Thank you for your e-mail. I am out of office until January 2nd, 2024.
I will respond to your e-mail as soon as possible upon my return.
For urgent matters please contact: b...@boku.ac.at
Thank you for your understanding.
With kind regards,
Elisabeth Laurent
>>> CCP4BB automatic digest system <lists...@jiscmail.ac.uk> 23.12.23 01:00 >>>
There are 4 messages totaling 667 lines in this issue.
Topics of the day:
1. Two-year postdoctoral position in time-resolved crystallography at IBS in
Grenoble
2. Postdoc opportunity at the PSI of Switzerland.
3. Relion issue with MPI
4. Relion issue with MPI
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Date: Fri, 22 Dec 2023 10:20:57 +0100
From: Elke De Zitter <elke.de-zit...@ibs.fr>
Subject: Two-year postdoctoral position in time-resolved crystallography at IBS
in Grenoble
Dear all,
We have an immediate opening for a two-year postdoctoral researcher in SNaX
team of the DYNAMOP group at the Institute for Structural Biology in Grenoble
(France). The successful candidate will work on the development and
optimization of bio-scavengers towards toxic organophosphorus compounds. To
attain this goal, the researcher will use time-resolved crystallography and in
silico protein design methods. The position is funded by the French National
Research Agency via the University Grenoble Alpes, and is open for a young
researcher.
Applicants must have obtained a Ph.D. in structural biology, biochemistry,
biophysics, physics, chemistry, or a related field, no more than two years
before the start of the project. The candidate must show a track-record of
publications in peer-reviewed journals, and is expected to be proficient in
English and highly motivated to learn new skills. The candidate will work in
the multidisciplinary DYNAMOP group and thus needs to be a good team player as
well as being capable of working independently. While the research will be
carried out in English, non-French-speaking candidates are expected to learn
the basics of French in order to facilitate communication and integration into
the laboratory.
Experience with one or more of the following skills would be highly evaluated:
protein design or the usage of artificial intelligence for structural biology,
protein expression and purification, protein crystallization and macromolecular
crystallography, serial crystallography, programming or scripting.
Interested candidates can apply via [
https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996
|
https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996
] . We advice to contact Elke De Zitter (elke.de-zit...@ibs.fr) to obtain more
information about the postdoctoral position and application procedure.
All the best,
Elke
Elke De Zitter
Institut de Biologie Structurale - IBS
group DYNAMOP
71 avenue des Martyrs
38044 Grenoble Cedex 9, France
+33 4 57 42 86 56
elke.de-zit...@ibs.fr
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------------------------------
Date: Fri, 22 Dec 2023 12:11:40 +0000
From: Panneels Valérie <valerie.panne...@psi.ch>
Subject: Postdoc opportunity at the PSI of Switzerland.
Dear Colleagues,
The Laboratory of Biomolecular Research at the Paul Scherrer Institute (PSI),
Switzerland, is advertising for a Postdoc position from the NanoArgovia
Programm of the Swiss Nanoscience Institute (SNI). This project is granted for
one year and extendable to 2 years.
The project is based on Electron Diffraction Crystallography on proteins either
photosensitive or involved in pharma applications. The PSI is the largest
research institute for natural and engineering sciences in Switzerland
(https://www.psi.ch/en) and hosts a synchrotron, the X-ray free electron laser
SwissFEL and an electron microscopy facility (https://www.psi.ch/en/emf). The
BIO division together with our PSI detector group has developed a unique
instrument for electron diffraction with a dedicated ED-detector based on PSI
detector technology.
Our laboratory (please consult https://www.psi.ch/en/lbr) is focused on
studying the mechanism of action of membrane proteins, including structural
dynamics, as well as studying the structural and functional role of tubulin in
the cell, with a focus on developping personalized medecine tools/strategies.
A selection of recent publications can be found here: https://www.psi.ch/en/lbr
The project will focus on the structural determination of proteins using
electron diffraction. Although most structures are determined at high
resolution using X-ray diffraction, the properties of electrons give them the
advantage to deliver even higher resolution and the possibility to see
hydrogens. The project will address several questions around mechanisms
involving hydrogen bond displacements in enzymes and membrane proteins.
The selected postdoc will crystallize the proteins, a soluble one and a
membrane protein, with already established protocols, optimize the crystal size
using focused ion beam scanning electron microscopy (FIB-SEM) milling and
collect the data at the transmission electron microscope in diffraction mode.
Similar experimental data will be compared to the performance of a table top
electron diffractometer prototype used in the pharma field.
All devices and state of the art equipment for protein expression, purification
and crystallisation are located at the Paul Scherrer Institute, including the
FIB/SEM device and a dedicated cryo-electron diffraction microsocope. The
tabletop electron diffractometer is close to it, in the region of Bale in
Switzerland.
The position is intended for 2 years and to be filled as soon as possible.
Experience in FIB/SEM-lamellae preparation, electron diffraction and/or
crystallography would be beneficial.
The applicants should send their CV and a cover letter to:
valerie.panne...@psi.ch<mailto:valerie.panne...@psi.ch> Informal inquiries can
be also addressed to the same e-mail.
Best wishes and happy time in this end of the year,
Valérie Panneels
__________________________________________
Valerie Panneels
Projects Leader
Paul Scherrer Institute
Forschungsstrasse 111
OSRA/005
5232 Villigen PSI
Switzerland
Tel: +41 56 310 21 04
E-Mail: valerie.panne...@psi.ch<mailto:valerie.panne...@psi.ch>
https://www.psi.ch/en/lbr/people/valerie-panneels
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------------------------------
Date: Fri, 22 Dec 2023 18:31:01 +0000
From: "Srivastava, Dhiraj" <dhiraj-srivast...@uiowa.edu>
Subject: Relion issue with MPI
Hi
I am trying to use relion and I am getting error when trying to use mpi (for 3d
classification and 3D auto-refine).
ERROR: out of memory in
/home/lvantol/relion5/relion/src/acc/cuda/custom_allocator.cuh at line 436
(error-code 2)
in: /home/lvantol/relion5/relion/src/acc/cuda/cuda_settings.h, line 65
ERROR:
A GPU-function failed to execute.
2D classification is working fine with significant GPU usage. I tried 3
different versions (4, 4 beta and 5 beta), one installed by vendor (Exxact) and
all have the same issue. I am able to do 3D auto-refine and 3D classification
on the same data set using our cluster without any problem. did anyone
encounter a similar issue earlier? How can I fix this problem?
Thank you
Dhiraj
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------------------------------
Date: Sat, 23 Dec 2023 08:35:34 +0900
From: Takanori Nakane <tnakane.prot...@osaka-u.ac.jp>
Subject: Re: Relion issue with MPI
Hi,
First of all, please report details of your hardware and your job.
- Type of GPU
- Number of GPU
- GPU memory size
- Box size
- Number of threads
- Number of MPI processes
- Full command line
Do you get the same error in ALL datasets (including our
tutorial dataset) or only on this particular dataset?
A very similar issue was reported in
https://github.com/3dem/relion/issues/1056
but I do not know what is the cause at the moment.
Best regards,
Takanori Nakane
On 12/23/23 03:31, Srivastava, Dhiraj wrote:
> Hi
> I am trying to use relion and I am getting error when trying to use mpi
> (for 3d classification and 3D auto-refine).
>
>
> ERROR: out of memory in
> /home/lvantol/relion5/relion/src/acc/cuda/custom_allocator.cuh at line
> 436 (error-code 2)
>
> in: /home/lvantol/relion5/relion/src/acc/cuda/cuda_settings.h, line 65
>
> ERROR:
>
> A GPU-function failed to execute.
>
>
> 2D classification is working fine with significant GPU usage. I tried 3
> different versions (4, 4 beta and 5 beta), one installed by vendor
> (Exxact) and all have the same issue. I am able to do 3D auto-refine
> and 3D classification on the same data set using our cluster without any
> problem. did anyone encounter a similar issue earlier? How can I fix
> this problem?
>
>
> Thank you
>
> Dhiraj
>
>
>
> ------------------------------------------------------------------------
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End of CCP4BB Digest - 21 Dec 2023 to 22 Dec 2023 (#2023-324)
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