search

czimaginginstitute / AreTomo2

BSD 3-Clause "New" or "Revised" License
41 stars 6 forks source link

$SB_EXECFILE error message #12

Open ncoudray opened 6 months ago

ncoudray commented 6 months ago

Hi,

I tried to run AreTomo2 (from SBgrid installation), and I get the following error message:

/data/apps/extern/sbgrid/share/capsules/lib/job.sh: line 126: 2156235 Segmentation fault (core dumped) "$SB_EXECFILE" "$@" I tried different versions (AreTomo2_1.0.0_Cuda118, AreTomo2_c7_Cuda122) which gave the same error. I noticed the v1.3.4 lead to the the same message (AreTomo_1.3.4_Cuda112_Feb22_2023, AreTomo_1.3.4_Cuda116_Feb22_2023).

However, older versions do work on the same images (and comparable cuda version) - (AreTomo_1.3.3_Cuda112_11212022, AreTomo_1.3.3_Cuda116_11212022, AreTomo_1.3.0_Cuda116_09292022).

Any idea why the newer version would fail with such a message on our cluster?

Thanks, Best, Nicolas

ncoudray commented 6 months ago

I figured in previous versions, I was using "-patch 1 1" to prevent patch processing. But this generated this error in the newest versions where "-patch 0 0" is required instead.

ncoudray commented 4 months ago

Actually, this error is still in the latest version we use on SBgrid and only seems to happen when -OutImod is set to "2" (AreTomo format). Everything runs well up to the last steps it seems.

Huang-XN commented 1 month ago

Hi @ncoudray, is there any way to solve it?

ncoudray commented 1 month ago

I haven't found a way to solve it. I used -OutImod option 1 instead and try to work with this outputt

Huang-XN commented 1 month ago

OK, I have tried with other number for -OutImod. But sometimes it worked, sometimes not.