Cryo-EM in the cloud

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Welcome to the Google group dedicated to discussing how to use and troubleshoot Amazon's EC2 to process electron microscopy data.

To learn more about how to set up and running refinements on Amazon's EC2: Electron microscopy image analysis in the cloud

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ilahi...@gmail.com

3/25/16

Using starcluster in different regions

For using starcluster to start a amazon cluster in a region other than us-east-1 change the following

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Using starcluster in different regions

For using starcluster to start a amazon cluster in a region other than us-east-1 change the following

3/25/16

irin tom

7/24/21

Advice on how to get rid of bad micrographs after CTF estimation

Hi all My name is Irin and I am new to CryoEM data processing. I have a data set which contain few

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Advice on how to get rid of bad micrographs after CTF estimation

Hi all My name is Irin and I am new to CryoEM data processing. I have a data set which contain few

7/24/21

Joe Batchelor

11/29/20

advice to set up AWS cluster in cisTEM

Dear Michael Cianfrocco, I came across your website while googling how to set up cisTEM for AWS. Any

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advice to set up AWS cluster in cisTEM

Dear Michael Cianfrocco, I came across your website while googling how to set up cisTEM for AWS. Any

11/29/20

dan.w...@gmail.com, Michael Cianfrocco2

7/31/20

Error message on installation running awls

Dear Dan, I'm not sure what this is coming from as it seems OK for me. If you want to list

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Error message on installation running awls

Dear Dan, I'm not sure what this is coming from as it seems OK for me. If you want to list

7/31/20

dnsu...@gmail.com3

7/14/20

AMI for cisTEM on AWS

I created my own AMI with cisTEM installed. I updated cistem_launch.py to use that, and made some

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AMI for cisTEM on AWS

I created my own AMI with cisTEM installed. I updated cistem_launch.py to use that, and made some

7/14/20

Doo Nam Kim

5/1/20

I can't install AWS command-line tools

(base) WE39390:install_cloud_tools kimd999$ ./install_cloud_tools_macOSX Install cryoem-cloud-tools

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I can't install AWS command-line tools

(base) WE39390:install_cloud_tools kimd999$ ./install_cloud_tools_macOSX Install cryoem-cloud-tools

5/1/20

ara...@gmail.com

5/14/19

Installation issue

Hello I am very new to this cloud cryoEM processing. I am trying to install this in my mac (OSX

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Installation issue

Hello I am very new to this cloud cryoEM processing. I am trying to install this in my mac (OSX

5/14/19

christopher.j...@gmail.com, mcia...@umich.edu2

4/1/19

cudapath

Hi Christopher, The cuda path should be /usr/local/cuda/ Mike

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cudapath

Hi Christopher, The cuda path should be /usr/local/cuda/ Mike

4/1/19

jli...@stanford.edu, mcia...@umich.edu4

2/24/19

how to use relion3.0?

I just use -i in ssh login but not -X. I think that cause the problem. Thanks.

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how to use relion3.0?

I just use -i in ssh login but not -X. I think that cause the problem. Thanks.

2/24/19

felj...@gmail.com, … Michael Cianfrocco3

2/12/19

awsls no instance found etc.

Hello - yes, as jliu321 said - your installation is working fine (assuming you haven't launched

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awsls no instance found etc.

Hello - yes, as jliu321 said - your installation is working fine (assuming you haven't launched

2/12/19

Martin Lawrence, mcia...@umich.edu2

11/26/18

Software Installation for AWS Command Line Tools

Hi Martin, Sorry for the hiccup - I think it must be a web browser issue? I see the link when I test

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Software Installation for AWS Command Line Tools

Hi Martin, Sorry for the hiccup - I think it must be a web browser issue? I see the link when I test

11/26/18

Rick Baker, mcia...@umich.edu2

10/9/18

requesting instance type through Relion gui

Hey Rick, Yes, you should be able to provide --instance p2.8xlarge in the command line box and it

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requesting instance type through Relion gui

Hey Rick, Yes, you should be able to provide --instance p2.8xlarge in the command line box and it

10/9/18

Rick Baker

9/12/18

Relion3 ami gives error running CTFFIND4

Hi Mike, thanks for making a Relion3 install on AWS. I was running it just now and I got an error

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Relion3 ami gives error running CTFFIND4

Hi Mike, thanks for making a Relion3 install on AWS. I was running it just now and I got an error

9/12/18

Rick Baker, mcia...@umich.edu5

9/10/18

AWS tools unexpectedly broken

¯\_(ツ)_/¯

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AWS tools unexpectedly broken

¯\_(ツ)_/¯

9/10/18

Cryo-EM in the cloud

8/14/18

Size of disk available for Warp installation on AWS

We have several large datasets that will not fit on the 800Gb disk For the Warp machine image on AWS,

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Size of disk available for Warp installation on AWS

We have several large datasets that will not fit on the 800Gb disk For the Warp machine image on AWS,

8/14/18

Rick Baker, mcia...@umich.edu5

8/13/18

Problem re-launching cryoSPARC after initial install

To clarify, once I deactivated the license, it registered the current AWS hardware I was using and

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Problem re-launching cryoSPARC after initial install

To clarify, once I deactivated the license, it registered the current AWS hardware I was using and

8/13/18

Cryo-EM in the cloud

8/12/18

Installing Warp on AWS

I am very interest in Dr. Dimitry's #Warp# software. Limited by the lack of a suitable windows

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Installing Warp on AWS

I am very interest in Dr. Dimitry's #Warp# software. Limited by the lack of a suitable windows

8/12/18

Shuobing Chen, Rick Baker3

7/18/18

Can not access cryosparc though web browser

Actually now that I look at this again you are trying to use the web address that was generated for

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FAQ

Can not access cryosparc though web browser

Actually now that I look at this again you are trying to use the web address that was generated for

7/18/18

Rick Baker2

7/18/18

cleaning up my awsls results

So stopped is different than terminated. I manually terminated to instance in my AWS console and it

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cleaning up my awsls results

So stopped is different than terminated. I manually terminated to instance in my AWS console and it

7/18/18

mcia...@umich.edu

6/15/18

Warp on AWS

Hi Anthony, Moving data up from external hard drives may take some time. But, perhaps the best way is

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EC2

Warp on AWS

Hi Anthony, Moving data up from external hard drives may take some time. But, perhaps the best way is

6/15/18

陈硕冰

5/29/18

unable to upload data

I'm now go though all example command and have trouble in uploading local data. It shows: rsync

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unable to upload data

I'm now go though all example command and have trouble in uploading local data. It shows: rsync

5/29/18

robinb...@gmail.com, mcia...@umich.edu3

5/29/18

Can not create volume

Hello Mike, Thanks so much for your help! It works. I write the wrong keywords. However I use "

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Can not create volume

Hello Mike, Thanks so much for your help! It works. I write the wrong keywords. However I use "

5/29/18

Jingqi, … mcia...@umich.edu7

5/4/18

instance fail to mount EBS volume

Hi Ali, This is very weird - I still suspect this is a python / software version issue. I have yet to

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instance fail to mount EBS volume

Hi Ali, This is very weird - I still suspect this is a python / software version issue. I have yet to

5/4/18

Rick Baker, mcia...@umich.edu2

4/25/18

Particles missing form final data.star file

Hi Rick, I haven't noticed this before - is it always the last iteration?

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Particles missing form final data.star file

Hi Rick, I haven't noticed this before - is it always the last iteration?

4/25/18

Ali Khan, mcia...@umich.edu2

3/20/18

Trouble uploading particle stacks

Hi Ali, That's a weird problem to have since I have patched that kind of issue a little while ago

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Trouble uploading particle stacks

Hi Ali, That's a weird problem to have since I have patched that kind of issue a little while ago

3/20/18

Rick Baker, Michael Cianfrocco11

3/13/18

Help with Rosetta on the cloud

I also see this output in the terminal that I launch from. Every few minutes or so it writes out a

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Help with Rosetta on the cloud

I also see this output in the terminal that I launch from. Every few minutes or so it writes out a

3/13/18

malyu...@gmail.com, Michael Cianfrocco2

3/7/18

P3 and C5 instances

Hi Andrey, I've tested the P3 instance using an NVIDIA container with RELION2 installed and I saw

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P3 and C5 instances

Hi Andrey, I've tested the P3 instance using an NVIDIA container with RELION2 installed and I saw

3/7/18

Michael Cianfrocco, Ali Khan3

3/2/18

cryoSPARC now available

Hi Ali, Thanks for the info about the installation - I just updated the website. Regarding parallel

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cryoSPARC now available

Hi Ali, Thanks for the info about the installation - I just updated the website. Regarding parallel

3/2/18

Jingqi, Michael Cianfrocco6

2/18/18

Any idea about this error?

Hi all, Problem solved by changing the output type from none to json in aws config file. Thanks.

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Any idea about this error?

Hi all, Problem solved by changing the output type from none to json in aws config file. Thanks.

2/18/18

ldel...@gmail.com, Michael Cianfrocco3

2/16/18

problem encountered trying cryo-EM in the cloud_ .aws_relion folder missing?

Hi Mike, in fact I did not have that permission on my IAM user. I have added it, remake Access key

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problem encountered trying cryo-EM in the cloud_ .aws_relion folder missing?

Hi Mike, in fact I did not have that permission on my IAM user. I have added it, remake Access key

2/16/18

Sarah Ur, Michael Cianfrocco12

1/29/18

IndexError: list index out of range

Hi Sarah, I'm sorry but it's hard for me to figure out what is happening on your shell.

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IndexError: list index out of range

Hi Sarah, I'm sorry but it's hard for me to figure out what is happening on your shell.

1/29/18