Dear Kay,
many thanks for your suggestions. We will look into this.
best
Demetres
On 11/29/2022 2:35 PM, Kay Diederichs wrote:
Dear Demetres,
I googled the Ubuntu 22.04 release notes and found
https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 which says "We’ve enabled
the
Dear Demetres,
I googled the Ubuntu 22.04 release notes and found
https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 which says
"We’ve enabled the userspace OOMD service and are shipping the systemd-oomd
package by default on the “Ubuntu Desktop” flavour, to avoid overloaded
Dear Demetres,
On Tue, Nov 29, 2022 at 10:25:17AM +0200, Demetres D. Leonidas wrote:
> Dear Kay,
>
> you are right and I do apologize for the misunderstanding. Point 1
> and 2 are sufficient.
You can probably avoid doing any of this by using the LIB= feature of
XDS on gzipped CBF files with the
Dear Kay,
you are right and I do apologize for the misunderstanding. Point 1 and 2
are sufficient.
best
Demetres
On 11/29/2022 10:00 AM, Kay Diederichs wrote:
Dear Demetres,
sounds a bit drastic!
The second point alone would certainly suffice, because then no forking is done.
What kind
Dear Demetres,
sounds a bit drastic!
The second point alone would certainly suffice, because then no forking is done.
What kind of hardware is that?
I would expect that on a contemporary workstation you have 8GB of RAM or more;
that would allow for 8 or more processes.
Do you have a swapfile?
marc-requ...@jiscmail.ac.uk>
Sent: Tuesday, November 29, 2022 6:34:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] xds crashes
Dear Kay,
after some digging and help from Max Nanao we found that the problem
was the memory. It was fulling rapidly. The workaround was to:
1. unzip the cbf
Dear Kay,
after some digging and help from Max Nanao we found that the problem
was the memory. It was fulling rapidly. The workaround was to:
1. unzip the cbf files prior to processing
2. use maximum number of jobs 1
3. use number of processors 4
4. run xds_par
Many thanks for all your
Dear Demetres,
I agree with what James says: this is the operating system trying to to
prevent, in an over-zealous way, the
forking of too many or too big (in terms of memory) processes.
In other words, XDS hasn't changed, but the operating system changed - it
applies different limits to its
Sounds like your kernel might think "forkxds" is creating a "fork
bomb". Too many sub-processes firing off in too short a time triggers
this. On one of my systems, I fixed it by editing
/etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more
pids than normal. This tends to
Dear all,
I do not know if this is the right list and I would like to apologize if
it is not.
We have repeatedly experienced xds crashes in machines running ubuntu
22.04.1 with the following message repeated several times at the
INTEGRATE step
/usr/local/bin/forkxds: line 60: 3427 Done
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