TeamTomo and latest Warp/M versions?

[Matt Larson]

We are trying to complete the https://teamtomo.org tutorial for EMPIAR-10164 (HIV VLPs) which combines Warp-RELION-M and Dynamo.

 Our environment is a Windows 10 PC with a single NVIDIA 1080 GPU. We are running the Warp 1.0.9 version, with the 'copy and replace' of files using the Warp nightly build 2020-11-04.  I believe this is the latest available release on the website of http://www.warpem.com/warp/?page_id=65 

 Prior to using the 2020-11-04 nightly build, we had crashes with the GUI during initial preprocessing. The use of the nightly build code appears to have resolved these.

 Now we are hitting an error when using the TeamTomo GoldNet model, where a TensorFlow.TFException: Attempting to use uninitialized value.conv2d_25/kernel, causes the step (https://teamtomo.org/walkthroughs/EMPIAR-10164/2d-preprocessing.html) to fail when using Pick Particles with the GoldNet model.  This step is to mask out beads prior to tomographic reconstruction.

 Before we go further to diagnose and troubleshoot Warp/M, is there a newer total build beyond the 2020-11-04?  We would like to work with the latest stable version of Warp and ideally the same version as TeamTomo has used to test the workflows.

 If anyone can point out where we can get the latest build for Warp with or without an installer, please let me know!

 Thanks,

  Matt

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Matt Larson

Associate Scientist

Computer Scientist/System Administrator

Cryo-EM Research Center

University of Wisconsin Madison

440 Henry Mall. Room 1220

Madison, WI 53706

https://cryoem.wisc.edu

[Alister Burt]

Hi Matt,

I don’t think there is a newer build available - sorry about the problems with the GoldNet. Do you get the same errors with the pretrained model included in your installation?

Cheers,

Alister

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[Matt Larson]

Hi Alister,

 Thanks for the response.  With our installation of Warp 1.09 we used the "Browse Public Repository" to pull down some pretrained models (http://www.warpem.com/warp/?page_id=135) and placed them in the C:\Program Files\Warp\boxnet2models as separate folders with the models. Other models pulled from the "Browse Public Repository" ran without issue here. Example: BoxNet2Mask_2018_0531 could run without issue here.

 We will plan to keep progressing forward as this may not be a critical step for all parts of the tutorial.

 I was asking with the GoldNet model in case we were being hit with a bug that is fixed in a newer build of Warp/M such as a newer Tensorflow distribution, etc. We've had some other issues with stability and crashing, including some harder crashes (blue screens) from processing that we are trying to work through.

 -Matt

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Matt Larson, PhD
Madison, WI  53705 U.S.A.