Fight­ing the Coro­n­avirus with FreeB­SD (Folding@Home)

Pho­to by Fusion Med­ical Ani­ma­tion on Unsplash

Here is a quick HOWTO for those which want to pro­vide some FreeB­SD based com­pute resources to help find­ing vac­cines. I have not made a port out of this and do not know yet if I get the time to make one. If some­one wants to make a port, go ahead, do not wait for me.

UPDATE 2020-03-22: 0mp@ made a port out of this, it is in “biology/lin­ux-foldin­gath­ome”.

  • Down­load the lin­ux RPM of the Folding@Home client (this cov­ers fah­client only).
  • Enable the lin­ux­u­la­tor (ker­nel moduls and linux_base (first part of chap­ter 10.2) is enough).
  • Make sure linprocfs/linsysfs are mount­ed in /com­pat/lin­ux/{proc|sys}.
  • cd /compat/linux
  • tar -xf /path/to/fahclient....rpm
  • add the “fah­client” user (give it a real home direc­to­ry)
  • make sure there is no /compat/linux/dev or alter­na­tive­ly mount devfs there
  • mkdir /compat/linux/etc/fahclient
  • cp /compat/linux/usr/share/doc/fahclient/sample-config.xml /compat/linux/etc/fahclient/config.xml
  • chown -R fahclient /compat/linux/etc/fahclient
  • edit /compat/linux/fahclient/config.xml: mod­i­fy user (manda­to­ry) / team (option­al: FreeB­SD team is 11743) / passkey (option­al) as appro­pri­ate (if you want to con­trol the client remote­ly, you need to mod­i­fy some more parts, but some­how the client “los­es” a filedescrip­tor and stops work­ing as it should if you do that on FreeB­SD)
  • If you have the home direc­to­ries of the users as no-exec (e.g. seper­ate ZFS datasets with exec=off): make sure the home direc­to­ry of the fah­client user has exec per­mis­sions enabled
  • cd ~fahclient (impor­tant! it tries to write to the cur­rent work direc­to­ry when you start it)
  • Start it: /usr/sbin/daemon /compat/linux/usr/bin/FAHClient /compat/linux/etc/fahclient/config.xml --run-as fahclient --pid-file=/var/run/fahclient.pid >/dev/null 2>&1

Per default it will now pick up some SARS-CoV‑2 (COVID-19) relat­ed fold­ing tasks. There are some more con­fig options (e.g. how much of the sys­tem resources are used). Please refer to the offi­cial Folding@Home site for more infor­ma­tion about that. Be also aware that there is a big rise in com­pute resources donat­ed to Folding@Home, so the pool of avail­able work units may be emp­ty from time to time, but they are work­ing on adding more work units. Be patient.

Send to Kin­dle

Lin­ux­u­la­tor explained: How to cre­ate Lin­ux bina­ries on FreeB­SD

There may by cas­es where you want to gen­er­ate a Lin­ux bina­ry on a FreeB­SD machine. This is not a prob­lem with the lin­ux­u­la­tor, but not with the default linux_base port.

As you may know, the linux_base port is designed to deliv­er an inte­grat­ed expe­ri­ence with FreeB­SD native pro­grams. As such some parts of the native FreeB­SD infra­struc­ture is used. If you would try to use a Lin­ux-com­pil­er to gen­er­ate Linux-bina­ries, you would run into the prob­lem that by default the FreeB­SD includes are used.

Pre­req­ui­sites

To have a ful­ly fea­tured and non-integrated Lin­ux envi­ron­ment on your FreeB­SD sys­tem either mount an exist­ing (and com­pat­i­ble) Lin­ux instal­la­tion some­where into your FreeB­SD sys­tem, or install a linux_dist port. This can be done addi­tion­al­ly to an already installed linux_base port.

Prepa­ra­tion

When you have a com­plete Lin­ux envi­ron­ment avail­able, you need to mount the FreeB­SD devfs to /path/to/complete_linux/dev, lin­procfs to /path/to/complete_linux/proc and lin­sys­fs to /path/to/complete_linux/sys to have a com­plete set­up.

Use it

Now you just need to chroot into this  /path/to/complete_linux and you configure/make/install or what­ev­er you need to do to gen­er­ate your desired Lin­ux bina­ry.

Send to Kin­dle

Lin­ux­u­la­tor D‑Trace probes com­mit­ted to cur­rent

A while ago I com­mit­ted the lin­ux­u­la­tor D‑Trace probes I talked about ear­li­er. I wait­ed a lit­tle bit for this announce­ment to make sure I have not bro­ken any­thing. Nobody com­plained so far, so I assume noth­ing obvi­ous­ly bad crept in.

The >500 probes I com­mit­ted do not cov­er the entire lin­ux­u­la­tor, but are a good start. Adding new ones is straight for­ward, if some­one is inter­est­ed in a junior-ker­nel-hack­er task, this would be one. Just ask me (or ask on emu­la­tion@), and I can guide you through it.

Send to Kin­dle

linux_base-c6

Seems I for­got to announce that the linux_base-c6 is in the Ports Col­lec­tion now. Well, it is not a replace­ment for the cur­rent default lin­ux base, the lin­ux­u­la­tor infra­struc­ture ports are miss­ing and we need to check if the ker­nel sup­ports enough of 2.6.18 that noth­ing breaks.

TODO:

To my knowl­edge, nobody is work­ing on any­thing of this. Any­one is wel­come to have a look and pro­vide patch­es.

Send to Kin­dle

Lin­ux­u­la­tor progress

This week­end I made some progress in the lin­ux­u­la­tor:

  • I MFCed the report­ing of some linux-syscalls to 9‑stable and 8‑stable.
  • I updat­ed my lin­ux­u­la­tor-dtrace patch to a recent ‑cur­rent. I already com­piled it on i386 and arundel@ has it com­piled on amd64. I count­ed more than 500 new DTrace probes. Now that DTrace res­cans for SDT probes when a ker­nel mod­ule is loaded, there is no ker­nel pan­ic any­more when the lin­ux mod­ule is loaded after the DTrace mod­ules and you want to use DTrace. I try to com­mit this at a morn­ing of a day where I can fix things dur­ing the day in case some prob­lems show up which I did not notice dur­ing my test­ing.
  • I cre­at­ed a PR for portmgr@ to repocopy a new linux_base port.
  • I set the expi­ra­tion date of linux_base-fc4 (only used by 7.x and upstream way past its EoL) and all depen­dent ports. It is set to the EoL of the last 7.x release, which can not use a lat­er linux_base port. I also added a com­ment which explains that the date is the EoL of the last 7.x release.
Send to Kin­dle