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--- hpc:faq [2020/11/26 12:46]
Yann Sagon [Can I run interactive tasks ?]
+++ hpc:faq [2023/12/13 08:37] (current)
Yann Sagon [Can I run interactive tasks ?]
@@ Line 2: / Line 2: @@
 ===== General =====
+==== Which cluster should I use ====
+You can use both clusters, but see [[hpc:hpc_clusters#the_clustersbaobab_and_yggdrasil|this link]] to help you choose the right cluster.
 ==== I'm lost, where can I find support ? ====
@@ Line 7: / Line 11: @@
+==== Citation, publication and acknowledgments ====
+Please see https://www.unige.ch/eresearch/en/services/hpc/terms-use/.
+==== The cluster is slow ====
+This may happen, but the problem is to determine what is slow:
+  * the login node: You shouldn't be running any job on the login node. Maybe another user is doing that and he is using all the cpus. In this, only the login node is slow, not the jobs running on the compute nodes.
+  * the compute node (the cpu, the storage)
+  * the storage (home, scratch, other): in this case, the whole cluster is impacted and your job can run slowly.
+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.
+===== Account =====
+==== When does my account expire ====
+  * If you have a non student account (Phd, postdoc, researcher), your account will expire at the same time your contract expire at UNIGE. Right now, there is a grace period after the end of your contract of around 6 months.
+  * If you have an outsider account, you need to check the expiration date you received when you filled the invitation.
+  * If you have an unige student account, you can check the expiration date with the ''chage'' command:
+<code>
+(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
+</code>
+==== I'm leaving UNIGE, can I continue to use Baobab HPC service? ====
+Yes it is possible as long as you collaborate tightly with your former research group. Your PI must invite you as [[hpc:access_the_hpc_clusters#outsider_account|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.
 ===== Storage =====
@@ Line 78: / Line 114: @@
 See [[hpc/slurm#interactive_jobs|Interactive jobs]]
+==== I'm not able to use all the cores of a compute node ====
+Indeed, we are reserving two cores per node for system tasks such as data transfer, and os stuff.
+<code>
+(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
+</code>
+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.
+ref: https://slurm.schedmd.com/core_spec.html
 ===== Troubleshooting =====
+==== Check ssh key ====
+If you connect to the cluster with an ssh key as authentication mechanism and you have trouble:
+  * check you have the correct private key: ''ssh-keygen -y -f id_rsa | cut -d' ' -f 2'' should correspond to ''cut -d' ' -f 2 id_rsa.pub''
 ==== Illegal instruction ====
-If you run a program and it crashes with an error ''"Illegal instruction"'' the reason is probably because you have compiled your program on login1 and your program is running on an older server on which the cpu lacks some specialized functionality that were used during the compilation on login1. \\
+If you run a program and it crashes with an error ''"Illegal instruction"'' the reason is probably because
-N.B. : login1 was running CentOS6, as of August 2019 all compute nodes run CentOS7
+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:
-  - Recompile your program with less optimization
+  - Recompile your program with less optimization, or compile on an older node. See [[hpc:hpc_clusters#for_advanced_users|Advanced users]]
   - Only run your program on newer servers. See [[hpc:slurm#specify_the_cpu_type_you_want|Specify the CPU type you want]] and [[hpc:hpc_clusters#compute_nodes|Compute nodes]].

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