I have signing of git commits turned on in my global git config on gadi. As long as I “module load” from vk83 or hh5, then the git version in those modules means that git commits are signed. If I try and use the system git, git commit’s fail - as written up here.
However, I have been trying to use runlog:True
in payu, and I get the following error:
$ qcat -e 118782756
Currently Loaded Modulefiles:
1) pbs 2) openmpi/4.1.4(default)
error: ssh-keygen -Y sign is needed for ssh signing (available in openssh version 8.2p1+)
error: unknown option -- Y?
usage: ssh-keygen [-q] [-b bits] [-t dsa | ecdsa | ed25519 | rsa] [-m format]
[-N new_passphrase] [-C comment] [-f output_keyfile]
ssh-keygen -p [-P old_passphrase] [-N new_passphrase] [-m format]
[-f keyfile]
ssh-keygen -i [-m key_format] [-f input_keyfile]
ssh-keygen -e [-m key_format] [-f input_keyfile]
...
fatal: failed to write commit object
Which means that the job which payu started to run the model is trying to commit using the system git (rather than the git in vk83). The expected result is that for each time “payu run” is executed, then one commit is made to the current configuration branch.
Note in the error log from PBS (above) the payu module from vk83 is not loaded inside the job. Which may be why the job us not using the vk83 git binary?
Saving that, there is a long set of environment variable created with the PBS job (below) maybe one of them should be point it to the vk83 git binary?
qstat -f 118782756
Job Id: 118782756.gadi-pbs
...
substate = 42
Variable_List = PBS_O_HOME=/home/603/as2285,PBS_O_LANG=en_US.UTF-8,
PBS_O_LOGNAME=as2285,
PBS_O_PATH=/g/data/vk83/apps/payu/1.1.3/bin:/home/603/as2285/.vscode-s
erver/cli/servers/Stable-5437499feb04f7a586f677b155b039bc2b3669eb/serve
r/bin/remote-cli:/home/603/as2285/.local/bin:/home/603/as2285/bin:/g/da
ta/hh5/public/apps/miniconda3/condabin:/opt/pbs/default/bin:/opt/nci/bi
n:/opt/bin:/opt/Modules/v4.3.0/bin:/bin:/usr/bin:/usr/local/sbin:/usr/s
bin:/opt/pbs/default/bin:/opt/pbs/default/bin:/opt/pbs/default/bin,
PBS_O_MAIL=/var/spool/mail/as2285,PBS_O_SHELL=/bin/bash,
PBS_O_TZ=:/etc/localtime,PBS_O_HOST=gadi-login-05.gadi.nci.org.au,
PBS_O_WORKDIR=/g/data/tm70/as2285/payu/MOM6-CICE6,PBS_O_SYSTEM=Linux,
PAYU_PATH=/g/data/vk83/apps/payu/1.1.3/bin,PAYU_FORCE=True,
MODULESHOME=/opt/Modules/v4.3.0,
MODULES_CMD=/opt/Modules/v4.3.0/libexec/modulecmd.tcl,
MODULEPATH=/g/data/vk83/modules:/etc/scl/modulefiles:/etc/scl/modulefi
les:/etc/scl/modulefiles:/opt/Modules/modulefiles:/opt/Modules/v4.3.0/m
odulefiles:/apps/Modules/modulefiles,PBS_NCI_HT=0,
PBS_NCI_STORAGE=scratch/tm70+gdata/tm70+gdata/qv56+gdata/ik11+gdata/vk
83,PBS_NCI_IMAGE=,PBS_NCPUS=48,PBS_NGPUS=0,PBS_NNODES=1,
PBS_NCI_NCPUS_PER_NODE=48,PBS_NCI_NUMA_PER_NODE=4,
PBS_NCI_NCPUS_PER_NUMA=12,PROJECT=tm70,PBS_VMEM=206158430208,
PBS_NCI_WD=1,PBS_NCI_JOBFS=10gb,PBS_NCI_LAUNCH_COMPATIBILITY=0,
PBS_NCI_FS_GDATA1=0,PBS_NCI_FS_GDATA1A=0,PBS_NCI_FS_GDATA1B=0,
PBS_NCI_FS_GDATA2=0,PBS_NCI_FS_GDATA3=0,PBS_NCI_FS_GDATA4=0,
PBS_O_QUEUE=normal,PBS_JOBFS=/jobfs/118782756.gadi-pbs
comment = Job run at Fri Jun 21 at 14:37 on (gadi-cpu-clx-2507:ncpus=48:mem
=201326592kb:jobfs=10485760kb)
etime = Fri Jun 21 11:07:37 2024
run_count = 1
Submit_arguments = -q normal -P tm70 -l walltime=172800 -l ncpus=48 -l mem=
192GB -l jobfs=10GB -N 1deg_jra55do_ia -l wd -j n -v PAYU_PATH=/g/data/
vk83/apps/payu/1.1.3/bin,PAYU_FORCE=True,
MODULESHOME=/opt/Modules/v4.3.0,
MODULES_CMD=/opt/Modules/v4.3.0/libexec/modulecmd.tcl,
MODULEPATH=/g/data/vk83/modules:/etc/scl/modulefiles:/etc/scl/modulefi
les:/etc/scl/modulefiles:/opt/Modules/modulefiles:/opt/Modules/v4.3.0/m
odulefiles:/apps/Modules/modulefiles -l storage=gdata/ik11+gdata/qv56+g
data/tm70+gdata/vk83 -- /g/data/vk83/apps/payu/1.1.3/bin/python3.9 /g/d
ata/vk83/apps/payu/1.1.3/bin/payu-run
executable = <jsdl-hpcpa:Executable>/g/data/vk83/apps/payu/1.1.3/bin/python
3.9</jsdl-hpcpa:Executable>
argument_list = <jsdl-hpcpa:Argument>/g/data/vk83/apps/payu/1.1.3/bin/payu-
run</jsdl-hpcpa:Argument>
project = tm70
Submit_Host = gadi-login-05.gadi.nci.org.au
Ping @jo-basevi