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Isabelle Laforest-Lapointe Laboratory code
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FATAL: failed to open /bin/sh for inspection: failed to open elf binary /bin/sh: read /bin/sh: input/output error #70

Closed jorondo1 closed 10 months ago

jorondo1 commented 11 months ago

j'ai cette erreur quand je roule le script suivant (que j'ai déjà roulé et qui fonctionnait bien par le passé): /home/def-ilafores/analysis/boreal_moss/scripts/sourmash_compare.sh avec la commande sbatch --array=1-140 $PWD/scripts/sourmash_compare.sh

voir log: /home/def-ilafores/analysis/boreal_moss/SM_abund/logs/sourmash-2059851_1.slurm.out

J'ai aussi essayé avec ml apptainer au lieu de la ligne module load et j'obtiens un autre type d'erreur, voir SM_abund/logs/sourmash-2060134_1.slurm.out

As-tu une idée de ce qui se passe?

jflucier commented 11 months ago

Je viens de lancer ca et tout a la'air de fonctionne:


|07:28:37|jflucier@ip34-rockylinux8:[boreal_moss]> sbatch --array=1 $PWD/scripts/sourmash_compare.sh
Submitted batch job 2285166
|07:28:41|jflucier@ip34-rockylinux8:[boreal_moss]> squeue -u jflucier
          JOBID     USER      ACCOUNT           NAME  ST  TIME_LEFT NODES CPUS       GRES MIN_MEM NODELIST (REASON) 
      2285166_1 jflucier def-ilafores       sourmash   R   23:59:58     1    2     (null)     25G cp2366 (None) 
|07:28:44|jflucier@ip34-rockylinux8:[boreal_moss]> tail -f /nfs3_ib/nfs-ip34/home/def-ilafores/analysis/boreal_moss/SM_abund/logs/sourmash-2285166_1.slurm.out 

Due to MODULEPATH changes, the following have been reloaded:
  1) blis/0.8.1          3) libfabric/1.10.1     5) ucx/1.8.0
  2) flexiblas/3.0.4     4) openmpi/4.0.3

loading env
cp: cannot create regular file '/nfs3_ib/nfs-ip34/home/def-ilafores/analysis/boreal_moss/SM_abund/temp/sourmash.4.7.0.sif': Permission denied

== This is sourmash version 4.7.0. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

select query k=31 automatically.
loaded query: S-1-POLPIL-B... (k=31, DNA)
--
loaded 10285 total signatures from 1 locations.
after selecting signatures compatible with search, 10285 remain.
Starting prefetch sweep across databases.
jflucier commented 10 months ago

est-ce ok cet issue?

jorondo1 commented 10 months ago

Il me semble que oui, je réouvrirai au besoin