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[AF>Le_Pommier] Jerome_C2005

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Message 44771 - Posted: 20 Apr 2021, 17:16:01 UTC

@David : Atlas tasks are not failing anymore, thanks a lof for the tip !
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tatayet64

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Message 44780 - Posted: 21 Apr 2021, 18:45:55 UTC

Hi,

All ATLAS Job are still KO for me.
Here is an exemple :
https://lhcathome.cern.ch/lhcathome/result.php?resultid=314031488

<core_client_version>7.16.6</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
19:03:12 (1338628): wrapper (7.7.26015): starting
19:03:12 (1338628): wrapper: running run_atlas (--nthreads 1)
[2021-04-21 19:03:12] Arguments: --nthreads 1
[2021-04-21 19:03:12] Threads: 1
[2021-04-21 19:03:12] Checking for CVMFS
[2021-04-21 19:03:17] Probing /cvmfs/atlas.cern.ch... OK
[2021-04-21 19:03:18] Probing /cvmfs/atlas-condb.cern.ch... OK
[2021-04-21 19:03:19] Probing /cvmfs/grid.cern.ch... OK
[2021-04-21 19:03:19] Probing /cvmfs/cernvm-prod.cern.ch... OK
[2021-04-21 19:03:21] Probing /cvmfs/sft.cern.ch... OK
[2021-04-21 19:03:22] Probing /cvmfs/alice.cern.ch... OK
[2021-04-21 19:03:22] VERSION PID UPTIME(M) MEM(K) REVISION EXPIRES(M) NOCATALOGS CACHEUSE(K) CACHEMAX(K) NOFDUSE NOFDMAX NOIOERR NOOPEN HITRATE(%) RX(K) SPEED(K/S) HOST PROXY ONLINE
[2021-04-21 19:03:22] 2.7.5.0 1338840 0 24652 83131 3 1 30021779 33554433 0 65024 0 0 n/a 527 139 http://cvmfs-stratum-one.cern.ch:8000/cvmfs/atlas.cern.ch DIRECT 1
[2021-04-21 19:03:22] CVMFS is ok
[2021-04-21 19:03:22] Efficiency of ATLAS tasks can be improved by the following measure(s):
[2021-04-21 19:03:22] The CVMFS client on this computer should be configured to use Cloudflare's openhtc.io.
[2021-04-21 19:03:22] Small home clusters do not require a local http proxy but it is suggested if
[2021-04-21 19:03:22] more than 10 cores throughout the same LAN segment are regularly running ATLAS like tasks.
[2021-04-21 19:03:22] Further information can be found at the LHC@home message board.
[2021-04-21 19:03:22] Using singularity image /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img
[2021-04-21 19:03:22] Checking for singularity binary...
[2021-04-21 19:03:22] Singularity is not installed, using version from CVMFS
[2021-04-21 19:03:22] Checking singularity works with /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img hostname
[2021-04-21 19:03:29] INFO: Converting SIF file to temporary sandbox... UBUNTU-FALOURD INFO: Cleaning up image...
[2021-04-21 19:03:29] Singularity works
[2021-04-21 19:03:29] Starting ATLAS job with PandaID=5031802625
[2021-04-21 19:03:29] Running command: /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /var/lib/boinc-client/slots/4 -B /cvmfs,/var /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img sh start_atlas.sh
[2021-04-21 19:03:39] Job failed
[2021-04-21 19:03:39] INFO:    Converting SIF file to temporary sandbox...
[2021-04-21 19:03:39] INFO:    Cleaning up image...
[2021-04-21 19:03:39] FATAL:   container creation failed: hook function for tag prelayer returns error: failed to create /var/lib/alternatives directory: mkdir /var/lib/alternatives: permission denied
[2021-04-21 19:03:39] ./runtime_log
[2021-04-21 19:03:39] ./runtime_log.err
19:13:40 (1338628): run_atlas exited; CPU time 15.787750
19:13:40 (1338628): app exit status: 0x1
19:13:40 (1338628): called boinc_finish(195)

</stderr_txt>
]]>


What can i do ?
Thanks for your help.
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Message 44806 - Posted: 24 Apr 2021, 16:29:32 UTC - in response to Message 44755.  
Last modified: 24 Apr 2021, 16:40:56 UTC

The feedback I got said there was a configuration change related to setuid in the latest singularity, and he pointed me to this page.

I didn't try to install a local singularity but I did try to:
openSUSE and SUSE have a small difference with upstream default. 
This means the SUID root binaries distributed by singularity are executable only by users belonging to the group 'singularity'.
Otherwise, users will get an error message like this one:
FATAL:   while executing /usr/lib/singularity/bin/starter-suid: permission denied
To add a user to the group singularity, execute (as root):
 # usermod -a -G singularity <user_login>
But when I execute:
sudo usermod -a -G singularity aurum
It responds with:
usermod: group 'singularity' does not exist

Ok, trying again:
sudo groupadd singularity
sudo usermod -a -G singularity aurum
Ok, so far so good. Just broke 1.1% which is first.
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Message 44807 - Posted: 24 Apr 2021, 16:46:53 UTC
Last modified: 24 Apr 2021, 16:48:42 UTC

Failed again. A perfect record: 100% failures for ATLAS.
[2021-04-24 09:34:41] Using singularity image /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img
[2021-04-24 09:34:41] Checking for singularity binary...
[2021-04-24 09:34:41] Singularity is not installed, using version from CVMFS
[2021-04-24 09:34:41] Checking singularity works with /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img hostname
[2021-04-24 09:34:42] Singularity isnt working: INFO:    Converting SIF file to temporary sandbox...
[2021-04-24 09:34:42] FATAL:   while extracting /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img: root filesystem extraction failed: extract command failed: WARNING: passwd file doesn't exist in container, not updating
[2021-04-24 09:34:42] WARNING: group file doesn't exist in container, not updating
[2021-04-24 09:34:42] WARNING: Skipping mount /etc/hosts [binds]: /etc/hosts doesn't exist in container
[2021-04-24 09:34:42] WARNING: Skipping mount /etc/localtime [binds]: /etc/localtime doesn't exist in container
[2021-04-24 09:34:42] WARNING: Skipping mount proc [kernel]: /proc doesn't exist in container
[2021-04-24 09:34:42] WARNING: Skipping mount /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/tmp [tmp]: /tmp doesn't exist in container
[2021-04-24 09:34:42] WARNING: Skipping mount /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/var/tmp [tmp]: /var/tmp doesn't exist in container
[2021-04-24 09:34:42] WARNING: Skipping mount /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
[2021-04-24 09:34:42] 
[2021-04-24 09:34:42] FATAL ERROR:write_file: failed to create file /image/root/usr/include/c++/4.8.2/ext/pb_ds/detail/cc_hash_table_map_/erase_fn_imps.hpp, because Too many open files
[2021-04-24 09:34:42] Parallel unsquashfs: Using 36 processors
[2021-04-24 09:34:42] 41269 inodes (41434 blocks) to write
[2021-04-24 09:34:42] 
[2021-04-24 09:34:42] : exit status 1
09:44:43 (47648): run_atlas exited; CPU time 1.082061
09:44:43 (47648): app exit status: 0x1
09:44:43 (47648): called boinc_finish(195)
</stderr_txt>
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Message 44897 - Posted: 6 May 2021, 8:11:33 UTC - in response to Message 44807.  

Looking into errors, I found that the problem is the use of wrong path by container :
09:56:16 (130425): wrapper (7.7.26015): starting
09:56:16 (130425): wrapper: running run_atlas (--nthreads 6)
[2021-05-06 09:56:16] Arguments: --nthreads 6
[2021-05-06 09:56:16] Threads: 6
[2021-05-06 09:56:16] Checking for CVMFS
[2021-05-06 09:56:16] Probing /cvmfs/atlas.cern.ch... OK
[2021-05-06 09:56:16] Probing /cvmfs/atlas-condb.cern.ch... OK
[2021-05-06 09:56:16] Running cvmfs_config stat atlas.cern.ch
[2021-05-06 09:56:16] VERSION PID UPTIME(M) MEM(K) REVISION EXPIRES(M) NOCATALOGS CACHEUSE(K) CACHEMAX(K) NOFDUSE NOFDMAX NOIOERR NOOPEN HITRATE(%) RX(K) SPEED(K/S) HOST PROXY ONLINE
[2021-05-06 09:56:16] 2.8.1.0 129901 5 25280 84062 2 3 4718377 6144001 0 130560 0 36 99.909 528 724 http://s1ral-cvmfs.openhtc.io/cvmfs/atlas.cern.ch http://192.168.2.1:3128 1
[2021-05-06 09:56:16] CVMFS is ok
[2021-05-06 09:56:16] Using singularity image /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img
[2021-05-06 09:56:16] Checking for singularity binary...
[2021-05-06 09:56:16] Singularity is not installed, using version from CVMFS
[2021-05-06 09:56:16] Checking singularity works with /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img hostname
[2021-05-06 09:56:18] INFO: Converting SIF file to temporary sandbox... fonck INFO: Cleaning up image...
[2021-05-06 09:56:18] Singularity works
[2021-05-06 09:56:18] Set ATHENA_PROC_NUMBER=6
[2021-05-06 09:56:18] Starting ATLAS job with PandaID=5047215526
[2021-05-06 09:56:18] Running command: /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /var/lib/boinc-client/slots/7 -B /cvmfs,/var /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img sh start_atlas.sh
[2021-05-06 09:56:20] Job failed
[2021-05-06 09:56:20] INFO:    Converting SIF file to temporary sandbox...
[2021-05-06 09:56:20] INFO:    Cleaning up image...
[2021-05-06 09:56:20] FATAL:   container creation failed: mount /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/rootfs/var/lib/package-list->/cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/underlay/var/lib/package-list error: while mounting /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/rootfs/var/lib/package-list: destination /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/underlay/var/lib/package-list doesn't exist in container
[2021-05-06 09:56:20] ./runtime_log.err
[2021-05-06 09:56:20] ./runtime_log

For testing, I changed temporarily write permission for /var/lib :
sudo chmod o+w /var/lib/

As you can see, all files are created there ...
$ ls -lh /var/lib/|grep boinc
drwxr-xr-x  2 boinc         boinc         4,0K mai    5 23:49 alternatives
lrwxrwxrwx  1 boinc         boinc           12 mai   22  2018 boinc -> boinc-client
drwxr-xr-x  8 boinc         boinc         4,0K mai    6 09:57 boinc-client
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 00:12 condor
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 00:28 cs
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:47 games
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 gssproxy
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 initramfs
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 machines
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 ntp
-rw-r--r--  1 boinc         boinc            0 mai    6 09:56 package-list
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 rpcbind
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 rpm
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 rpm-state
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 texmf

There are some parts missing at the mount point :
$ ls /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/
$
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Message 45025 - Posted: 28 May 2021, 6:36:03 UTC - in response to Message 44897.  

Looking into errors, I found that the problem is the use of wrong path by container :
09:56:16 (130425): wrapper (7.7.26015): starting
09:56:16 (130425): wrapper: running run_atlas (--nthreads 6)
[2021-05-06 09:56:16] Arguments: --nthreads 6
[2021-05-06 09:56:16] Threads: 6
[2021-05-06 09:56:16] Checking for CVMFS
[2021-05-06 09:56:16] Probing /cvmfs/atlas.cern.ch... OK
[2021-05-06 09:56:16] Probing /cvmfs/atlas-condb.cern.ch... OK
[2021-05-06 09:56:16] Running cvmfs_config stat atlas.cern.ch
[2021-05-06 09:56:16] VERSION PID UPTIME(M) MEM(K) REVISION EXPIRES(M) NOCATALOGS CACHEUSE(K) CACHEMAX(K) NOFDUSE NOFDMAX NOIOERR NOOPEN HITRATE(%) RX(K) SPEED(K/S) HOST PROXY ONLINE
[2021-05-06 09:56:16] 2.8.1.0 129901 5 25280 84062 2 3 4718377 6144001 0 130560 0 36 99.909 528 724 http://s1ral-cvmfs.openhtc.io/cvmfs/atlas.cern.ch http://192.168.2.1:3128 1
[2021-05-06 09:56:16] CVMFS is ok
[2021-05-06 09:56:16] Using singularity image /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img
[2021-05-06 09:56:16] Checking for singularity binary...
[2021-05-06 09:56:16] Singularity is not installed, using version from CVMFS
[2021-05-06 09:56:16] Checking singularity works with /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img hostname
[2021-05-06 09:56:18] INFO: Converting SIF file to temporary sandbox... fonck INFO: Cleaning up image...
[2021-05-06 09:56:18] Singularity works
[2021-05-06 09:56:18] Set ATHENA_PROC_NUMBER=6
[2021-05-06 09:56:18] Starting ATLAS job with PandaID=5047215526
[2021-05-06 09:56:18] Running command: /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /var/lib/boinc-client/slots/7 -B /cvmfs,/var /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img sh start_atlas.sh
[2021-05-06 09:56:20] Job failed
[2021-05-06 09:56:20] INFO:    Converting SIF file to temporary sandbox...
[2021-05-06 09:56:20] INFO:    Cleaning up image...
[2021-05-06 09:56:20] FATAL:   container creation failed: mount /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/rootfs/var/lib/package-list->/cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/underlay/var/lib/package-list error: while mounting /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/rootfs/var/lib/package-list: destination /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/underlay/var/lib/package-list doesn't exist in container
[2021-05-06 09:56:20] ./runtime_log.err
[2021-05-06 09:56:20] ./runtime_log

For testing, I changed temporarily write permission for /var/lib :
sudo chmod o+w /var/lib/

As you can see, all files are created there ...
$ ls -lh /var/lib/|grep boinc
drwxr-xr-x  2 boinc         boinc         4,0K mai    5 23:49 alternatives
lrwxrwxrwx  1 boinc         boinc           12 mai   22  2018 boinc -> boinc-client
drwxr-xr-x  8 boinc         boinc         4,0K mai    6 09:57 boinc-client
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 00:12 condor
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 00:28 cs
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:47 games
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 gssproxy
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 initramfs
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 machines
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 ntp
-rw-r--r--  1 boinc         boinc            0 mai    6 09:56 package-list
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 rpcbind
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 rpm
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 rpm-state
drwxr-xr-x  2 boinc         boinc         4,0K mai    6 09:56 texmf

There are some parts missing at the mount point :
$ ls /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/3.7.2/var/singularity/mnt/session/
$


same problem where I've been posting all night long here :

https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=5633&postid=45024#45024

so is the local installation of singularity the only available solution out there?
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Message 45026 - Posted: 28 May 2021, 6:44:24 UTC - in response to Message 45025.  

When you read the messages in the folders, you can find the answer!
Singularity is downloaded from the Atlas-Server, when local no singularity could be found!
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Message 45029 - Posted: 28 May 2021, 7:34:32 UTC - in response to Message 45026.  
Last modified: 28 May 2021, 7:35:35 UTC

When you read the messages in the folders, you can find the answer!
Singularity is downloaded from the Atlas-Server, when local no singularity could be found!


yes and that's exactly where the emssage is coming from... from the singularity downloaded from the server and apparently ther eis something wrong with the package since he can't find some folder from the img donwloaded @maeax
do you want maybe the task unit to prove it to you?
here it is:
https://lhcathome.cern.ch/lhcathome/result.php?resultid=317300586
and as you can see the singularity is downloaded, probed as working fine but still there are pieces missing which echoes the messages posted earlier in this thread for example this one:
https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=5647&postid=44897
so since I'm not the only one let's not pretend that the package is okey... OR there are some missing informations then
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Message 45055 - Posted: 16 Jun 2021, 1:39:21 UTC - in response to Message 45029.  

I'm having issues with the native ATLAS app with just these same behaviors.

Getting error messages that a given directory under /var/lib isn't present and can't be created.

I tried adding the Singularity group and adding both my username and boinc to the group.

This is happening on two Linux boxes of mine...
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Message 45060 - Posted: 16 Jun 2021, 13:49:05 UTC - in response to Message 45055.  

Working workarounds can be find in these posts.
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Message 45180 - Posted: 11 Aug 2021, 20:08:25 UTC
Last modified: 11 Aug 2021, 20:24:19 UTC

Having the same issue here. it has been a while.
Steps ran:
Installed cvmfs.
create default.local
sudo apt-get install singularity
sudo apt-get install squashfs-tools
Ubuntu 20.04. Plenty of ram - set to run 1 Atlas task, machine has 16 gb ram. Initially thought there was an error while changing number of CPUs per task.
Task in question:

https://lhcathome.cern.ch/lhcathome/result.php?resultid=323595231

Has anyone found a working fix for this?
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Message 45181 - Posted: 11 Aug 2021, 20:55:30 UTC - in response to Message 45180.  
Last modified: 11 Aug 2021, 20:55:58 UTC

sudo apt-get install singularity

Even though it says "Singularity works", I haven't had that version of singularity work in years, on Ubuntu 20.04.2 and earlier.

This is what worked for me about six months ago, though it is a fairly safe bet that things have changed by now.
But it might get you started. (First uninstall the version you have, with sudo apt remove singularity, though it probably won't find it anyway).

First: install Dependencies:
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
wget \
pkg-config \
git \
cryptsetup

To correct broken packages (examples):
sudo apt install libseccomp2=2.4.3-1ubuntu1
sudo apt install libssl1.1=1.1.1f-1ubuntu2

Second: install GO
sudo snap install go --classic
Result: go 1.16.2 from Michael Hudson-Doyle (mwhudson) installed

go get -u github.com/golang/dep/cmd/dep
(wait for the download!)

Check version: go version

-----------------------------------------------------------------------------------
Install Singularity (check latest version at https://github.com/hpcng/singularity/releases):
See: https://sylabs.io/guides/3.7/user-guide/quick_start.html

go get -d github.com/sylabs/singularity

export VERSION=3.7.2 && \
wget https://github.com/hpcng/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
tar -xzf singularity-${VERSION}.tar.gz && \
cd singularity

./mconfig && \
make -C ./builddir && \
sudo make -C ./builddir install

Check Version: singularity --version
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wolfman1360

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Message 45182 - Posted: 11 Aug 2021, 22:31:49 UTC - in response to Message 45181.  

sudo apt-get install singularity

Even though it says "Singularity works", I haven't had that version of singularity work in years, on Ubuntu 20.04.2 and earlier.

This is what worked for me about six months ago, though it is a fairly safe bet that things have changed by now.
But it might get you started. (First uninstall the version you have, with sudo apt remove singularity, though it probably won't find it anyway).

First: install Dependencies:
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
wget \
pkg-config \
git \
cryptsetup

To correct broken packages (examples):
sudo apt install libseccomp2=2.4.3-1ubuntu1
sudo apt install libssl1.1=1.1.1f-1ubuntu2

Second: install GO
sudo snap install go --classic
Result: go 1.16.2 from Michael Hudson-Doyle (mwhudson) installed

go get -u github.com/golang/dep/cmd/dep
(wait for the download!)

Check version: go version

-----------------------------------------------------------------------------------
Install Singularity (check latest version at https://github.com/hpcng/singularity/releases):
See: https://sylabs.io/guides/3.7/user-guide/quick_start.html

go get -d github.com/sylabs/singularity

export VERSION=3.7.2 && \
wget https://github.com/hpcng/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
tar -xzf singularity-${VERSION}.tar.gz && \
cd singularity

./mconfig && \
make -C ./builddir && \
sudo make -C ./builddir install

Check Version: singularity --version

First off - thank you so much. We're currently well above 10 minutes of CPU time, so it appears to be working. This was all very much above my head and I simply copy and pasted a lot of this with the substitutions of version numbers and directories. Hopefully nothing goes wrong in the future as I am still very much new to Linux for the most part.
hopefully this, along with a few other things, can be pinned. I'm finding a lot of things are very scattered - especially as they relate to native - and there are a lot of different instructions that are now out of date or do not work for this project.
For reference, this is what just worked for me. I still have a few questions, but that's for another topic.
sudo apt remove singularity
sudo apt autoremove (not sure if this is needed, but it didn't break anything, yet)
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
wget \
pkg-config \
git \
cryptsetup

To correct broken packages (examples):
sudo apt install libseccomp2=2.4.3-1ubuntu1
sudo apt install libssl1.1=1.1.1f-1ubuntu2

Second: install GO
sudo snap install go --classic
Result: go 1.16.6 from Michael Hudson-Doyle (mwhudson) installed
Check version: go version
go get -d github.com/hpcng/singularity
export VERSION=3.8.0 && \
wget https://github.com/hpcng/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
tar -xzf singularity-${VERSION}.tar.gz && \
cd singularity-3.8.0

./mconfig && \
make -C ./builddir && \
sudo make -C ./builddir install

Good luck and thank you again.
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Jim1348

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Message 45184 - Posted: 11 Aug 2021, 23:07:13 UTC - in response to Message 45182.  

You are quite welcome. Nothing is easy with native, especially singularity.
It all depends on which version of Linux you have, and what libraries it contains.

I am glad it worked this time.
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wolfman1360

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Message 45185 - Posted: 12 Aug 2021, 0:05:00 UTC - in response to Message 45184.  

You are quite welcome. Nothing is easy with native, especially singularity.
It all depends on which version of Linux you have, and what libraries it contains.

I am glad it worked this time.

As am I. I usually install the standard Ubuntu 20.04 along with any updates. I know I had major issues with debien.
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David Cameron
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Message 45272 - Posted: 30 Aug 2021, 9:32:06 UTC

Hi all,

I recently switched one of my CentOS 7 machines to use Singularity from CVMFS and got the same problem described in this thread:

FATAL: container creation failed: hook function for tag prelayer returns error: failed to create /var/lib/condor directory: mkdir /var/lib/condor: permission denied


I am running the boinc client via systemd in /var/lib/boinc and it seems the issue comes from mounting the whole /var directory into the container.

I worked around the problem by moving the BOINC data dir to /home/boinc as described here: https://boinc.berkeley.edu/forum_thread.php?id=13919

However those instructions didn't work exactly out of the box, I had to set ProtectHome=false to allow access to /home and add the new dir to ReadWritePaths. My working settings are

# /etc/systemd/system/boinc-client.service.d/override.conf
[Service]
ProtectHome=false
BindPaths=/home/boinc
WorkingDirectory=/home/boinc
ReadWritePaths=-/etc/boinc-client /home/boinc
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[AF>Le_Pommier] Jerome_C2005

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Message 45329 - Posted: 11 Sep 2021, 10:50:48 UTC
Last modified: 11 Sep 2021, 10:52:37 UTC

Jesus. The wonderful world of Linux :D

We are quite far from the "initial boinc spirit" here : allow anybody to install, subscribe to a project, it works.

I fully agree it is necessary and great to have people involved in such test (I am a humble one of them), but what's the point of all this if it can't be packaged in a "simple a workable" way for boinc users ?
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