Re: [ccp4bb] [ccpem] relion benchmark with recent GPUs

[mesters]

Hi,

a dedicated/fast stand-alone workstation will be in most cases a better 
choice for running single jobs than running on multiple machines as the 
network capabilities are a limiting factor once all nodes try to access 
the disk with the data (unless locally stored on each node on an 
ultra-fast M.2 SSD). Obviously, if a central computing service is 
provided to you (for free), the situation may be a different one if time 
does not play that big a role or, you plan to run multiple jobs in parallel.


You are correct to note that I/O operations are very important and often 
one badly chosen/implemented "element(s)" slows down everything. A 
well-balanced I/O speed between DDR memory, GPU (and its memory), CPU 
and fast SSD will be needed for a stand-alone machine to be 
useful/compatible.


My thoughts / two cents / feedback:

CPU: 1 CPU with 32 cores
GPU: 2 GPUs with 16-24 GB GDDR each
DDR: 256 GB (minimally 128 GB)
SSD: 1 TB M.2 PCIe 3.0 x 4 (for the dataset being processed)
2nd SSD: 1 TB standard SSD (not PCIe 3.0 x 4) for the linux/software etc.
Raid: 2 x 12TB HDD Disks (for general dataset storage)
Motherboard: maximum (all possible) number of PCIe lanes implemented and 
with 10GB ethernet (for example to connect 2 dedicated machines with one 
another)


- 32 core CPU will do fine unless budget plays no role or, you want to 
outperform the GPUs: The 3990X will out-render an RTX 2060 Super. Extra 
money is better spent on professional GPUs and 256 GB DDR memory 
(instead of the minimum 128 GB)
- 2 GPUs with 16-24 GB GDDR each in order to optimize data shuffling: 2 
GPU cards can be each run at PCIe 3.0 x16 speed instead of more cards at 
x8 speed. More memory on the card is more efficient/important than the 
total number of cards / cuda-cores. With 2 cards you will have less 
problems with heat production in the case and no problem with the supply 
of power. Many do not notice that because of heat, CPUs and especially 
GPUs are throttled severely: Consumer RTX cards are not designed for the 
purpose of running 4 of them on one motherboard / in one case! The hot 
air is not "exported" out of the case by consumer RTX cards. Finally, 
Nvidia still generously allows to install the cuda drivers on consumer 
RTX cards but actually not in the environment of a central university 
facility (read the small print)! Further, the cuda software profits from 
having professional quadro cards installed such as the RTX 5000 or 6000, 
which in addition do not get that hot!
- 256 GB for big datasets, minimally 128 GB but with the ability for 
later upgrade -> octa-channel mainboard
- 1 TB M.2 PCIe 3.0 x 4 ultra-fast SSD disk for placing the dataset 
under process as it will be read more than once during processing: Many 
mainboards allow to install only one ultra-fast M.2 disk, for all other 
software including Linux and Relion you will thus need a normal SSD. Buy 
a Samsung 980 Pro for placing the data to be processed as these will 
last longer but be prepared to replace it after some time because of the 
heavy I/O burden
- Motherboard with maximum possible number of PCIe lanes -> Threadripper 
motherboard: No consumer motherboard supplies the maximum possible 
number of lanes! X299 motherboards (Intel) and several proposedly 
high-end Intel CPUs suffer from the same "problem". Beware, PCIe lanes 
or other "ports" may become disabled once you plug-in further M.2 SSD 
disks etc. Make really sure to study/scrutinize the small print in the 
manual of the motherboard, it will pay off.


Cheers,

Jeroen


  Am 25.03.21 um 13:29 schrieb Pierre-Damien Coureux:

Hi everyone

we are thinking in buying new nodes for our data processing with 
relion. We still have technical questions that need to be addressed 
and I couldn't find recent benchmarks for the answers:


- what's the best choice between buying 2 nodes with 4xGPU or 1 node 
with 8xGPU with RTX 3080/3090 cards. In terms of speed calculation, is 
1 node with 8xGPU still equivalent to 3 nodes with 4xGPU ?


- Comparing RTX 3080 (8704 cores, 10 Go GDDR, 2-Slot height) and RTX 
3090 cards (10496 cores, 24 Go GDDR, 3-Slot height), would 4x3090 GPU 
cards be more advantageous in one node  if you can run relion with 2 
mpi/card (because of the 24 Go RAM/card) instead of having one node 
with 8x3080 GPU cards and run 1 mpi/card?


- for a node with 8xGPU with RTX 30XX cards, because of the speed of 
the cards, would the RAID SSD drive Bus speed (1 Go/s) be enough to 
"feed" all the GPU without slowing down the system ? Is extra 
PCI-Express card with SSD at 3 Go/s a preferred choice for this kind 
of node ?


Any feedback is welcome

Pierre-Damien Coureux




--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/ 
Visiting 
Professorship (South Bohemian University) in Biophysics

Logo Uni Lübeck
*University of Lübeck*
Center for Structural 

[ccp4bb] Postdoc position at CHESS

[Doletha Marian Szebenyi]

The Macromolecular Diffraction and High Pressure Biology resources at the
Cornell High Energy Synchrotron Source (MacCHESS and CHEXS/HP-Bio, respectively)
have an opening for a Postdoctoral Associate to develop applications of high
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folding, adaptation to extreme environments, and the origin of life. The
primary method to be used is pressurization of macromolecular crystals in a
diamond anvil cell (HP-MX), but other techniques such as high-pressure small
angle X-ray scattering (HP-SAXS) will also be available. A Ph.D. degree in a
relevant field (e.g. structural biology or biophysics) is required.
Experience in crystallography is highly desirable, and experience working with
samples in "non-standard" environments is a plus. The ability to identify
suitable systems for study, through researching previous work and establishing
suitable collaborations, is essential. In addition to pursuing his/her own study
of pressure effects, the successful candidate will be expected to assist
research groups seeking to use high-pressure techniques at CHESS for their work.
Good clear communication skills are a must, including fluency in the English
language. Appointments are for one year at a time and are renewable for
additional years, contingent upon availability of funds and employee
performance.

Located on an Ivy League university campus in picturesque upstate New York,
the Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user
base of structural biologists, chemists, physicists, and engineers.
MacCHESS is an NIH-supported National Resource providing support for structural
biology at CHESS, and CHEXS is an NSF-supported facility incorporating several
projects, including high-pressure biology.

Applications should be submitted at http://academicjobsonline.org/
(posting #18189) and should include a cover letter, a CV, a list of
publications, and a detailed summary of research experience and interests.
Please arrange to have at least three letters of recommendation sent, as per
instructions on the academicjobsonline website. The starting date is negotiable.
For more information about the position, contact Dr. Marian Szebenyi at
dm...@cornell.edu.

Diversity and Inclusion are a part of Cornell University’s heritage. We’re a
recognized employer and educator valuing AA/EEO, Protected Veterans, and
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[ccp4bb] Lectureship at Leicester (LISCB)!

[Peter Moody]

We have just posted an advertisement for a lecturer in structural biology
at Leicester Institute for Structural and Chemical Biology.

Closing date for applications 22 April

see https://jobs.le.ac.uk/vacancies/2983/lecturer-in-structural-biology.html

for more information.


We would love to hear from you.
Peter

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Re: [ccp4bb] Maniatis: Molecular Cloning

[Tim Gruene]

Dear Aviv, dear Jeroen,

thank you very much for the links to the latest edition! We always
called it 'the Maniatis'...

I was also pointed at "Current Protocols in Molecular Biology", edited
by F. M. Ausubel et al.
https://www.wiley.com/en-us/Current+Protocols+in+Molecular+Biology+-p-9780471503385?purchasedProduct=%2Fen-us%2FCurrent%2BProtocols%2Bin%2BMolecular%2BBiology%2B-p-9780471503385#
as an alternative

Best regards,
Tim

On Fri, 26 Mar 2021 13:11:08 +
Aviv Paz  wrote:

> Dear Tim,
> 
> Here is a link to the new version (with some author changes):
> https://www.cshlpress.com/default.tpl?cart=1616763922770582099=T=full=oop_title&--eqSKUdatarq=934
> 
> All the best,
> 
> Aviv Paz, Ph.D.
> Associate Research Scientist | Hauptman-Woodward Medical Research
> Institute Adjunct Associate Professor of Oncology | Roswell Park
> Comprehensive Cancer Center p: +1 716 898 8619 | f: +1 716 898 8660
> e: a...@hwi.buffalo.edu
> Hauptman-Woodward Medical Research Institute
> 700 Ellicott Street | Buffalo, NY 14203-1102
> hwi.buffalo.edu
> 
> 
> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] Register now for Instruct-ERIC ‘Structure Meets Function’ webinar – 13 April

[Claudia Alén Amaro]

Dear All

Featuring expert speakers from Instruct Centres across Europe, the 
Instruct-ERIC webinar series, Structure Meets 
Function, highlights some of the 
latest developments in structural biology, demonstrating how integrative 
methods are enabling scientists to decipher the mechanisms that underpin health 
and disease.



[https://instruct-eric.eu/upload/fClQXH9ZFeSmEEapnDrjMSOcvC877mXy.png]



Registration is open for the ninth 
webinar in the series, which will be hosted by Instruct Centre Finland 
 on 13 April 2021, 11:00 - 12:30 
CEST. The upcoming webinar will feature talks on the application of structural 
biology methods, (native mass spectrometry,  crystallography, sample 
preparation for advances structural analyses) to better understand key aspects 
of macromolecular structures and interactions.



Talk 1: Biocomplex: Sample preparation strategies for biomolecular complexes
Speaker: Minna Poranen



Talk 2: Switching on ADP-ribosylation at the DNA damage site
Speaker: Lari Lehtiö



Talk 3: High-resolution native mass spectrometry as a versatile tool in 
structural biology
Speaker: Juha Rouvinen



Moderator: Sarah Butcher



You can view the full abstracts and register 
 on the Instruct-ERIC website, where 
you can also watch recordings of the previous 
webinars.



Questions can be submitted in advance of the webinar by sending them to 
paul...@instruct-eric.org.



We hope that you can join the webinar - please feel free to share this message 
with anyone who might be interested in attending.



Best wishes,

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My former email address clau...@instruct-eric.eu is unavailable. Please resend 
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[instructlogo]

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[ccp4bb] Q Integrating cryo-EM into your existing drug development process

[Hans Raaijmakers]

Thursday, April 1 | 8:30 a.m. PDT | 11:30 a.m. EDT | 5:30 p.m. CEST

Join a discussion on integrating cryo-EM into your existing drug development 
process

Attend our upcoming Ask the Experts Q session on integrating cryo-EM into 
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Re: [ccp4bb] Maniatis: Molecular Cloning

[mesters]

Authors have changed, Maniatis is out but Sambrook is still on board

Molecular Cloning: A laboratory Manual by Green & Sambrook, ISBN: 
9781936113422


Best regards

Jeroen

eAm 26.03.21 um 14:02 schrieb Tim Gruene:

Hello erveryone,

does anyone know whether Maniatis/Fritsch/Sambrock "Molecular Cloning"
are still being printed and sold? I could not find it by ISBN
(0‐87969‐309‐6) at my favourite book store.

Or is there anything comparable?

Best regards,
Tim



--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/ 
Visiting 
Professorship (South Bohemian University) in Biophysics

Logo Uni Lübeck
*University of Lübeck*
Center for Structural and Cell Biology in Medicine
*Institute of Biochemistry*

Tel +49 451 3101 3105 (secretariate 3101)
Fax +49 451 3101 3104
jeroen.mest...@uni-luebeck.de 
www.biochem.uni-luebeck.de 

*Ratzeburger Allee 160
23538 Lübeck, Schleswig-Holstein
Germany*




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Re: [ccp4bb] Maniatis: Molecular Cloning

[Aviv Paz]

Dear Tim,

Here is a link to the new version (with some author changes):
https://www.cshlpress.com/default.tpl?cart=1616763922770582099=T=full=oop_title&--eqSKUdatarq=934

All the best,

Aviv Paz, Ph.D.
Associate Research Scientist | Hauptman-Woodward Medical Research Institute 
Adjunct Associate Professor of Oncology | Roswell Park Comprehensive Cancer 
Center
p: +1 716 898 8619 | f: +1 716 898 8660
e: a...@hwi.buffalo.edu
Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203-1102
hwi.buffalo.edu



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[ccp4bb] Maniatis: Molecular Cloning

[Tim Gruene]

Hello erveryone,

does anyone know whether Maniatis/Fritsch/Sambrock "Molecular Cloning"
are still being printed and sold? I could not find it by ISBN
(0‐87969‐309‐6) at my favourite book store.

Or is there anything comparable?

Best regards,
Tim

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] advert for postdoc

[Amedeo Caflisch]

Dear Madams, dear Sirs,

I hope this message finds you in good health.
I would very much appreciate it if you could post the attached advert 
for a postdoctoral position.
(It is in ASCII, i.e., plain text, format but I can also prepare a pdf 
document if needed).


Thank you in advance.

Sincerely,
Amedeo Caflisch
*cafli...@bioc.uzh.ch

*Director
Department of Biochemistry
University of Zurich


===

*University of Zurich
Department of Biochemistry*


 Postdoctoral researcher in cryo-EM

The research groups of Prof. Amedeo Caflisch (Department of 
Biochemistry) and Prof. Cristina Nevado (Department of Chemistry) at the 
University of Zurich are looking for a post-doctoral associate with 
strong experience in cryo-electron microscopy and single-particle analysis.


The researcher is expected to contribute expertise in single-particle 
cryo-EM to support ongoing collaborative projects aiming at the 
optimization and characterization of in-house designed proteolysis 
targeting chimeric (PROTAC) molecules that show nanomolar affinity on 
cancer-relevant targets. On a second stage, the postdoctoral researcher 
will have the possibility to manage her/his own independent research 
project within the main research focus areas of the host laboratory. The 
researcher will have access to the Center for Microscopy and Image 
Analysis in the same building on campus

https://www.zmb.uzh.ch/en/Instruments-and-tools/ElectronMicroscopes.html


   Your responsibilities

The activities of this position involve mainly:

 * Protein expression (mainly in /E. coli/) and purification
 * Cryo-EM sample handling and preparation protocols including negative
   staining and sample vitrification
 * Process single particle cryo-EM data including handling raw data,
   interpretation, 3D reconstruction and map refinement, and model building
 * Structure-based optimization of small-molecule ligands and PROTACs


   Your profile

Experience on data-processing and structure solution of *small size 
protein complexes (<150 kDa)* is desired. The candidate should be about 
to receive their PhD degree or have less than three years of previous 
post-doctoral experience. Applications from senior researchers will not 
be considered.



   What we offer

Our well-funded drug discovery research program combines inspiring 
international research environment with access to state-of-the-art 
scientific infrastructure. Our alumni value their comprehensive 
training: about 25% of them are offered a tenure track assistant 
professorship position, with the vast majority of the rest finding 
employment in large pharma or biotech industry.



   Place of work

Irchel campus, CH-8057 Zurich, Switzerland


   Start of employment

Starting date: by arrangement (immediate entry possible).
Length: 3 years with an initial 1-year contract.

Applications are to be submitted as a single PDF file to 
*cafli...@bioc.uzh.ch*
and must contain a cover letter, a concise summary of past 
accomplishments in cryo-EM, a CV (of maximum two pages), and at least 
one letter of support or the names and contact details of two (former) 
advisors.





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