M not responding

[shyamal narayan]

Hi Dimitry and others,

I am running M (v1.0.9) and there was no problem. However, after sometime there is no progress and it stuck on a tilt series (TS_749, please see attached) for almost an hour now. 

Did anyone have a similar problem? and is there a way to fix this?

Please let me know,

Thank you,

Shyamal

[Alister Burt]

Hi Shyamal,

I have a weird recurring issue which is similar, M sometimes hangs when trying to write files at the end of a refinement. In my case it seems to be some file permissions issue, even though everywhere I have full access unclicking the read-only checkbox and applying recursively down through the directory seems to fix it!

Cheers,

Alister

On 18 Aug 2020, at 17:41, shyamal narayan <narayan...@gmail.com> wrote:



Hi Dimitry and others,

I am running M (v1.0.9) and there was no problem. However, after sometime there is no progress and it stuck on a tilt series (TS_749, please see attached) for almost an hour now. 

Did anyone have a similar problem? and is there a way to fix this?

Please let me know,

Thank you,

Shyamal

<Screenshot 2020-08-18 at 17.34.59.png>

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[Pranav Shah]

Good catch Alister! Yeah I had forgotten about this problem.

@Shyamal, if you are running MobaXTerm, you can run chmod +rwx -R on your data folder.

I would suggest chmod 777 -R but that could be dangerous since your data is on a shared network.

To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/2005BF4A-3B98-483D-A345-5FE886F9B4C4%40gmail.com.

--

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

--

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

[shyamal narayan]

Thank you, Alister and Pranav.

Couldn't have figured this out.

I will re-run as you suggested while recording the warpworker.exe window, to see the error if and when it crashes.

Thanks again,

Shyamal

To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/CAHNYQ5q39EFDXiSAsjRxj4Uor%2BREKxUV1q3eUswhRBbQ1Epnsw%40mail.gmail.com.

[范潇]

Hi Shyamal,

I got a similar problem and I am also searching for solution. It seems you've already refined some TS successfully but I've get stuck at the beginning. I found that the Warpwokers will exit when this happen, but the UI is still running. I'm wondering is there any difference between TS_749 and the others? BTW, if I uncheck the "Image warp grid" and "Volume warp grid" option, there's no problem with the refinement.

Best,

Xiao

在 2020年8月18日星期二 UTC-4上午11:41:53，shyamal mosalaganti写道：

[Dimitry Tegunov]

Hi everyone,

there is nothing at the weight precalculation step that could take hours. Even in the worst case scenario of thousands of particles and super fine grid resolution, it should be quicker. So Alister's explanation seems more likely. If true, it would be a filesystem issue unrelated to M. Although our file servers also run Linux, I've never experienced it.

Generally, the weight precalculation step can crash if some particles' positions in the tilt images are outside those images. I added some code to exclude individual particle tilts from refinement if that happens in this updated version: http://deployment.warpem.com/nightly/Warp_20200802.zip (copy and replace files in installation directory).

Side note: I'll be adding experimental versions that I've been sharing with some users to test bug fixes as nightly builds under http://www.warpem.com/warp/?page_id=65 from now on. They definitely won't be updated every night, but I can at least make an effort to upload them in the late hours :-)

Cheers,

Dimitry

[shyamal narayan]

Hi Dimitry,

Thanks for the explanation. I will try the updated version.

Thanks again,

Shyamal 

On 18. Aug 2020, at 23:19, Dimitry Tegunov <teg...@gmail.com> wrote:



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[shyamal narayan]

Hi Alister, Dimitry & others,

So based on your suggestions, i re-ran M with changing permissions. It ran through most of my data ~480/570 tilt series before finally crashing with the following error (see below).

I will re-run it using the patched version which Dimitry recommended. Nevertheless, any ideas why this happened?

Thanks,

Shyamal 

To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/2005BF4A-3B98-483D-A345-5FE886F9B4C4%40gmail.com.

[Dimitry Tegunov]

Hi Shyamal,

that's exactly the dreaded "particle outside of image boundaries" error I mentioned. Hope the update helps!

Cheers,

Dimitry

On Wednesday, August 19, 2020 at 8:18:51 AM UTC+2, shyamal mosalaganti wrote:

Hi Alister, Dimitry & others,

So based on your suggestions, i re-ran M with changing permissions. It ran through most of my data ~480/570 tilt series before finally crashing with the following error (see below).

I will re-run it using the patched version which Dimitry recommended. Nevertheless, any ideas why this happened?

Thanks,

Shyamal 

On Tue, Aug 18, 2020 at 6:01 PM Alister Burt <alist...@gmail.com> wrote:

Hi Shyamal,

I have a weird recurring issue which is similar, M sometimes hangs when trying to write files at the end of a refinement. In my case it seems to be some file permissions issue, even though everywhere I have full access unclicking the read-only checkbox and applying recursively down through the directory seems to fix it!

Cheers,

Alister

On 18 Aug 2020, at 17:41, shyamal narayan <narayan...@gmail.com> wrote:



Hi Dimitry and others,

I am running M (v1.0.9) and there was no problem. However, after sometime there is no progress and it stuck on a tilt series (TS_749, please see attached) for almost an hour now. 

Did anyone have a similar problem? and is there a way to fix this?

Please let me know,

Thank you,

Shyamal

<Screenshot 2020-08-18 at 17.34.59.png>

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[shyamal narayan]

Hi all,

Just an update: the patched version of Warp/M runs fine without any crashes. 

Thank you all for chipping in suggestions.

Cheers,

Shyamal

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[alist...@gmail.com]

Hi all,

Sorry to open this up again, I'm running the latest version patched with the nightly build files and am getting the following error which looks similar to Shyamal's? Is this the same?

Cheers,

Alister

Running on GPU #1 (13633 MB free) through WarpWorker0f33726d-37a9-4dd8-9aae-da47ab22d1f6

Received "SetHeaderlessParams", with 3 arguments, for GPU #1, 13633 MB free

Set headerless parameters to 2, 2, 0, float

0.000

Received "MPAPreparePopulation", with 1 arguments, for GPU #1, 13633 MB free

Preparing hex64 for refinement... 2020-08-31 15:52:41.517185: I D:\Dev\tensorflow\tensorflow\core\platform\cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2

2020-08-31 15:52:41.764715: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1405] Found device 0 with properties:

name: Quadro RTX 5000 major: 7 minor: 5 memoryClockRate(GHz): 1.815

pciBusID: 0000:17:00.0

totalMemory: 16.00GiB freeMemory: 13.32GiB

2020-08-31 15:52:41.777151: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1405] Found device 1 with properties:

name: Quadro RTX 5000 major: 7 minor: 5 memoryClockRate(GHz): 1.815

pciBusID: 0000:73:00.0

totalMemory: 16.00GiB freeMemory: 13.31GiB

2020-08-31 15:52:41.787661: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1484] Adding visible gpu devices: 0, 1

2020-08-31 15:52:44.142108: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:965] Device interconnect StreamExecutor with strength 1 edge matrix:

2020-08-31 15:52:44.148279: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:971]      0 1

2020-08-31 15:52:44.153252: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:984] 0:   N N

2020-08-31 15:52:44.157953: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:984] 1:   N N

2020-08-31 15:52:44.163503: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 12889 MB memory) -> physical GPU (device: 0, name: Quadro RTX 5000, pci bus id: 0000:17:00.0, compute capability: 7.5)

2020-08-31 15:52:44.180712: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:1 with 12885 MB memory) -> physical GPU (device: 1, name: Quadro RTX 5000, pci bus id: 0000:73:00.0, compute capability: 7.5)

2020-08-31 15:52:44.229194: I d:\dev\warp2\tfutility\graph.cpp:369] not cuda_malloc

2020-08-31 15:52:44.244059: I d:\dev\warp2\tfutility\graph.cpp:262] Loading SavedModel from: D:\WM5984_180924_DCheR_minicells\species/2d294638/hex64_noisenet

2020-08-31 15:52:44.364399: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1484] Adding visible gpu devices: 0, 1

2020-08-31 15:52:44.369927: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:965] Device interconnect StreamExecutor with strength 1 edge matrix:

2020-08-31 15:52:44.379757: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:971]      0 1

2020-08-31 15:52:44.386214: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:984] 0:   N N

2020-08-31 15:52:44.391790: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:984] 1:   N N

2020-08-31 15:52:44.398918: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 12889 MB memory) -> physical GPU (device: 0, name: Quadro RTX 5000, pci bus id: 0000:17:00.0, compute capability: 7.5)

2020-08-31 15:52:44.418976: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1097] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:1 with 12885 MB memory) -> physical GPU (device: 1, name: Quadro RTX 5000, pci bus id: 0000:73:00.0, compute capability: 7.5)

2020-08-31 15:52:44.490732: I d:\dev\warp2\tfutility\graph.cpp:182] Restoring SavedModel bundle.

2020-08-31 15:52:44.898505: I d:\dev\warp2\tfutility\graph.cpp:215] Running LegacyInitOp on SavedModel bundle.

done.

Preparing data:

Done.

16.692

Received "LoadGainRef", with 5 arguments, for GPU #1, 13259 MB free

Loaded gain reference and defect map: , False, False, False,

0.003

Received "MPARefine", with 5 arguments, for GPU #1, 13259 MB free

Loading tilt series and masks...

12716 MB after loading raw data of tomo_ts105.mrc.tomostar

Calculating spectral weights...

12714 MB after spectra estimation of tomo_ts105.mrc.tomostar

Precomputing gradient weights...

Unhandled Exception:

Unhandled Exception:

Unhandled Exception:

Unhandled Exception: System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

Unhandled Exception:

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

Unhandled Exception: System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

Unhandled Exception: System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

Unhandled Exception:

Unhandled Exception:

Unhandled Exception: Unhandled Exception: Unhandled Exception: System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

Unhandled Exception: Unhandled Exception: Unhandled Exception:

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

Unhandled Exception: System.Exception

   at Warp.TiltSeries.<>c__DisplayClass87_15.<PerformMultiParticleRefinement>b__56(Int32 iwiggle, Int32 threadID) in D:\Dev\warp2\WarpLib\TiltSeries.cs:line 3967

   at Warp.Tools.Helper.<>c__DisplayClass48_0.<ForCPU>b__0(Object id) in D:\Dev\warp2\WarpLib\Tools\Helper.cs:line 679

   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)

   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)

   at System.Threading.ThreadHelper.ThreadStart(Object obj)

[teg...@gmail.com]

Hi Alister,

did you specify a larger pixel size for your species than the raw data by any chance? Just noticed that it leads to the same error due to a recently introduced change.

Cheers,

Dimitry

[Alister Burt]

Hi Dimitry,

I did indeed, I’ll resize to the raw data pixel size and run again - thanks for the quick response!

Cheers,

Alister

On 1 Sep 2020, at 13:59, teg...@gmail.com <teg...@gmail.com> wrote:

Hi Alister,

To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/1f69e19a-9792-4887-9154-e5956753ee20n%40googlegroups.com.

[teg...@gmail.com]

This should fix it: http://deployment.warpem.com/nightly/Warp_20200901.zip

[alist...@gmail.com]

Perfect - everything now running without any issues, thanks!

Alister