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hello
on opensuse 15.4
when trying to install
i get the following error
:~> singularity run --app install salome_meca-lgpl-2021.0.0-2-20211014-scibian-9.sif
ERROR : No setuid installation found, for unprivileged installation use: ./mconfig --without-suid
i do not understand what it means
singularity is 3.8.3 from opensuse repo
jean pierre aubry
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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Hi Jean-Pierre,
I see that you finally updated to 15.4. Your "problem" happens with all OpenSUSE users. By default, OpenSUSE limits what a simple user can do with singularity. If you read the file "/usr/share/doc/packages/singularity/README.SUSE" it explains what is happening.
You need to add your user to the singularity group in order to have full rights to use it from within that user. That can be achieved easily with:
# usermod -a -G singularity <user_login>
(run as root)
Do so, log out and log in for the change to take place. Then you should be able to run singularity without any issues.
Best regards,
Fer
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hello Irvise
thanks for that prompt answer
unfortunately it does not change anything
> singularity run --app install salome_meca-lgpl-2021.0.0-1-20210811-scibian-9.sif
ERROR : No setuid installation found, for unprivileged installation use: ./mconfig --without-suid
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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Hi Jean-Pierre,
since I still had not done this in my OpenSUSE 15.4 installation, I tried to see if I get the same result, but I cannot replicate your case... I did, however, copy all that I did so that you can see if there is a difference with what you tried and what you got. There are a few things that will be different as I tried this from a chrooted environment, which is not your case.
fernando@linux:~/bin/salome_meca> singularity run salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
FATAL: while executing /usr/lib/singularity/bin/starter-suid: permission denied
Please read /usr/share/doc/packages/singularity/README.SUSE to get help
fernando@linux:~/bin/salome_meca> sudo usermod -a -G singularity fernando
fernando@linux:~/bin/salome_meca> singularity run salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
FATAL: while executing /usr/lib/singularity/bin/starter-suid: permission denied
Please read /usr/share/doc/packages/singularity/README.SUSE to get help
fernando@linux:~/bin/salome_meca> su - fernando
Password:
fernando@linux:~> cd bin/salome_meca/
fernando@linux:~/bin/salome_meca> singularity run salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
WARNING: Running inside a weak chrooted environment, prefer pivot_root instead of chroot
ERROR : Aborting as Singularity cannot run correctly without modifications to your environment
fernando@linux:~/bin/salome_meca>
As you can see, I initially got the error that I was not allowed to run singularity. I added myself to the group, reloaded my environment with su (so that I don't have to log out and back in) and then I could run it. The final error is because of the chrooted environment.
Here is the information about my singularity installation. I am using the one provided by the default repository. Does your look the same? You can get this information by running "sudo zypper info singularity".
Information for package singularity:
------------------------------------
Repository : Main Repository
Name : singularity
Version : 3.8.3-150400.1.64
Arch : x86_64
Vendor : SUSE LLC <https://www.suse.com/>
Installed Size : 153.5 MiB
Installed : Yes
Status : up-to-date
Source package : singularity-3.8.3-150400.1.64.src
Upstream URL : https://github.com/hpcng/singularity
Summary : Application and environment virtualization
Description :
Singularity provides functionality to make portable
containers that can be used across host environments.
If it still does not work, tell me, as you could potentially get Apptainer (the renamed and updated version of singularity) running in OpenSUSE 15.4.
Regards,
Fer
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your post confuses me
i cannot see the result of a successful installation in it
could you be a bit more clear
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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Yes, I did not paste a successful installation because I was in a chrooted environment (which singularity does not like). Here is the same system finally running the installation:
fernando@localhost:~/bin/salome_meca> singularity run --app install salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
Installation successfully completed.
To start salome_meca, just use:
/home/fernando/bin/salome_meca/salome_meca-lgpl-2021.1.0-1-20220405-scibian-9
or (in the installation directory):
./salome_meca-lgpl-2021.1.0-1-20220405-scibian-9
If you want to check your configuration, use:
singularity run --app check salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
fernando@localhost:~/bin/salome_meca> ./salome_meca-lgpl-2021.1.0-1-20220405-scibian-9 --soft
*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
runSalome running on linux.fritz.box
Searching for a free port for naming service: 2810 - OK
Searching Naming Service + found in 0.1 seconds
Searching /Kernel/Session in Naming Service +++++++++++_IceTransSocketUNIXConnect: Cannot connect to non-local host localhost.localdomain
_IceTransSocketUNIXConnect: Cannot connect to non-local host localhost.localdomain
+Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 14: reading configurations from ~/.fonts.conf is deprecated. please move it to /home/fernando/.config/fontconfig/fonts.conf manually
++****************************************************************
Warning: module HexoticPLUGIN is improperly configured!
Module HexoticPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
Warning: module GHS3DPLUGIN is improperly configured!
Module GHS3DPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
Warning: module GHS3DPRLPLUGIN is improperly configured!
Module GHS3DPRLPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
Warning: module BLSURFPLUGIN is improperly configured!
Module BLSURFPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
Warning: module NETGENPLUGIN is improperly configured!
Module NETGENPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
Warning: module HYBRIDPLUGIN is improperly configured!
Module HYBRIDPLUGIN will not be available in GUI mode!
****************************************************************
****************************************************************
Warning: module GMSHPLUGIN is improperly configured!
Module GMSHPLUGIN will not be available in GUI mode!
****************************************************************
found in 7.0 seconds
Start SALOME, elapsed time : 7.5 seconds
fernando@localhost:~/bin/salome_meca>
This is my end result. Can you paste the information about your singularity installation as I showed you mine in the previous post?
Regards,
Fer
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hello
here is the copy of the sequence
dedalus@localhost:~> sudo zypper info singularity
[sudo] password for root:
Loading repository data...
Reading installed packages...
Information for package singularity:
------------------------------------
Repository : Main Repository
Name : singularity
Version : 3.8.3-150400.1.64
Arch : x86_64
Vendor : SUSE LLC <https://www.suse.com/>
Installed Size : 153.5 MiB
Installed : Yes
Status : up-to-date
Source package : singularity-3.8.3-150400.1.64.src
Upstream URL : https://github.com/hpcng/singularity
Summary : Application and environment virtualization
Description :
Singularity provides functionality to make portable
containers that can be used across host environments.
dedalus@localhost:~> singularity run --app install salome_meca-lgpl-2021.0.0-1-20210811-scibian-9.sif
INFO: squashfuse not found, will not be able to mount SIF
INFO: fuse2fs not found, will not be able to mount EXT3 filesystems
INFO: Converting SIF file to temporary sandbox...
Installation successfully completed.
To start salome_meca, just use:
/tmp/rootfs-2043008892/salome_meca-lgpl-2021.0.0-1-20210811-scibian-9
or (in the installation directory):
./salome_meca-lgpl-2021.0.0-1-20210811-scibian-9
If you want to check your configuration, use:
singularity run --app check salome_meca-lgpl-2021.0.0-1-20210811-scibian-9.sif
INFO: Cleaning up image...
dedalus@localhost:~> ./salome_meca-lgpl-2021.0.0-1-20210811-scibian-9
bash: ./salome_meca-lgpl-2021.0.0-1-20210811-scibian-9: No such file or directory
dedalus@localhost:~>
i hope that helps you as it doe not help me very much
jean pierre aubry
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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Hi Jean-Pierre,
that gives a bit more information.
Could you install these two programs? "zypper in e2fsprogs squashfs"
If that still does not work, you could also try:
"zypper dup --recommends" and uninstall singularity and then run "zypper in --recommends singularity".
Regards,
Fer
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hello Irvise
it gives that:
dedalus@localhost:~> sudo zypper in e2fsprogs squashfs
[sudo] password for root:
Loading repository data...
Reading installed packages...
'e2fsprogs' is already installed.
No update candidate for 'e2fsprogs-1.46.4-150400.3.3.1.x86_64'. The highest available version is already installed.
'squashfs' is already installed.
No update candidate for 'squashfs-4.4-1.1.x86_64'. The highest available version is already installed.
Resolving package dependencies...
Nothing to do.
jean pierre aubry
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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in fact following some [unwise?] advice i installed apptainer
this created a symlink to apptainer
giving
which singularity
/usr/local/bin/singularity
killing this and reverting to /usr/bin/singularity
i can install, giving this
which singularity
/usr/bin/singularity
dedalus@localhost:~> singularity run --app install salome_meca-lgpl-2021.0.0-1-20210811-scibian-9.sif
Installation successfully completed.
To start salome_meca, just use:
/home/dedalus/salome_meca-lgpl-2021.0.0-1-20210811-scibian-9
or (in the installation directory):
./salome_meca-lgpl-2021.0.0-1-20210811-scibian-9
If you want to check your configuration, use:
singularity run --app check salome_meca-lgpl-2021.0.0-1-20210811-scibian-9.sif
dedalus@localhost:~> ./salome_meca-lgpl-2021.0.0-1-20210811-scibian-9
INFO: Could not find any nv files on this host!
*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
runSalome running on localhost.localdomain
Searching for a free port for naming service: 2812 - OK
Searching Naming Service + found in 0.1 seconds
Searching /Kernel/Session in Naming Service ++++++++++++++No protocol specified
No protocol specified
Traceback (most recent call last):
File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 181, in waitNSPID
os.kill(thePID,0)
ProcessLookupError: [Errno 3] No such process
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 694, in useSalome
clt = startSalome(args, modules_list, modules_root_dir)
File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 639, in startSalome
session=clt.waitNSPID("/Kernel/Session",mySessionServ.PID,SALOME.Session)
File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 183, in waitNSPID
raise RuntimeError("Process %d for %s not found" % (thePID,theName))
RuntimeError: Process 24162 for /Kernel/Session not found
--- Error during Salome launch ---
or this for astk
dedalus@localhost:~> singularity run -B /dedalus/arbeit salome_meca-lgpl-2021.0.0-1-20210811-scibian-9.sif shell -- astk
*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
dedalus@localhost:~> No protocol specified
No protocol specified
application-specific initialization failed: couldn't connect to display ":0"
Error in startup script: invalid command name "wm"
while executing
"wm withdraw ."
(file "/opt/salome_meca/Salome-V2021-s9/tools/Code_aster_frontend-2021001/lib/astk/astk.tcl" line 28)
Last edited by jeanpierreaubry (2022-08-30 10:06:05)
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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Hi JP,
I am a bit mixed. Did you managed to use apptainer? I don't think that you correctly installed apptainer, as far as I know, it does not create a symlink to singularity. It installs as apptainer.
It seems that you have a locally built singularity (as it comes from /usr/local/bin/singularity). After deleting it, your system is probably using the singularity binary from /usr/bin, which is the one provided by OpenSUSE, that is probably why it runs now, just like in my system.
Regarding the issues trying to get something running. I forgot to mention I am using a newer singularity Code_Aster image than yours. I just went to the download page and noticed that there is a newer singularity image that was uploaded a week ago.
Could you try to use that newer singularity container? The earlier singularity images were a bit problematic for me too, hopefully updating the singularity file fixes the issues you have.
Best regards and sorry that this is taking longer than expected,
Fer
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the provided link in the download section gives
https://code-aster.org/V2/%E2%80%99/FICHIERS/singularity/salome_meca-lgpl-2021.1.0-2-20220817-scibian-9.sif%E2%80%99
Not Found
The requested URL was not found on this server.
besides that how long does it takes you to download from code_aster,
i remember last time it took me more than a single day
can you install and run with the opensuse provided singularity
sudo zypper info singularity
Loading repository data...
Reading installed packages...
Information for package singularity:
------------------------------------
Repository : Main Repository
Name : singularity
Version : 3.8.3-150400.1.64
Arch : x86_64
Vendor : SUSE LLC <https://www.suse.com/>
Installed Size : 153.5 MiB
Installed : Yes
Status : up-to-date
Source package : singularity-3.8.3-150400.1.64.src
Upstream URL : https://github.com/hpcng/singularity
Summary : Application and environment virtualization
Description :
Singularity provides functionality to make portable
containers that can be used across host environments.
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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It seems someone made a typo with the download URL, the correct URL is https://www. code-aster.org/FICHIERS/singularity/salome_meca-lgpl-2021.1.0-2-20220817-scibian-9.sif
I am using the OpenSUSE provided singularity package. I had no problems with it, I thought that you had been using it all the time : ), that may explain why you were getting different errors initially.
Seeing your last error messages (Salome/ASTK failing to run) I would assume that the problem now is with the singularity image, not with singularity the program or your system. That is why I would ask you to use a newer image (.sif) file.
I know that the download is absolutly terrible. If you cannot download the new file, I could upload the .sif file that I use to my server and give you a download link.
Best regards,
Fer
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I know that the download is absolutly terrible. If you cannot download the new file, I could upload the .sif file that I use to my server and give you a download link.,
Fer
thanks that would be a jolly good idea
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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Hi JP,
it took a while to get it uploaded, here is the link: irvise.xyz/salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
This is not the newest one, but the second to newest (which is only in the archive, it was never linked to in the Downloads page). This is the one that worked for me.
I tried to download the latest version for hours, but the connection always dies, even when using wget -c. I managed to download most of it at high speeds but then it always just dies...
Anyhow, I hope this helps. Tell me if you have any other issues.
Regards,
Fer
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hello
thanks
but i cannot see any valid link in your post
jean pierre aubry
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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I left the https part out. Careful with the space
link: https:// irvise.xyz/salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
Regards,
Fer
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hello Irvise
thanks for the uploaded file
i am afraid it did not change anything
here is the output:
dedalus@localhost:~/opt/salome-meca> singularity run --app install salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
Installation successfully completed.
To start salome_meca, just use:
/home/dedalus/opt/salome-meca/salome_meca-lgpl-2021.1.0-1-20220405-scibian-9
or (in the installation directory):
./salome_meca-lgpl-2021.1.0-1-20220405-scibian-9
If you want to check your configuration, use:
singularity run --app check salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
dedalus@localhost:~/opt/salome-meca> ./salome_meca-lgpl-2021.1.0-1-20220405-scibian-9
INFO: Could not find any nv files on this host!
*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
runSalome running on localhost.localdomain
Searching for a free port for naming service: 2820 - OK
Searching Naming Service + found in 0.1 seconds
Searching /Kernel/Session in Naming Service ++++++++++++++No protocol specified
No protocol specified
Traceback (most recent call last):
File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 181, in waitNSPID
os.kill(thePID,0)
ProcessLookupError: [Errno 3] No such process
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 694, in useSalome
clt = startSalome(args, modules_list, modules_root_dir)
File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 639, in startSalome
session=clt.waitNSPID("/Kernel/Session",mySessionServ.PID,SALOME.Session)
File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 183, in waitNSPID
raise RuntimeError("Process %d for %s not found" % (thePID,theName))
RuntimeError: Process 4240 for /Kernel/Session not found
--- Error during Salome launch ---
dedalus@localhost:~/opt/salome-meca> singularity run -B /dedalus salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif shell -- astk
*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
dedalus@localhost:~/opt/salome-meca> No protocol specified
No protocol specified
jean pierre aubry
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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Thank for the output. This is getting tough...
Mmmm... Okay... Here is the situation:
1. Our systems (libraries, programs, etc) are mostly identical to the bit level. There should be no problem with singularity, related libraries, etc.
2. Now we are using the exact same .sif file. So regarding singularity, there should be no issues.
This leaves me with a few possible points.
1. You do not seem to have an Nvidia card or the drivers are not loaded. Try to run the launch script with --soft:
./salome_meca-lgpl-2021.1.0-1-20220405-scibian-9 --soft
1.1 If you have Nvidia GFX, you should install the drivers and make sure they are in use. But for the time being, lets get the singularity container running.
2. I noticed that you are running the singularity container from /opt/salome-meca. That should be fine if you have the necessary rights. I am using $HOME/bin, which for sure should not have any issues with permissions. Could you try to "install" and run the singularity container from within your $HOME?
3. What filesystem are you using? I know singularity has issues with AFS, but otherwise, it should just work. If you are running it locally in a normal OpenSUSE Leap install, you are probably using BTRFS or EXT4, which should just work.
4. Your singularity is failing to launch with an error "No protocol specified", that is a bit strange, but it is not the first time I have seen it... I am not 100% sure how to fix it...
5. Could you try launching a shell inside the container? You should be able to do that with "singularity shell salome...........sif"
Otherwise I have no better idea on how to approach this problem...
Best regards,
Fer
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hello Irvise
here my answers point by point
1- i do not have an nividia card the komptuer is a basic lenovo laptop
the previous version of singularity salome-meca worked well under 15.1
the output with --soft (the same as before)
dedalus@localhost:~/opt/salome-meca> ./salome_meca-lgpl-2021.1.0-1-20220405-scibian-9 --soft*****************************************************
INFO : Running salome_meca in software rendering mode
*****************************************************
runSalome running on localhost.localdomain
Searching for a free port for naming service: 2823 - OK
Searching Naming Service + found in 0.1 seconds
Searching /Kernel/Session in Naming Service ++++++++++++++No protocol specified
No protocol specified
Traceback (most recent call last):
File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 181, in waitNSPID
os.kill(thePID,0)
ProcessLookupError: [Errno 3] No such process
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 694, in useSalome
clt = startSalome(args, modules_list, modules_root_dir)
File "/opt/salome_meca/appli_V2021/bin/salome/runSalome.py", line 639, in startSalome
session=clt.waitNSPID("/Kernel/Session",mySessionServ.PID,SALOME.Session)
File "/opt/salome_meca/Salome-V2021-s9/modules/KERNEL_V9_7_0/bin/salome/orbmodule.py", line 183, in waitNSPID
raise RuntimeError("Process %d for %s not found" % (thePID,theName))
RuntimeError: Process 23393 for /Kernel/Session not found
--- Error during Salome launch ---
dedalus@localhost:~/opt/salome-meca>
2- $HOME/opt/salome-meca is owned by myself with the necessary rights as far as i know
3- this directory is btrfs on the same ssd i have a working directory that is ext4
4- i noticed that quite a few (not to say all) of my presonnal scripts used to perform some tasks (for example take a screen shot) print this "No protocol specified" in the terminal which did not happen earlier as far as i remember
5- here is the output
dedalus@localhost:~/opt/salome-meca> singularity shell salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif --soft
Singularity> ls
salome_meca-lgpl-2021.1.0-1-20220405-scibian-9 salome_meca-lgpl-2021.1.0-1-20220405-scibian-9.sif
Otherwise I have no better idea on how to approach this problem...
as i doubt the salome-meca team will ever answer this question we are left alone
i am very sad
up to 15.2 code_aster stand alone was a nice piece of software
with a comprehensive documentation
this containerized version of salome-meca sucks, with no documentation and no help
jean pierre aubry
Last edited by jeanpierreaubry (2022-08-31 13:28:10)
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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Code_Asterの開発者
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hello AsterO'dactyle
thanks for the link
first of all
as you can see from the log message it looks like the trouble is not due do nividia driver
as it occurs with the option --soft
second
what do you suggest as best linux distribution to ensure a trouble free salome-meca installation and use?
which one is mostly used among the development team
i am a structural engineer, i like fiddling with my komputer, but the end i want to produce some structural analysis?
jean pierre aubry
consider reading my book
freely available here https://framabook.org/beginning-with-code_aster/
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