You can use both clusters, but see this link to help you choose the right cluster.
Since you are reading this FAQ, we suppose you already know how to find the documentation. If you need any further explanation, advice, tips, etc. contact us at: hpc@unige.ch . We will try to answer your request as soon as possible.
This may happen, but the problem is to determine what is slow:
What to do: be sure you aren't the cause. Check with htop
on the login node. If you see that all the cpus are in use, please take a screenshot and send it to us at hpc@unige.ch.
chage
command:(baobab)-[yourusername@login2 ~]$ chage -l yourusername Last password change : Apr 01, 2022 Password expires : never Password inactive : never Account expires : never Minimum number of days between password change : 0 Maximum number of days between password change : 99999 Number of days of warning before password expires : 7
Yes it is possible as long as you collaborate tightly with your former research group. Your PI must invite you as outsider. For technical reason, your account needs to be expired prior doing the request for the invitation. We'll then reactivate your account. You'll keep your data.
Where should I store my files ? What should I do if I deleted something by mistake ? Is there a backup ? How can I restore a delete file ? What amount of storage space is available ? My job creates lots of temporary small files and everything is slow…
Please check the Storage page for details.
Alternatively, if you need to store a large quantity of data, you could use another service such as the “Academic NAS” : https://catalogue-si.unige.ch/en/stockage-recherche
You can find information about available applications here
Please check this documentation.
Baobab is a GNU/Linux only machine, like the majority of academic clusters. If you have a windows software that could run on a Windows cluster, contact us at hpc@unige.ch, perhaps we could find some solutions.
Yes we can install it, but you should pay the required license. Send us a request at hpc@unige.ch.
No, please check the Singularity documentation.
Have a look at this scheduler “rosetta stone”, available here:
http://slurm.schedmd.com/rosetta.pdf
No never. You must use SLURM to run any test. The debug
partition is dedicated to small tests.
In that case you can use the job arrays feature of SLURM. Please, have a look at the documentation Job array
See here
No. Unfortunately you can't. If we raised this limit, you will have to wait longer before having your pending jobs started. We think that the 4 days limit is a good trade-off.
However there could be two work-around if you experience an issue with this limit:
See here
To get the priority calculation details of the jobs in the pending queue, you can use the command: sprio -w
. You can also have a look at the weights, by typing sprio -l
.
Yes, you can. But it is really awkward because you cannot be sure when your job will start.
See Interactive jobs
Indeed, we are reserving two cores per node for system tasks such as data transfer, and os stuff.
(yggdrasil)-[root@admin1 ~]$ scontrol show node cpu001 NodeName=cpu001 Arch=x86_64 CoresPerSocket=18 CPUAlloc=0 CPUEfctv=34 CPUTot=36 CPULoad=0.01 AvailableFeatures=GOLD-6240,XEON_GOLD_6240,V9 ActiveFeatures=GOLD-6240,XEON_GOLD_6240,V9 Gres=(null) NodeAddr=cpu001 NodeHostName=cpu001 Version=23.02.1 OS=Linux 4.18.0-477.10.1.el8_8.x86_64 #1 SMP Tue May 16 11:38:37 UTC 2023 RealMemory=187000 AllocMem=0 FreeMem=185338 Sockets=2 Boards=1 CoreSpecCount=2 CPUSpecList=17,35 <==================== this means we have two specialization cores <<<< State=IDLE ThreadsPerCore=1 TmpDisk=150000 Weight=10 Owner=N/A MCS_label=N/A Partitions=debug-cpu BootTime=2023-08-10T12:08:11 SlurmdStartTime=2023-08-10T12:09:00 LastBusyTime=2023-08-11T10:06:42 ResumeAfterTime=None CfgTRES=cpu=34,mem=187000M,billing=34 AllocTRES= CapWatts=n/a CurrentWatts=0 AveWatts=0 ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
If you really need to use all the cores of a compute node, you can override this parameter: –core-spec=0
. This will implicitly lead to an exclusive allocation of the node.
If you connect to the cluster with an ssh key as authentication mechanism and you have trouble:
ssh-keygen -y -f id_rsa | cut -d' ' -f 2
should correspond to cut -d' ' -f 2 id_rsa.pub
If you run a program and it crashes with an error “Illegal instruction”
the reason is probably because
you have compiled your program on Baobab login node and your program is running on an older compute node
on which the CPU lacks some specialized functionality that were used during the compilation.
You have two possibilities: