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Add SLURM support #1

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CFGrote opened this issue Dec 17, 2024 · 3 comments
Open

Add SLURM support #1

CFGrote opened this issue Dec 17, 2024 · 3 comments
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@CFGrote
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CFGrote commented Dec 17, 2024

SLURM is missing from the list of supported schedulers

@CFGrote CFGrote self-assigned this Dec 17, 2024
@CFGrote
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CFGrote commented Dec 17, 2024

Running into problems when

setup.sh
...
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:179,
                 from ./stdio.h:60,
                 from argv-iter.h:17,
                 from argv-iter.c:20:
./stdio.h:496:1: error: ‘gets’ undeclared here (not in a function); did you mean ‘fgets’?
  496 | _GL_WARN_ON_USE (gets, "gets is a security hole - use fgets instead");
      | ^~~~~~~~~~~~~~~
make[2]: *** [Makefile:2140: argv-iter.o] Error 1
make[2]: Leaving directory '/home/grotec/Repositories/orderedPainting/coreutils-8.11/lib'
make[1]: *** [Makefile:2165: all-recursive] Error 1
make[1]: Leaving directory '/home/grotec/Repositories/orderedPainting/coreutils-8.11/lib'
make: *** [Makefile:1695: all] Error 2
  GEN      version.h
  CC       sort.o
In file included from /usr/include/pthread.h:23,
                 from sort.c:26:
../lib/stdio.h:496:1: error: ‘gets’ undeclared here (not in a function); did you mean ‘fgets’?
  496 | _GL_WARN_ON_USE (gets, "gets is a security hole - use fgets instead");
      | ^~~~~~~~~~~~~~~
make: *** [Makefile:2615: sort.o] Error 1
20241217_095954 Make of GNU sort failed

@CFGrote
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CFGrote commented Dec 17, 2024

commented section 3 coreutils in setup.sh. building then completes

@CFGrote
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CFGrote commented Dec 17, 2024

this seems to do the trick.
furthermore:

  • module load R (or provide R in other ways)
  • adjust qsub comand compilations in main .sh file (ordererdPainting.sh)

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