EMEBSDDI version 5_0_20200714_ on Linux (Ubuntu 20.04) fails, apparently jumps over indexing step

[hakonanes]

Hello!

Running EMEBSDDI on Windows with binaries from Bluequartz (EMsoft-5.0.20200714.-Win64.zip) works nicely, but on Linux with the same pattern and NML file fails with the output:

> EMEBSDDI sic_4h_ebsddi.nml 


 Copyright (C) 2001-2019 Marc De Graef Research Group/CMU
 EMsoft comes with ABSOLUTELY NO WARRANTY.
 This is free software, and you are welcome to redistribute it
 under certain conditions; see License.txt file for details.


 Program name         : EMEBSDDI.f90
 Purpose              : Program to index EBSD patterns using a dynamically calculated pattern dictionary
 Platform             : Linux
 Source code version  : 5_0_20200714_
 Source code Revision : 
 Build Date/Time      : 2020-07-14 15:49:24Z

 See https://github.com/EMsoft-org/EMsoft/wiki for selected help pages.

 Jul 14 2020   6:56:34.695 PM


Number of command line arguments detected:           1
 Array size analysis
 ===================
 Ne           :         1024
 Nd           :         1024
 L            :         9216
 size result array  :      4194304
 size_in_bytes_dict :              37748736
 size_in_bytes_expt :              37748736
 Total allocations on GPU (Mb):                    76
 reading from xtalfile si_carbide_4h\si_carbide_4h.xtal
Orientation space sampling mode set to RFZ
Point group number and number of cubochoric sampling points :  25,  100
 Number of unique orientations sampled =        :  666187
--> Initializing OpenCL device
--> Allocating various arrays for indexing
Preprocessing experimental patterns
Creating temporary file :/home/hakon/.config/EMsoft/tmp/1_4h.data
 -> Number of threads set to  4
Starting processing of experimental patterns
 pattern size :  96 x   96
Completed row   5 of  350 rows
[...]
Completed row 350 of  350 rows
 -> experimental patterns preprocessed
Number of experimental patterns processed per second :    4819.7

 -> computing Average Dot Product map (ADP)

 -> Number of threads set to  4
 Jul 14 2020   6:57:43.601 PM
  actual number of OpenMP threads  =            4
Indexing duration (system_clock, s)                :
         3.514
Number of pattern comparisons per second           :
**************
Number of experimental patterns indexed per second :
     20916.336

At line 899 of file /home/hakon/kode/emsoft/EMsoft/Source/EMsoftHDFLib/EMh5ebsd.f90
Fortran runtime error: Index '0' of dimension 2 of array 'eulerarray' outside of expected range (1:666624)

Error termination. Backtrace:
#0  0x7f8fd444ecd1 in ???
#1  0x7f8fd444f819 in ???
#2  0x7f8fd444fe96 in ???
#3  0x5599c41a5320 in __emh5ebsd_MOD_h5ebsd_writefile
	at /home/hakon/kode/emsoft/EMsoft/Source/EMsoftHDFLib/EMh5ebsd.f90:899
#4  0x5599c411e868 in EBSDDIdriver
	at /home/hakon/kode/emsoft/EMsoft/Source/EMOpenCLLib/Indexingmod.f90:1288
#5  0x5599c40d22b9 in emebsddi
	at /home/hakon/kode/emsoft/EMsoft/Source/DictionaryIndexing/EMEBSDDI.f90:86
#6  0x5599c40d22f6 in main
	at /home/hakon/kode/emsoft/EMsoft/Source/DictionaryIndexing/EMEBSDDI.f90:54

I would have though I did something wrong, however it works fine on Windows... Anyone experiencing the same on Linux?

[hakonanes]

Also, don't know if it is related to this issue, but after a successful indexing on Windows, the dot product file dataset Scan 1/EBSD/Data/FZcnt is 666187 while the dataset Scan 1/EBSD/Data/DictionaryEulerAngles has the shape (666624, 3). The point group number is 25 (space group 186).

[marcdegraef]

Hi Håkon, FZcnt is the true number of Euler angle triplets in the fundamental zone for a given value of N, the cubochoric sampling number. Many of the arrays that are used for indexing must have dimensions that are a multiple of 16 when they are sent to  or used for the GPU computations, so those arrays will be over-dimensioned with respect to the FZcnt value. We typically pad them with zeros so you can ignore the actual values.   When reading the dot product file, I would first read FZcnt, and then user that as the maximum index into the other arrays. Marc.

…

On 7/15/20 4:51 AM, Håkon Wiik Ånes wrote: Also, don't know if it is related to this issue, but after a successful indexing on Windows, the dot product file dataset |Scan 1/EBSD/Data/FZcnt| is 666187 while the dataset |Scan 1/EBSD/Data/DictionaryEulerAngles| has the shape (666624, 3). The point group number is 25 (space group 186). — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#120 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB26VWATQVBTGWOMKL57YR3R3VUZVANCNFSM4OZW26BA>.

[hakonanes]

Of course, thanks for the quick response!

[hakonanes]

Just to be 100% sure, am I correct in assuming that the indices in the TopMatchIndices dataset are 1-indices, and not 0-indices, into the DictionaryEulerAngles dataset? I.e. a TopMatchIndices element of value 1 points to the first element in DictionaryEulerAngles?

[hakonanes]

I still experience this issue. Apparently indexmain is 0 when it tries to index into the Euler angle dictionary array in various routines.