [[Sysadmin:Bioinformatics Packages\|ea-utils]]		* [[Sysadmin:Bioinformatics Packages\|ea-utils]]
	* [[Sysadmin:Bioinformatics Packages\|AdapterRemoval]]		* [[Sysadmin:Bioinformatics Packages\|AdapterRemoval]]
Line 36:		Line 36:
	* mapdamage2		* mapdamage2

	~~Survey kit~~:		If the server will host surveying software, add these:
	* Docker		* Docker
			* ODM
	* WebODM		* WebODM

Craigje at 14:58, 21 May 2020

2020-05-21T14:58:34Z

← Older revision		Revision as of 14:58, 21 May 2020
Line 11:		Line 11:
	* modules		* modules
	* rsync		* rsync
	* ~~unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)~~		* rclone

	~~On a cluster, add these: (should not most of these be in the above list too?)~~
	* C3 tools (see [[Sysadmin:C3\|the C3 tools page]]) - possibly deprecated, Ansible is a good replacement
	* openldap		* openldap
	* openldap-clients		* openldap-clients
Line 20:		Line 17:
	* pam_ldap		* pam_ldap
	* nss-pam-ldapd		* nss-pam-ldapd
			* unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)

			On a high-performance computing server or cluster, add these:
			* C3 tools (see [[Sysadmin:C3\|the C3 tools page]]) - possibly deprecated, Ansible is a good replacement
	* Slurm		* Slurm
	* OpenMPI (latest version)		* OpenMPI (latest version)

	~~On a jumbo~~ server, add these: ~~(this is more a bioinformatics package)~~		If your server will be used for bioinformatics, add these:
	* rclone
	* [[Sysadmin:Bioinformatics Packages\|ea-utils]]		* [[Sysadmin:Bioinformatics Packages\|ea-utils]]
	* [[Sysadmin:Bioinformatics Packages\|AdapterRemoval]]		* [[Sysadmin:Bioinformatics Packages\|AdapterRemoval]]
Line 35:		Line 35:
	* PMD tools		* PMD tools
	* mapdamage2		* mapdamage2

			Survey kit:
			* Docker
			* WebODM

	Python libraries (Python 3):		Python libraries (Python 3):

Charliep at 14:42, 21 May 2020

2020-05-21T14:42:01Z

← Older revision		Revision as of 14:42, 21 May 2020
Line 13:		Line 13:
	* unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)		* unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)

	On a cluster, add these:		On a cluster, add these: (should not most of these be in the above list too?)
	* C3 tools (see [[Sysadmin:C3\|the C3 tools page]]) - possibly deprecated, Ansible is a good replacement		* C3 tools (see [[Sysadmin:C3\|the C3 tools page]]) - possibly deprecated, Ansible is a good replacement
	* openldap		* openldap
Line 20:		Line 20:
	* pam_ldap		* pam_ldap
	* nss-pam-ldapd		* nss-pam-ldapd
			* Slurm
			* OpenMPI (latest version)

	On a jumbo server, add these:		On a jumbo server, add these: (this is more a bioinformatics package)
	* rclone		* rclone
	* [[Sysadmin:Bioinformatics Packages\|ea-utils]]		* [[Sysadmin:Bioinformatics Packages\|ea-utils]]

Craigje at 19:01, 20 May 2020

2020-05-20T19:01:35Z

← Older revision		Revision as of 19:01, 20 May 2020
Line 11:		Line 11:
	* modules		* modules
	* rsync		* rsync
			* unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)

	On a cluster, add these:		On a cluster, add these:

Craigje at 15:46, 12 May 2020

2020-05-12T15:46:42Z

← Older revision		Revision as of 15:46, 12 May 2020
Line 10:		Line 10:
	* ntp - get a time server		* ntp - get a time server
	* modules		* modules
			* rsync

	On a cluster, add these:		On a cluster, add these:

Craigje at 14:12, 4 May 2020

2020-05-04T14:12:34Z

← Older revision		Revision as of 14:12, 4 May 2020
Line 1:		Line 1:
	These software packages should be installed on every machine we provision, regardless of their purpose. A script in /~~root~~/~~install~~ on ~~tools~~ has ~~a model for~~ a dirt-simple script to do this, though it ~~could probably~~ be improved and/or developed ~~into~~ an Ansible playbook.		These software packages should be installed on every machine we provision, regardless of their purpose. A script [https://gitlab.cluster.earlham.edu/sysadmin/server-scripts/tree/master on GitLab] has a dirt-simple script to do this, though it should be improved and/or developed (including making an Ansible playbook for easy install on a bunch of cluster nodes).
	* nano - text editor		* nano - text editor
	* vim - text editor		* vim - text editor

Craigje at 13:37, 9 March 2020

2020-03-09T13:37:35Z

← Older revision		Revision as of 13:37, 9 March 2020
Line 9:		Line 9:
	* gcc - most recent C compiler (modules can support as many versions as we'd like but we need at least one)		* gcc - most recent C compiler (modules can support as many versions as we'd like but we need at least one)
	* ntp - get a time server		* ntp - get a time server
			* modules

	On a cluster, add these:		On a cluster, add these:

Craigje at 14:54, 18 February 2020

2020-02-18T14:54:45Z

← Older revision		Revision as of 14:54, 18 February 2020
Line 2:		Line 2:
	* nano - text editor		* nano - text editor
	* vim - text editor		* vim - text editor
			* emacs - text editor
	* nfs-common for Debian or nfs-utils for CentOS - allow NFS mounts		* nfs-common for Debian or nfs-utils for CentOS - allow NFS mounts
	* wget - wget a file from the Internet		* wget - wget a file from the Internet
Line 17:		Line 18:
	* nss-pam-ldapd		* nss-pam-ldapd

	On a ~~phat node~~, add these:		On a jumbo server, add these:
	* rclone		* rclone
	* [[Sysadmin:Bioinformatics Packages\|ea-utils]]		* [[Sysadmin:Bioinformatics Packages\|ea-utils]]

Craigje at 18:20, 8 November 2019

2019-11-08T18:20:30Z

← Older revision		Revision as of 18:20, 8 November 2019
Line 29:		Line 29:
	* PMD tools		* PMD tools
	* mapdamage2		* mapdamage2

			Python libraries (Python 3):
			* Pandas
			* Numpy
			* Scipy