Re: [ccp4bb] [External] Re: [ccp4bb] Relion issue with MPI

[Suparno]

Try separating the MPI process and threads. For example if you have 4 GPUs, use 
0,1:2,3. You can do this in ‘Which GPUs to use’ under compute tab. 

Additionally, use a scratch directory and do not put particles in RAM. You can 
skip padding and gridding as well. Hope this helps!

Suparno.

Sent from my iPhone

> On Dec 22, 2023, at 7:23 PM, Srivastava, Dhiraj  
> wrote:
> 
> 
> It was reported by me but the problem was not solved. I thought ccp4bb has 
> much bigger user base and may be someone has experienced this issue. 
> It is something related to os (rocky linux) or mpi in my computer. Data set 
> is not a problem as i can process same data set with exactly same parameters 
> on a much less powerful computer without any problem. Also 2D classification 
> on my computer is using gpu without any problem. Its only mpi processes of 
> relion which are failing. Cryosparc is not a problem either.
> Thanks
> Dhiraj 
> From: Takanori Nakane 
> Sent: Friday, December 22, 2023 5:35 PM
> To: Srivastava, Dhiraj 
> Cc: CCP4BB@JISCMAIL.AC.UK 
> Subject: [External] Re: [ccp4bb] 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
> > 
> > 
> > 
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> > 
> > 
> 
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Re: [ccp4bb] [External] Re: [ccp4bb] Relion issue with MPI

[Srivastava, Dhiraj]

It was reported by me but the problem was not solved. I thought ccp4bb has much 
bigger user base and may be someone has experienced this issue.
It is something related to os (rocky linux) or mpi in my computer. Data set is 
not a problem as i can process same data set with exactly same parameters on a 
much less powerful computer without any problem. Also 2D classification on my 
computer is using gpu without any problem. Its only mpi processes of relion 
which are failing. Cryosparc is not a problem either.
Thanks
Dhiraj

From: Takanori Nakane 
Sent: Friday, December 22, 2023 5:35 PM
To: Srivastava, Dhiraj 
Cc: CCP4BB@JISCMAIL.AC.UK 
Subject: [External] Re: [ccp4bb] 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
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>



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Re: [ccp4bb] CCP4BB Digest - 21 Dec 2023 to 22 Dec 2023 (#2023-324) (out of office)

[Elisabeth Laurent]

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  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 
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 +
From:Panneels Valérie 
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 

Re: [ccp4bb] Relion issue with MPI

[Takanori Nakane]

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





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 







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[ccp4bb] Relion issue with MPI

[Srivastava, Dhiraj]

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




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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[ccp4bb] Postdoc opportunity at the PSI of Switzerland.

[Panneels Valérie]

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  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
https://www.psi.ch/en/lbr/people/valerie-panneels




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[ccp4bb] Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble

[Elke De Zitter]

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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