I am using Matlab to do some image processing on a cluster that uses Sun Grid Engine. On my personal laptop the code runs fine but when I run it on the cluster I get several errors of files that cannot be found. For example a .nii (nifti) file that exists (I can read it when I run matlab interactively in the shell) is not found. An excerpt from the output log:
{^HError using load_nii_ext (line 97)
Cannot find file
"/path/imageFile.nii".
And I also get errors from an xml structured file (that needs to have a .mps extension to be readable by a postprocessing toolbox, which all worked fine on my own laptop). Another excerpt from the output log:
/path/pointSetFile.mps exists
{^HError using readpointsmps (line 24)
Failed to read XML file
/path/pointSetFile.mps.
In this second error message the first line is the output I get from including in the script,
if exist(strcat(folder, fileName), 'file') == 2
disp([strcat(folder, fileName) ' exists'])
end
So it's weird that 1) I can see the files, 2) I can open them manually with Matlab, 3) according to the matlab function exist() they do indeed exist, but when the functions xmlread() and read_niigz() want to open them they suddenly can't be found.
As extra information: I run the scripts with the flags -nodisplay -nodesktop -nosplash, and I currently run the scripts as 2 tasks with the SGE. Memory should be good, I give it 5GB and all my images combined are about 1.5GB.
I'm using absolute paths starting at the root /, have been reading the paths letter by letter about 200 times now and have no clue anymore what's going on.
I have solved the problems now.
@Xiangrui Li pointed out in the comments that the missing .nii files were due to interference with the unzipping, reading and deletion of the .nii and .nii.gz files. That was indeed the problem. Thanks!
I found that the second problem was due to umlauts in the filenames. Apparently there was a difference between how the system and matlab and even other processes involved encode the filenames. Removing the characters with umlauts solved the problem.