<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline !important; float: none;" class="">Oh dear I never saw Tom’s original mail, appareantly mailing list owners are not automativally subscribers….</span><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;"><br class=""><div class="">Let me anwer now!</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On 20. Oct 2020, at 14:51, Johannes Buchner <<a href="mailto:jbuchner@mpe.mpg.de" class="">jbuchner@mpe.mpg.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">On 19.10.20 14:58, Tom Dwelly wrote:<br class=""><blockquote type="cite" class="">Hi Jonas<br class=""><br class="">I have a few questions about using the MPE SciServer system. I am<br class="">sending this to the list in case any of these issues have been<br class="">encountered by other users.<br class="">Apologies for where I have got the SciServer nomenclature wrong.<br class=""><br class=""><br class="">1) Is it possible to ssh from an external machine into a container<br class="">session running on SciServer compute?<br class=""></blockquote><br class="">This would make SciServer many times more attractive to use for me.<br class=""><br class=""></div></div></blockquote><div class=""><br class=""></div><div class="">It is not possible to enter a interactive container that way no, however you can use the SciServer Python API to do interactive work on your machine using the resources on the SciServer (database, file sharing) and you can also use it to launch compute jobs, so running your software inside a new container.</div><div class=""><br class=""></div><div class="">The MPE version of it is here:</div><div class=""><a href="https://github.com/jonashaase/SciScript-Python" class="">https://github.com/jonashaase/SciScript-Python</a></div><div class=""><br class=""></div><div class="">I put some small example at the end of the getting started document</div><div class=""><a href="https://datashare.mpcdf.mpg.de/s/1e0CF3yRNcgDL4V" class="">https://datashare.mpcdf.mpg.de/s/1e0CF3yRNcgDL4V</a></div><div class="">And there is a example usage file with the code as well.</div><div class="">Admittedly a lot of it could be made more userfriendly...</div><br class=""><blockquote type="cite" class=""><div class=""><div class="">Cheers,<br class=""> Johannes<br class=""><br class=""><blockquote type="cite" class="">2) Is there any way for a user to set up persistent settings (e.g.<br class="">.bashrc file, ssh settings etc) that are sourced/used by new terminal<br class="">sessions within any compute container?<br class=""><br class=""></blockquote></div></div></blockquote><div class=""><br class=""></div><div class="">You can change .bashrc and everything else the idies user has access to and it should stay the same as long as the container is not deleted. However as soon as you start a new container that will all be gone since /home/idies gets re-built from the original image. </div><div class=""><br class=""></div><div class="">Only the volumes mounted inside /home/idies/workspace/ are persistent, so you could of course source a setup scrip inside your user volume which sets the environment in a way you like. </div><div class=""><br class=""></div><div class="">I am of course happy to adjust the compute images to set up the environment better. I am sure I missed a few things, in particular in connection with the x-ray software.</div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><blockquote type="cite" class="">3) Is it possible for users to install standard linux packages (e.g. via<br class="">apt) within a container session?<br class=""><br class=""></blockquote></div></div></blockquote><div class=""><br class=""></div><div class="">apt-get not, but conda and pip work.</div><div class=""><br class=""></div><div class="">The reason is that we enforce that the user in the container is ‘idies’ and not root as it most often is in a Docker container. </div><div class="">Its mostly a security issue: We don’t want anyone with root to be able to write onto the mounted disks on the underlying system and somehow launch a escalation attack there. </div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><blockquote type="cite" class="">3a) if not, please can you add emacs to the default list of installed<br class="">packages in the standard SciServer compute image?<br class=""><br class=""></blockquote></div></div></blockquote><div class=""><br class=""></div><div class="">absolutely, no problem!</div><div class=""><br class=""></div><div class="">@everyone: Please let me know if any software or libraries you need are missing and I’ll install them as quickly as possible.</div><div class=""><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><blockquote type="cite" class=""><br class="">4) Any idea why 'git clone' operations like the following are failing<br class="">within a compute container?<br class=""><br class=""></blockquote></div></div></blockquote><div class=""><br class=""></div><div class="">unfortunately not, this should work.</div><div class="">I will look into it!</div><div class=""><br class=""></div></div><div class=""><br class=""></div>cheers</div><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;">Jonas</div><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;"><div class=""><br class=""></div></div><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-ligatures: normal; font-variant-position: normal; font-variant-caps: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">—<br class="">Jonas Haase<br class="">Max Planck Institute for Extraterrestrial Physics (MPE)<br class="">Giessenbachstr. 1, 85748 Garching, Germany</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">X5 1.3.08<br class="">+49 89 30000 3706</div></span></div></div></div></div></div>
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