July 2024 – the iCSF Operating System was upgraded from Scientific Linux 7.9 to Alma 9.4. As a result, there’s a possibility certain pieces of software will require re-installing, or perhaps additional modulefiles will need to be loaded in your environment.<\/p>\n
We list below, the known problems and workarounds discovered so far.<\/p>\n
Your own testing of your jobs will help us. If you discover any such things in your own jobs, please do let us know!<\/p>\n
PLEASE NOTE: The incline256 nodes will soon be retired and replaced entirely with 2TB nodes. Therefore we recommend connecting to and using the newly upgraded incline2000 (incline2000.itservices.manchester.ac.uk) nodes.<\/strong><\/p>\n If you would like to report a problem with a piece of software, please fill out the following request form<\/a> and do include the following:<\/p>\n R\/Rstudio fails to open. <\/p>\n Users are encouraged to use the latest version of R and Rstudio. The latest version of R addresses a number of security concerns found in previous versions. Older version of R will not run on the incline2000 nodes. <\/p>\n Known applications affected: R & Rstudio<\/a> (follow link for more info.)<\/p>\n Please ensure you are connecting to incline2000 and loading the latest version of R and Rstudio<\/p>\n Please read the R & Rstudio<\/a> page for further info.<\/p>\n We have now taken some old nodes out of service. These were accessed via the addresses When logging in to the you may receive one or both the following errors about host identification:<\/p>\n The easiest way to fix this if logging in from Linux (e.g., our X2GO desktop), or from MacOSX or in MobaXterm is to run the following command(s) in your terminal window (note: you must not<\/strong> be logged in to the iCSF at this point):<\/p>\n You should then log in using ssh:<\/p>\n you will be asked to accept the new key:<\/p>\n It is safe<\/strong> to do so – answer July 2024 – the iCSF Operating System was upgraded from Scientific Linux 7.9 to Alma 9.4. As a result, there’s a possibility certain pieces of software will require re-installing, or perhaps additional modulefiles will need to be loaded in your environment. We list below, the known problems and workarounds discovered so far. Your own testing of your jobs will help us. If you discover any such things in your own jobs, please do let us.. Read more »<\/a><\/p>\n","protected":false},"author":7,"featured_media":0,"parent":90,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1306","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/1306","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=1306"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/1306\/revisions"}],"predecessor-version":[{"id":1529,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/1306\/revisions\/1529"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/90"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=1306"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}\r\nssh -X incline2000.itservices.manchester.ac.uk\r\n<\/pre>\n
How to report an issue<\/h2>\n
\n
Known Issues and Workarounds<\/h2>\n
R & Rstudio not working<\/h3>\n
Solution<\/strong><\/h4>\n
\r\n# Connect to incline2000\r\nssh -X incline2000.itservices.manchester.ac.uk\r\n\r\n# Load latest version of R\r\nmodule load apps\/gcc\/R\/4.4.1\r\n\r\n# Load latest version of rstudio\r\nmodule load apps\/binapps\/rstudio\/2024.04.2-any-r\r\n<\/pre>\n
Host Key Error on incline\/icsf Nodes<\/h3>\n
incline2000.itservices.manchester.ac.uk<\/code> and icsf.itservices.manchester.ac.uk<\/code> and incline256.itservices.manchester.ac.uk<\/code>. Those addresses are still valid but they will now log you into one of the new incline2000 nodes. This may cause you to see an error when logging in. See below on how to fix it:<\/p>\nincline2000.itservices.manchester.ac.uk<\/code> nodes using:<\/p>\n\r\nssh -X username@incline2000.itservices.manchester.ac.uk\r\n #\r\n # (optional - the error may occur below with or without -X)\r\n<\/pre>\n
\r\n@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\r\n@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @\r\n@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\r\nIT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!\r\nSomeone could be eavesdropping on you right now (man-in-the-middle attack)!\r\nIt is also possible that a host key has just been changed.\r\nThe fingerprint for the ED25519 key sent by the remote host is\r\nSHA256:1xTLr+ipUFWUHBeSq3ZF5lnOMGy73OzuQOzJFA2oZm8.\r\nPlease contact your system administrator.\r\nAdd correct host key in \/home\/username<\/em>\/.ssh\/known_hosts to get rid of this message.\r\nOffending ECDSA key in \/home\/username<\/em>\/.ssh\/known_hosts:3\r\n remove with:\r\n ssh-keygen -f \"\/home\/username<\/em>\/.ssh\/known_hosts\" -R \"incline2000\"<\/strong>\r\nHost key for incline2000 has changed and you have requested strict checking.\r\nHost key verification failed.\r\n<\/pre>\n
Solution<\/strong><\/h4>\n
\r\n# Do this on your laptop\/PC in a terminal NOT<\/strong> logged in to the iCSF\r\nssh-keygen -f \"\/home\/username<\/em>\/.ssh\/known_hosts\" -R 10.99.203.69\r\nssh-keygen -f \"\/home\/username<\/em>\/.ssh\/known_hosts\" -R incline2000.itservices.manchester.ac.uk\r\n #\r\n # Use the correct path and username reported in your<\/em> error!\r\n # It may be different to that shown here and where username<\/em> is\r\n # whatever username you use on YOUR laptop\/PC.\r\n<\/pre>\n
\r\nssh -X username<\/em>@incline2000.itservices.manchester.ac.uk\r\n<\/pre>\n
\r\nThe authenticity of host 'incline2000.itservices.manchester.ac.uk (10.99.203.69)' can't be established.\r\nECDSA key fingerprint is xx:xx:xx:xx:xx......:xx<\/em>.\r\nAre you sure you want to continue connecting (yes\/no)? yes<\/strong>\r\n #\r\n # Type yes<\/strong> and press Enter\r\n<\/pre>\n
yes<\/code> at the prompt. You will then be logged in to one of the 2TB compute nodes.<\/p>\n","protected":false},"excerpt":{"rendered":"