astk from s.m. 2023 refuses to start

BrunoZilli

hello everybody,
I downloaded s.m. 2023.1.0-4-20240327. All was fine up to the astk launch. I've got back this message:

launch..

:~/salome_meca$ ./salome_meca-lgpl-2023.1.0-4-20240327-scibian-10.sif

..messages back:

running salome_meca in software rendering mode
++ using container salome_meca-lgpl-2023.1.0-4-20240327-scibian-10.sif
++ using software rendering mode (should use mesa_salome starter)
<INFO> Optional module not found : tkpng
searched in /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/astk/not_defined
Error in startup script: can't create directory "/local00": read-only file system
while executing
"file mkdir "$astk::tmpdir""
(procedure "init_gene" line 96)
invoked from within
"init_gene $root"
(file "/opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/astk/astk.tcl" line 36)

Note: I've got several versions of s.m. on the same machine, ubuntu 20.04 with singularity 3.9.7-bionic.
All of them work well, astk s.m. 2022 too.

I was wondering if astk was intentionally switched out from this version of s.m..

Please give me any feedback on this issue.

Thank you in advance for any help.

Bruno

Ect

BrunoZilli

Hello, I'm struggling with the same error:

Singularity> as_run 00-thermal.export /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:93: DeprecationWarning: invalid escape sequence \+ mat = re.search('^([-a-zA-Z_0-9@\+]+)=(.*$)', line) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:611: DeprecationWarning: invalid escape sequence \. name = re.sub('\.gz$', '', src) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:856: DeprecationWarning: invalid escape sequence \s exp = re.compile('^processor\s+:\s+([0-9]+)', re.MULTILINE) pas d'acccès en écriture dans /local00/tmp/astk_etienne

In this post post the solution is to bind the local00 directory to something on your filesystem:

singularity run --bind /tmp:/local00/tmp salome_meca-lgpl-2023.1.0-4-20240327-scibian-10-vanilla.sif shell

as_run started the calculation with a bit of gibberish at the beginning, but it seems to run

/opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:93: DeprecationWarning: invalid escape sequence \+ mat = re.search('^([-a-zA-Z_0-9@\+]+)=(.*$)', line) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:611: DeprecationWarning: invalid escape sequence \. name = re.sub('\.gz$', '', src) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:856: DeprecationWarning: invalid escape sequence \s exp = re.compile('^processor\s+:\s+([0-9]+)', re.MULTILINE) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/build.py:1430: DeprecationWarning: invalid escape sequence \( expr = re.compile('^[A-Za-z_0-9]+ *= *[OPERPROCMACROFORM]+ *\(.*', /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/build.py:1553: DeprecationWarning: invalid escape sequence \. pattern='TOTAL_JOB +: +([0-9\.]+) +: +([0-9\.]+) +: +([0-9\.]+) +: +([0-9\.]+)') /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/build.py:1614: DeprecationWarning: invalid escape sequence \s mat = re.search('^ *SUPPR +([^\s]+)', line) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/build.py:1661: DeprecationWarning: invalid escape sequence \. mat = re.search('^ *TESSUPPR +([-_a-zA-Z0-9\.]+)', line) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/build.py:1701: DeprecationWarning: invalid escape sequence \# linc = re.findall('^\#include *[\"\<]{1}(.*)[\"\>]{1}', code, re.MULTILINE) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/build.py:1718: DeprecationWarning: invalid escape sequence \# mat = re.search('^\#include.*%s' % osp.basename(other), code, re.MULTILINE) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/calcul.py:579: DeprecationWarning: invalid escape sequence \. mat = re.search('%s +([0-9\.]+) +([0-9\.]+) +([0-9\.]+) +([0-9\.]+)' % 'Total', txt) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/calcul.py:763: DeprecationWarning: invalid escape sequence \g content = exp.sub('\g<1>%s = %s' % (para, pval), content) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/calcul.py:818: DeprecationWarning: invalid escape sequence \. mat = re.search('JOBID *= *([0-9a-zA-Z\._\-]+)', txt) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/calcul.py:821: DeprecationWarning: invalid escape sequence \. mat = re.search('QUEUE *= *([0-9a-zA-Z\._\-]+)', txt) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/calcul.py:825: DeprecationWarning: invalid escape sequence \. mat = re.search('STUDYID *= *([0-9a-zA-Z\._\-]+)', txt) /opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/rex.py:72: DeprecationWarning: invalid escape sequence \@ exp = re.compile('\@%s\@(.*)\@FIN%s\@' % (ch, ch), re.MULTILINE | re.DOTALL)

Cheers
Etienne

jeanpierreaubry

hello

i am running into the same trouble, as well for as_run, when issuing the commands from the shell

i am using apptainer version 1.1.0-rc.3 on Ubuntu 20.04.5 LTS

this occurs in the .sif container as well as on sandboxed directory
while it runs smoothly on the 2021 and 2022 versions

jean pierre aubry

sb1966

jeanpierreaubry

Hi,
Facing same issue here. I am using it in software rendering mode on Linux Mint 21.3 which is based on Ubuntu 22.04. The initial screen for astk appears, but then it does not do anything further..

My singularity version is singularity-ce version 3.11.4-jammy

Would like to draw the attention of the developers.

Regards and Thanks.

Sukumar

jeanpierreaubry

sb1966 Would like to draw the attention of the developers.

"where there's life there's hope"
but i refrain myself from hoping too much!

bosman

Hi!

I'm running the latest Salome-Meca in Debian 12 using Singularity 4.1, that I compiled myself, and everything seems to be working fine, if the correction are made to nvliblist.conf.
The only issue I have found, and not been able to fix, is "interactive follow up" in ASTK.
It complains about unable to execute the terminal.

jeanpierreaubry

hello bosman

thanks for the hint
i find out three instance of this nvliblist.conf on my komputer*
they are in 3 different dir
$HOME/appatainer/etc/ etc/singularity/ /usr/local/appatainer
which one has to be modified

and how to know which are the relevant library entry to put in it?

cristianoltfs

In 2022.1.0 "AsterStudy", "Run" is OK:

=====================

$ singularity run salome_meca-lgpl-2022.1.0-1-20221225-scibian-9.sif

INFO : Running salome_meca in software rendering mode

runSalome running on pop-os
Searching for a free port for naming service: 2810 - OK
Searching Naming Service + found in 0.1 seconds
Searching /Kernel/Session in Naming Service ++++++++****************************************************************
Warning: module HexoticPLUGIN is improperly configured!
Module HexoticPLUGIN will not be available in GUI mode!

=====================

In 2023.1.0 "AsterStudy", "Run" is not run:

=====================

$ singularity run salome_meca-lgpl-2023.1.0-4-20240327-scibian-10.sif

running salome_meca in software rendering mode
++ using container salome_meca-lgpl-2023.1.0-4-20240327-scibian-10.sif
++ using software rendering mode (should use mesa_salome starter)
SalomeApp_Engine_i::Load() isMultiFile = 0
AsterStudy: dim.-23-19:00:25.685 Opening AsterStudy JSON file...

=====================

MuhammadQasim

Dear @Ect Etienne,

I am also receiving similar error. Have you solved it?

''singularity run /home/sines/Documents/Salome_Meca2023/salome_meca-lgpl-2023.1.0-4-20240327-scibian-10.sif shell -- as_run 291p0p0.export

running salome_meca in software rendering mode
++ using container salome_meca-lgpl-2023.1.0-4-20240327-scibian-10.sif
++ using software rendering mode (should use mesa_salome starter)
/opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:93: DeprecationWarning: invalid escape sequence +
mat = re.search('^{[-a-zA-Z_0-9@+]+}=(.*$)', line)
/opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:611: DeprecationWarning: invalid escape sequence .
name = re.sub('.gz$', '', src)
/opt/salome_meca/2023.1.0_scibian_univ/tools/Code_aster_frontend-202310/lib/python3.7/site-packages/asrun/system.py:856: DeprecationWarning: invalid escape sequence \s
exp = re.compile('^processor\s+:\s+([0-9]+)', re.MULTILINE)
pas d'acccès en écriture dans /local00/tmp/astk_sines

EXIT_CODE=4
Error raised when executing command: as_run 291p0p0.export
ERROR:salomeContext:SystemExit 4 in method _runSession.''

Best,
Misaq

k_zurawski

I have the same DeprecationWarning which I think could be easily fixed if root password for the system in container was available for us.

hberro

k_zurawski

If you run

sudo singularity shell file.sif

You will get a shell as root. There is no need for a sudo password, that's an irrelevant concept for a container.

However, even being root the filesystem is readonly.

The only way to be able to modify something (like create a permanent /local00) is by

creating a sandbox from the sif
running sudo singularity shell --writable

Nevertheless, binding any local directory (where you have write access!) to /local00 inside the container is a much easier and more straightforward solution.

This is possible through the launcher script which accepts the -B flag.

BrunoZilli

Hello Etienne

singularity run --bind /tmp:/local00/tmp salome_meca-lgpl-2023.1.0-4-20240327-scibian-10.sif shell
singularity> astk

It works fine.

Fantastic.

Thank you.

Best Regards

Bruno