Posts by [AF>Le_Pommier] Jerome_C2005

1) Message boards : News : Molecules are coming! (Message 539)
Posted 10 Feb 2020 by [AF>Le_Pommier] Jerome_C2005
Post:
I don't control anything about it. I added the application in beta on the interface and that's it.

Mmmm dommage...

Il doit bien y avoir un moyen vu qu'ils ont prévu une case à cocher pour ça... mais bon c'est pas grave :)
2) Message boards : News : Molecules are coming! (Message 532)
Posted 8 Feb 2020 by [AF>Le_Pommier] Jerome_C2005
Post:
One question : I can see that the new application was already listed and checked in the application list of my profile, even though I had not check the "accept test application" checkbox.

I actually checked it anyway, because I want to help with the testing, but wouldn't it be better not to add such beta app automatically to the list, especially if the test checkbox is not checked ?
3) Message boards : Number crunching : Native Linux WU refuses to suspend (Message 264)
Posted 9 Nov 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
Damotbe will confirm but I think the previous dev (the trainee) did completely stop the VM task for linux once he had come up with the native client, he thought it was a better solution.

So I don't think you can do this now, there is no choice.

He was also planning to do the same with windows and mac OS but his training period ended before that :)
4) Message boards : Science : Preliminary results? (Message 254)
Posted 4 Nov 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
Thanks a lot for this very interesting feedback, even if most of us won't understand "a variable part of it", this is typically the kind of "high level information" that pleases the crunching community and shows us we are helping an initiative with a lot of value !

Bon courage, nous sommes là pour aider :)
5) Message boards : Number crunching : Everything is bad (Message 246)
Posted 3 Nov 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
For linux and CPU core affinity issue (causes to be stuck into a single core instead of spreading harmoniously), here is a script provided by damotbe, it worked well with me (in Debian), I translate here his instructions :

while [[ 1 -eq 1 ]]; do for pid in $(pgrep nwchem); do taskset -p 0xffffffff $pid; done; sleep 60; done

Every minute it will force affinity of nwChem.

Depending on configuration it must be ran in root (or sudo), ideally inside a "screen" session. (install and use screen utility)

I used it straight away (not in screen) and it worked well for the tasks already running. I stopped it and its effect is lasting until the end of these tasks.


Alternative of screen (I did not test this) : create a affinity.sh and give it execution rights

touch affinity.sh
chmod +x affinity.sh

then add inside

#!/bin/bash
while [[ 1 -eq 1 ]]; do
    for pid in $(pgrep nwchem); do
        taskset -p 0xffffffff $pid
    done
    sleep 60
done

then execute is as a service with nohup (to be run again when booting the machine)

nohup sudo ./affinity.sh 2>/dev/null >/dev/null &


*** I did not write these scripts and provide no kind of support for them ***
6) Message boards : Number crunching : Work units complete but won't upload (Message 184)
Posted 20 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
Try to stop network traffic in boinc (activity menu) and then restart it, try to hold / unhold individual task upload (transfer tab), try to close boinc / launch it again... ?
7) Message boards : Number crunching : Native Linux WU refuses to suspend (Message 183)
Posted 20 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
[quote]A much higher percentage (compared to overall installed market share of OS'es) of the user base that crunch BOINC have native Linux machines doing the work.

BoincStats disagrees.

Only linux is summarized there (173k) but if you sum up only the first 10 rows of windows versions you are above of 300k...
(and the RAC of only the first windows row is more than twice the global linux)

So I don't know where you get that idea from.

It appears that each year the percentage of Linux machines increases in the BOINC user base (especially among the high-end equipment) and so, in the future, increasing amount of work done on your project will likely be native Linux WU's.

And for that I need proof too. I don't say that linux base is not increasing, I say it will never be bigger than windows.

And for the Mac, oh well, I know, I know... (I'm a Mac user)
8) Message boards : Number crunching : Very little CPU usage (Message 67)
Posted 7 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
vbox now allows VM to run inside VM.

If you refer to the last remark in my previous message, I was meaning "you cannot run any kind of virtualization software from a virtualized environment (like the linux VM (/cloud) machine I'm renting to a service provider called OVH)", I even tried installing VB inside of it (it will accept it), but when trying to run any actual VM inside of it, it will crash the whole host (VM) machine...

This is not the same as "VB inside VB", AFAIK (?)
9) Message boards : Number crunching : VM job unmanageable (Message 66)
Posted 7 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
This is a very interesting thread I read a good part of it : people still experience this issue in recent time depending on LHC subproject.

It seems to be a very subtle problem depending on many factors :

- amount of RAM and resources available on the machine + boinc parameters about memory, task switch frequency...
- how many VM tasks you run concurrently (it seems that "the less the better"),
- the version of VB installed on the machine (it seems "the most recent is not necessarily the best one"),
- the OS used,
- the version of the VB boinc wrapper that is being implemented by the project application (all LHC subprojects don't use the same wrapper version)
- and maybe other factors...

So it's a bit of an alchemy !!
10) Message boards : Number crunching : Very little CPU usage (Message 50)
Posted 6 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
First thing Michael : sorry I misunderstood, having your own linux VM (on your windows) to run the native non VM linux task should be more or less equivalent than the "native VM windows task", agreed.

About the overhead of running *anything* in a VM on a host system : I very strongly contest that you only "loose" 1% CPU. I have some experience in using VM, the reason why I switched to Mac back in the days is when they turned to Intel that allowed windows VM on the Mac, and during several years I used it intensively (not anymore) and the "VM own processes" (the programs used to run and encapsulate whatever you are doing in the VM) were always using a fair amount of CPU (VirtualBox processes, or Parallels Desktop processes).

And with boinc I can see the same happening with that VB process that encapsulates the boinc VM tasks (I don't have any at the moment and I forgot its name on the Mac), that process (plus another one, I need to test again) always eats a good amount of CPU outside of the VM boinc tasks themselves. I'll have a closer look after we finish our AF RAID in a week, I'll try to run QCPIA again on my Mac.


Damotbe : if you switch back with the VM app for linux again I won't be able to help anymore, I only run it on the OVH linux VM machine that I have, I cannot run any VM in it.
11) Message boards : Number crunching : VM job unmanageable (Message 49)
Posted 6 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
I didn't see that with Nanohub on my iMac.

And for LHC yes they did, but no idea how...
12) Message boards : Number crunching : Very little CPU usage (Message 40)
Posted 5 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
@Michael : but running a VM it is consuming a certain amount of CPU just for "running the VM" (I always had "a good 10% CPU" in mind ?), so there you are paying twice the cost ?

Of course this is better than "loosing most the CPU" that the current versions of the app seem not able to use properly in certain conditions (obviously linked to parallel multi-tasks) but it cannot be a long term solution, right ? (whatever the reason, let's think it will be fixed)
13) Message boards : Number crunching : VM job unmanageable (Message 39)
Posted 5 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
I remember this was an old recurrent issue with LHC when they started with VM applications years ago (and Boinc/Rob Walton was fighting to get a stable working wrapper), it would especially happen when "mixing" several VM tasks at the same time (and other VM projects like RNA...).

I don't know how they solved this, I never had it anymore (I think) with any LHC sub-projects.

Some days ago I think I found one QCPIA task in that same status on my iMac, but I also think it was at the start of the AF RAID and I must have I killed it and didn't want to try anything by that time.

Try to search / discuss on the LHC forum ?
14) Message boards : News : Public opening (Message 29)
Posted 4 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
Yépaaaaa !
15) Message boards : Cafe : Welcome onboard ! (Message 1)
Posted 3 Oct 2019 by [AF>Le_Pommier] Jerome_C2005
Post:
It's official ! QuChemPedIA is a beta project :)

Long live to QCPIA !




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