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I'm running an array job (400 Matlab R2018b tasks) in the HPC of my university. After having qsub the .sh file in the terminal, the 400 tasks start by they are immediately killed.

In the .o file of each task no errors are reported but only the following warning

Warning: Name is nonexistent or not a directory: /share/apps/.../NAG/mbl6a24dnl/mex.a64

In case it might be useful to know: I call the MOSEK solver in my Matlab .m file. In particular, at the beginning of my Matlab .m file I have 

addpath /share/apps/mosek-9.2/9.2/toolbox/r2015aom

Also, this is my .sh file

#$ -S /bin/bash #$ -l h_vmem=7G #$ -l tmem=7G #$ -l h_rt=480:0:0 #$ -cwd #$ -j y #Run 400 tasks #$ -t 1-400 #$ -N count2 date hostname #Output the Task ID echo "Task ID is $SGE_TASK_ID" /share/apps/matlabR2018b -nodisplay -nodesktop -nojvm -nosplash -r "main; ID = $SGE_TASK_ID; f; exit"

Provided that I have contacted the administrator to ask about this (no reply yet), is there anything I can do can in the immediate to fix it and run my code?

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  • /.../ is not a valid part of a pathname (unless you really have a link in there called ...). I assume this is an ellipsis that you should replace by an actual directory (possibly a version number of matlab). Commented May 9, 2020 at 10:44
  • @Paul_Pedant sorry, the pathname is fine, I just did not report it here. Commented May 9, 2020 at 10:52
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    I assumed you posted the error message verbatim: the missing file is /share/apps/.../NAG/mbl6a24dnl/mex.a64 although the report may elide long names itself. I see your cross-post in StackOverflow, and it seems probable your PC has this NAG library installed and your Uni HPC does not. Commented May 9, 2020 at 11:31
  • @Paul_Pedant Thanks. Can I ask whether this warning can cause my tasks to be killed? I would like to know whether it is just a warning and hence the error is somewhere else Commented May 9, 2020 at 13:38

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I don't know MatLab at all: I was just pointing out that the warning message remarks on a very specific filename.

When I google for mexa64, it always comes up as a file extension .mexa64, never as mex.a64. So there may be some ambiguity in a filename somewhere.

There is a NAG Installers note at "www.nag.co.uk/doc/inun/mb24/l6idml/in.html" which includes the pathname: /opt/NAG/mbl6i24dml/mex.a64/a00aa.mexa64; which may explain something, as both variations are in there.

I also wondered why this is a warning, yet processes get killed. It seems that .mexa64 is a code library, and MatLab will try to compile it from source if it can't find it. So maybe, after the warning, it tries to build the library, and records a failure somewhere else (or fails to report it). Possibly the source is also not available or not found correctly.

I hope your Uni administrator knows more than I do. It seems likely you would not have permissions to rectify this issue on the server in any case.

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