Re: superslow make on a cluster over the network

Help: Forums, postings and threads

Forums, postings and threads

Click on the Forum title, e.g. on the "Forums by Category" page, to read a sequence of postings to the Forum and its threads all in one page. If you are only interested in one thread or the thread following a specific posting, click the thread or the posting, which takes you to a smaller page, which contains only the part you are interested in and may be easier to navigate.

Layout of the posting thread(s)

The posting threads can be shown with/without the text of the postings ("Inline depth"). In addition the depth of the thread can be controlled ("Outline depth"). For both cases several values are provided, which can be toggled. Note that the displayed values are those, which can be chosen, they do not correspond to the actual display status of the thread(s).

Add message

Add a new posting thread to this Forum

Show subscribers

Click "Show subscribers" to get the List of all subscribers, who receive e-mail from postings to this Forum, if they have not explictly unsubscribed from a posting thread. This includes:

Subscribers to the forum
Explicit subscribers to the posting or any of its ancestors
The author of the posting (if he has not unsubscribed)
The authors of any ancestor posting (if they have not unsubscribed)

Some browsers display old pages from the cache

Some browsers (e.g. Firefox) display a page from the cache even though the page has been updated. As a result, one may not get the latest messages in the forum's outline or the logon ID of the previous session appears on the upper right corner. If one suspects that he or she does not get the latest content of a page, try clearing up the personal data from the browser's cache as the following:

Tools -> Clear Private Data -> Clear Private Data (from browser Firefox)

Tools -> Delete Private Data (from browser Opera)

then reflesh the current page to get the latest content.

Details on "Inline depth" and "Outline depth"

Threads and the follow-up messages are numbered. There is one line per posting, normally starting with the posting number. The URLs of a posting and its responses reflect the depth of the follow-up postings. Watch the URLs to see how this is done. Depending on the chosen display options, the thread-display may be incomplete; the number of messages at the next level is, however, displayed, e.g. "…3 message(s)". You may not see all contributors unless you choose "All".

Messages are "chained" if there are only replies at the first level, i.e. 1/1.html, 1/1/1.html etc. In case of "chained" messages the message number is replaced by the icon and there is no indentation.

Inline: Display the subject line only or also the text of the posting(s); for the choice "All" the "Outline" choices are switched off.

Argument Default value Alternative Comment

1 0 1 no text / full text of posting

2 1 All text for level 1 only / text for All postings

Argument	Default value	Alternative		Comment
1	0	1		no text / full text of posting
2	1	All		text for level 1 only / text for All postings

Outline: Choose the depth of the posting thread, successive toggle controls provide increasing detail.

Argument Default value Alternative Comment

1 2 1 2 levels / 1 level (original posting)

2 3 2 3 levels / 2 levels

3 3 All 3 levels / all levels (all postings)

Argument	Default value	Alternative	Comment
1	2	1	2 levels / 1 level (original posting)
2	3	2	3 levels / 2 levels
3	3	All	3 levels / all levels (all postings)

Hi Valery,

On Tue, 03 Nov 2009 22:36:38 GMT, Valery Taranenko wrote:
>...
> normally, on a computer with a local HDD, the make (of a 20 user files)
> w/ link takes 1 min. now, on a cluster, with a remote disk storage, i
> have to ssh to a computational node, and then the make takes 30 min or
> more. the problem is--i suspect--is a network load (I/O). "Making
> dependency for file ..." takes several min for each file(!). i suspect,
> make needs to transfer many files over the network (it's Gb Ethernet).
> not only making dependencies takes long, compilations do too. the make
> process is awfully slow. i cannot stand it :(
>...

If you're running on a computational node are there other jobs running on it? Also, it may be that there's a high network throughput anyway with lots of jobs. Both would certainly slow things down, and that being the case there isn't really a problem with Geant4 per se - it's going to happen with any buildsystem.

> does anybody knows how to bring the speed back to 1 min? i can do the
> so-called prestaging (copping the files to a local note hdd and run from
> there) but in this case all paths will be different, it will be
> basically a new g4 installation, which is too much.
<...

"Prestaging" is what I would recommend - but I'm a little unclear on what you mean by the paths being different. What you can do is in your Makefile (it sounds like you're using the Geant4 makefile system) is:

set G4WORKDIR to something like /tmp/geant4 - that should be on a locally mounted filesystem on *nix systems
set G4EXLIB to 'nothing' so that the application gets built directly without an intermediate library, i.e G4EXLIB :=

This should ensure that all created files are written locally. You'll have to copy the executable from wherever it is in /tmp to somewhere where it's available across the cluster - you can always add an 'install' target to the makefile to do this.

Cheers,

Ben.