noise2map error

[Pranav Shah]

Hi Dimitry,

I had emailed this problem to the group but it seems it hasnt landed here (or atleast I cannot see it). Therefore, I am posting this directly into the group.Apologies if it is repeated. The premise of question is that, I am trying to denoise my tomograms (for shiggles) and I am running into an error after running the following command:

 Noise2Map.exe --observation1 even --observation2 odd --angpix 10 --batchsize 4 --dont_flatten_spectrum --iterations 10000 --gpuid_preprocess 0

Loading model, 23351 MB free.
2020-10-26 17:25:35.301274: 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
2020-10-26 17:25:35.311183: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1405] Found device 0 with properties:
name: Quadro RTX 6000 major: 7 minor: 5 memoryClockRate(GHz): 1.77
pciBusID: 0000:d9:00.0
totalMemory: 24.00GiB freeMemory: 22.80GiB
2020-10-26 17:25:35.311220: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1484] Adding visible gpu devices: 0
2020-10-26 17:25:36.882537: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:965] Device interconnect StreamExecutor with strength 1 edge matrix:
2020-10-26 17:25:36.882559: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:971]      0
2020-10-26 17:25:36.882565: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:984] 0:   N
2020-10-26 17:25:36.884983: 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 22117 MB memory) -> physical GPU (device: 0, name: Quadro RTX 6000, pci bus id: 0000:d9:00.0, compute capability: 7.5)
2020-10-26 17:25:36.897024: I d:\dev\warp2\tfutility\graph.cpp:369] not cuda_malloc
2020-10-26 17:25:36.898218: I d:\dev\warp2\tfutility\graph.cpp:262] Loading SavedModel from: C:\Users\warp\AppData\Roaming\Warp\noisenet3dmodel_64
2020-10-26 17:25:36.956355: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:1484] Adding visible gpu devices: 0
2020-10-26 17:25:36.956432: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:965] Device interconnect StreamExecutor with strength 1 edge matrix:
2020-10-26 17:25:36.956438: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:971]      0
2020-10-26 17:25:36.956442: I D:\Dev\tensorflow\tensorflow\core\common_runtime\gpu\gpu_device.cc:984] 0:   N
2020-10-26 17:25:36.956505: 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 22117 MB memory) -> physical GPU (device: 0, name: Quadro RTX 6000, pci bus id: 0000:d9:00.0, compute capability: 7.5)
2020-10-26 17:25:37.055940: I d:\dev\warp2\tfutility\graph.cpp:182] Restoring SavedModel bundle.
2020-10-26 17:25:37.259247: I d:\dev\warp2\tfutility\graph.cpp:215] Running LegacyInitOp on SavedModel bundle.
Loaded model, 18827 MB remaining.


Unhandled Exception: System.IO.IOException: The handle is invalid.

   at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
   at System.Console.GetBufferInfo(Boolean throwOnNoConsole, Boolean& succeeded)
   at Noise2Map.Program.ClearCurrentConsoleLine() in D:\Dev\warp2\Noise2Map\Program.cs:line 605
   at Noise2Map.Program.Main(String[] args) in D:\Dev\warp2\Noise2Map\Program.cs:line 480

Could you help me understand the first cause of death?

best,

Pranav

[teg...@gmail.com]

Hi Pranav,

that's an odd one – looks like it just couldn't clear the console line. Is it some non-standard console, i.e. not cmd.exe? Is it reproducible?

Unrelated, please also use --dont_augment for tomograms.

Cheers,

Dimitry

[Pranav Shah]

Yup, the program is now running in cmd.exe. Who woulda thunk?
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

On Mon, Oct 26, 2020 at 10:16 PM Pranav Shah
<prana...@strubi.ox.ac.uk> wrote:
>
> Yeah this is MobaXTerm for windows. It is reproducible in the
> non-standard terminal. Will try this in cmd and see what happens. and
> thanks for the --dont_augment flag.
>
> 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

> > --
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