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Error when using antsApplyTransforms to large data #564

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david-hoffman opened this issue Apr 10, 2018 · 26 comments
Closed

Error when using antsApplyTransforms to large data #564

david-hoffman opened this issue Apr 10, 2018 · 26 comments

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@david-hoffman
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I get this error when using antsApplyTransforms to large data.

** ERROR: NWAD: wrote only 0 of 3650505600 bytes to file
@cookpa
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cookpa commented Apr 10, 2018

This appears to be a NIFTI library error. Are you sure you have sufficient disk space to write the file?

@david-hoffman
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@cookpa I believe I do (~8TB free)

@cookpa
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cookpa commented Apr 10, 2018

OK, then I think the error is caused by integer overflow:

https://github.com/InsightSoftwareConsortium/ITK/blob/a652fd46a9b47acf68f290ca41aa8e5f8a38a56d/Modules/ThirdParty/MINC/src/libminc/nifti/nifti1_io.c#L5169

if size_t is 32 bits, then it would not be able to represent the size of the file.

Do you have the latest ANTs? How did you compile?

@david-hoffman
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I compiled earlier today following the instructions here: https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Windows-10

@david-hoffman
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There's no error if I run the command on a linux box. Something strange about WSL.

@dorianps
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dorianps commented Apr 10, 2018 via email

@david-hoffman
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@dorianps I don't think it's a swap issue, I have plenty of RAM (512 GB). Plus, the swap in WSL is 2GB and the swap on the Linux box I used is 4GB.

@cookpa
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cookpa commented Apr 11, 2018

Related?

microsoft/WSL#597

It seems the WSL was setting the Linux swap size to a small value, resulting in memory allocation failures. The thread above suggests this is fixed in the "creators update", which might be worth a try if you don't already have it.

@dorianps
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dorianps commented Apr 11, 2018 via email

@david-hoffman
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This is what I get, again I don't think it's a memory issue

hoffmand@HOFFMAND-WW1:~$ free -m
             total       used       free     shared    buffers     cached
Mem:        524204      82316     441888         17         33        184
-/+ buffers/cache:      82098     442105
Swap:         8192         21       8170

@dorianps
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dorianps commented Apr 11, 2018 via email

@dorianps
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dorianps commented Apr 11, 2018 via email

@david-hoffman
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@dorianps it did show as an error during compilation so I installed it (I also updated the instructions here).

I have run into problems with some python libraries under windows because the default integer is uint32 not uint64. I didn't think this would extend to WSL, but it may have.

@dorianps
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dorianps commented Apr 11, 2018 via email

@david-hoffman
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@dorianps I doubt that, I had just run antsRegistration in the same terminal with no issues (albeit on smaller data).

@cookpa
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cookpa commented Apr 11, 2018

Thanks for the Wiki update @david-hoffman .

From the WSL issue above,

By default native Linux will not allowing you to map an address range larger than your swap file size.

As I read it, the swap size is the limiting factor here. According to your free output above this is 8Gb, but earlier you mentioned it being 2 Gb. Did you change it? Can you increase it further and see if the problem goes away?

@ptsii
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ptsii commented Feb 9, 2019

Did anyone solve this? I just got the same issue. I don't think it is memory, as it happened with one file (of several I was trying to save) that is relatively small:
** ERROR: NWAD: wrote only 0 of 3612672 bytes to file
(that can't be big enough to be a swap problem, can it?)

@zz10001
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zz10001 commented Nov 8, 2019

Did anyone solve this? I just got the same issue. I don't think it is memory, as it happened with one file (of several I was trying to save) that is relatively small:
** ERROR: NWAD: wrote only 0 of 3612672 bytes to file
(that can't be big enough to be a swap problem, can it?)

Have you sovle it? I have met the same trouble like this.
image
but it really enough memrory and exist this file

@dorianps
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dorianps commented Nov 8, 2019 via email

@zz10001
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zz10001 commented Nov 8, 2019

Sorry, It not on WSL, it occurs when I crop image to 64128128 use simpleitk

@cookpa
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cookpa commented Nov 8, 2019

I think there's probably more than one way to get this error. If the buffer can only write a subset of the data, this error will be generated. But the numbers reported may not be accurate in case of overflow or if there are I/O errors other than a short write.

If you're seeing this error with ITK outside of ANTs then you might want to ask on the ITK forum.

https://discourse.itk.org

@ptsii
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ptsii commented Nov 8, 2019 via email

@zz10001
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zz10001 commented Nov 9, 2019

Thanks for your help.

@david-hoffman
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Dead issue

@tashrifbillah
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tashrifbillah commented Jun 9, 2020 •
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Same problem on Cent OS 7 Linux:

11821 Total elapsed time: 534.8
11822 ** ERROR: NWAD: wrote only 68812448 of 92274688 bytes to file
11823 ** ERROR: NWAD: wrote only 129105568** ERROR: NWAD: wrote only 392864 of 276824064 bytes to file
11824 Transform reader for /tmp/tmp6a11_1hd/warp1.nii.gz caught an ITK exception:
11825
11826 itk::ExceptionObject (0x351f3d0)
11827 Location: "unknown"
11828 File: /data/pnl/soft/pnlpipe3/pnlpipe/soft_dir/ANTs-build/ITKv5/Modules/IO/TransformBase/include/itkTransformFileReader.hxx
11829 Line: 129
11830 Description: itk::ERROR: TransformFileReaderTemplate(0x3512e80): Could not create Transform IO object for reading file /tmp/tmp6      a11_1hd/warp1.nii.gz
11831   Tried to create one of the following:
11832     HDF5TransformIOTemplate
11833     HDF5TransformIOTemplate
11834     MatlabTransformIOTemplate
11835     MatlabTransformIOTemplate
11836     TxtTransformIOTemplate
11837     TxtTransformIOTemplate
11838   You probably failed to set a file suffix, or
11839     set the suffix to an unsupported type.
11840
11841
11842 ** ERROR: NWAD: wrote only 67337888 of 92274688 bytes to file
11843 ** ERROR: NWAD: wrote only 64519840 of 92274688 bytes to file
11844 ** ERROR: NWAD: wrote only 64224928 of 92274688 bytes to file
11845 ** ERROR: NWAD: wrote only 50888352 of 92274688 bytes to file
11846 ** ERROR: NWAD: wrote only 62881440 of 92274688 bytes to file
11847 ** ERROR: NWAD: wrote only 65732256 of 92274688 bytes to file
11848 ** ERROR: NWAD: wrote only 63995552 of 92274688 bytes to file
11849 ** ERROR: NWAD: wrote only 44203680 of 92274688 bytes to file
11850 ** ERROR: NWAD: wrote only 63110816 of 92274688 bytes to file
11851 ** ERROR: NWAD: wrote only 63078048 of 92274688 bytes to file

On the following host:

GiB Mem :    251.6 total,    111.1 free,     79.1 used,     61.5 buff/cache
GiB Swap:     14.6 total,      6.8 free,      7.8 used.    169.0 avail Mem

My NIFTI data type:

data_type       INT16
dim0            3
dim1            176
dim2            256
dim3            256

As @cookpa mentioned, I think it is related to my little swap memory.

Edit:
My issue was space shortage in my /tmp/ directory.

@vkyprmr vkyprmr mentioned this issue Mar 19, 2021
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@caixh39
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caixh39 commented Aug 31, 2021 •
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It seem that each nii.gz file registrated will generate some temp files in /tmp/*Warp.nii.gz and Affine.mat in ubuntu system, as below:
image

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7 participants
@cookpa @david-hoffman @ptsii @dorianps @caixh39 @tashrifbillah @zz10001