CDT Cluster: Care and Feeding
Note that this page is currently being developed contact iainr@infREMOVE_THIS.ed.ac.uk for more information. This page covers the design, configuration and maintenance of the CDT cluster(s) AKA the James and Charles machines. If you just want to use the cluster then look at compuing.help instead.Overview
The cluster is made up of a set of nodes specced for GPU coding (the Charles machines), a set specced for CPU coding (the James machines) and two large memory nodes (anne and mary). The cluster nodes are named after the first Kings and queens of the United Kingdom (the James's, Charles' Anne and Mary )I current head nodes are hood.inf.ed.ac.uk and renown.inf.ed.ac.uk (both virual). The head nodes are purely for submitting jobs and copying files from /afs or other otherwise inaccessible filesystems, feel free to kill any processes which are hogging the CPU. execution nodes are only sshable via cluster infrastructure nodes such as fondant or escience7 this is to stop students logging in and running jobs outsde of the scheduler.Hardware
As originally purchased the cluster consisted of:- 10 off Dell Poweredge R730 (the charles machines) , 2 x Xeon(R) CPU E5-2640 v3 @ 2.60GHz 16 Core, 64G RAM, 4T HDD, 1 or 2 Tesla K40m
- 21 off Dell Poweredge R815 (the james machines), 4 x AMD Opteron(tm) Processor 6376 16 core, 256G RAM, 4T HDD
- 2 off Dell Poweredge R815 (anne and mary), 4 x AMD Opteron(tm) Processor 6376 16 core, 1T RAM, 2T HDD
- 4 off Dell Poweredge T630, 2 x Xeon(R) CPU E5-2620 v3 @ 2.40GHz 12 Core 64G RAM 1T HDD with some Titan X(maxwell) cards and the rest Titan-X (pascal) cards.
- 4 off Scan/Asus 3xs_hpc-t6a with Titan-X (pascal) cards
OS
These nodes were installed with an early version of SL7, the charles machines have all been reinstalled with the full DICE release of SL7. The james are currently being reinstalled piecemeal with the full DICE SL7. The main difference is the partitioning scheme and the use of ext4 rather than ext3.Scheduler
We were initially asked not to install a scheduler but to allow open access and there was the possibility that students might get either bare metal or VM based access to install different operating systems, as of May 2016 nothing has come of this. In Arpil 2016 we were asked to install gridengine to provide a comparable system to ECDF/Eddie. Installation of hadoop based frameworks has been mooted at various tilmes but has not progressedShared filesystem
Gridengine needs a shared filesystem to operate, because gridnegine is not kerberizes this filesystem can't be on afs. Also becuase the jobs are forked off from sgeexecd on the compute nodes we need to have non afs user home directories. In order to provide this we have used gluster which is the standard redhat distributed/enterprise filesystem. There are mounted as /mnt/mscteach_gridengine_common for the gridengine admin filesystem and /mnt/mscteach_home for the user home directories the two filesystems are configured as follows filesystems are currenty mounted via systemd and fstab e.g charles11.inf.ed.ac.uk:/cdt-gridengine-common 402910080 1029248 381400832 1% /mnt/cdt_gridengine_common note that although it appears that the filesstem is mounted off charles 11 it's distributed across four fileservers i.e.gluster> volume info cdt-gridengine-common Volume Name: cdt-gridengine-common Type: Distributed-Replicate Volume ID: 26e1a62a-ffd9-40f7-a425-f929537bc1ee Status: Started Number of Bricks: 2 x 2 = 4 Transport-type: tcp Bricks: Brick1: charles11:/disk/gluster/brick_charles11_01/data Brick2: charles12:/disk/gluster/brick_charles12_01/data Brick3: charles13:/disk/gluster/brick_charles13_01/data Brick4: charles14:/disk/gluster/brick_charles14_01/data Options Reconfigured: performance.readdir-ahead: on gluster> Distributed means that the files are spread over two (or more) bricks, Replicated means that there are two (or more) copies of any file on multiple bricks. In this case it;s like a disk raid setup with 2 replicated 2 disk stripessimilarly for the home directories
[anne]root: gluster gluster> volume info Volume Name: cdt-gridengine-home Type: Distributed-Replicate Volume ID: 49a16c6a-1d07-4aea-b9a5-c6b0f5ae2b10 Status: Started Number of Bricks: 7 x 2 = 14 Transport-type: tcp Bricks: Brick1: anne:/disk/gluster/brick_anne_01/data Brick2: mary:/disk/gluster/brick_mary_01/data Brick3: charles03:/disk/gluster/brick_charles03_01/data Brick4: charles04:/disk/gluster/brick_charles04_01/data Brick5: charles05:/disk/gluster/brick_charles05_01/data Brick6: charles06:/disk/gluster/brick_charles06_01/data Brick7: charles09:/disk/gluster/brick_charles09_01/data Brick8: charles10:/disk/gluster/brick_charles10_01/data Brick9: charles07:/disk/gluster/brick_charles07_01/data Brick10: charles08:/disk/gluster/brick_charles08_01/data Brick11: charles15.inf.ed.ac.uk:/disk/gluster/brick_charles15 Brick12: charles16.inf.ed.ac.uk:/disk/gluster/brick_charles16 Brick13: charles17.inf.ed.ac.uk:/disk/gluster/brick_charles17_01/data Brick14: charles18.inf.ed.ac.uk:/disk/gluster/brick_charles18_01/data Options Reconfigured: network.inode-lru-limit: 9000 performance.md-cache-timeout: 60 performance.stat-prefetch: on features.cache-invalidation-timeout: 600 features.cache-invalidation: on performance.readdir-ahead: on gluster>which is like 2 replicated 7 disk stripes. for most gluster issues we'd recommend the https://access.redhat.com/documentation/en/red-hat-gluster-storage/redhat documents
Common gluster issues
- "too many symboic links" on login. this has started to appear and seems to be a race condition between systemd mounting the filesystem and the links being in place.
umount /home
followed bymount -a
will fix.
- filesystem failing to mount. THis is ususally indicative that lots of nodes in the filesystem are no longer talking to each other. log onto the machine listed in fstab as the mount and chec that glusterd is running
[forthea]iainr: ps auxww|grep glusterd root 1039 0.0 0.0 605060 24708 ? Ssl 10:28 0:01 /usr/sbin/glusterd -p /var/run/glusterd.pid --log-level INFO root 1278 0.0 0.1 778204 57384 ? Ssl 10:28 0:01 /usr/sbin/glusterfs -s localhost --volfile-id gluster/glustershd -p /var/lib/glusterd/glustershd/run/glustershd.pid -l /var/log/glusterfs/glustershd.log -S /var/run/gluster/864101a86f98b91e4af178b78b1602a1.socket --xlator-option *replicate*.node-uuid=5ab018c5-c637-4910-b31a-b0935ab28ee8 root 1284 2.1 0.1 1627476 46460 ? Ssl 10:28 7:49 /usr/sbin/glusterfsd -s forthea --volfile-id mscteach-gridengine-common.forthea.disk-gluster-brick_forthea_01-data -p /var/lib/glusterd/vols/mscteach-gridengine-common/run/forthea-disk-gluster-brick_forthea_01-data.pid -S /var/run/gluster/5d6a98a082c13ef0e162a9026afe6516.socket --brick-name /disk/gluster/brick_forthea_01/data -l /var/log/glusterfs/bricks/disk-gluster-brick_forthea_01-data.log --xlator-option *-posix.glusterd-uuid=5ab018c5-c637-4910-b31a-b0935ab28ee8 --brick-port 49152 --xlator-option mscteach-gridengine-common-server.listen-port=49152 root 1285 0.0 0.3 695560 113744 ? Ssl 10:28 0:00 /usr/sbin/glusterfs -s localhost --volfile-id gluster/nfs -p /var/lib/glusterd/nfs/run/nfs.pid -l /var/log/glusterfs/nfs.log -S /var/run/gluster/c689254873f7f171afe7d97355c08e4a.socket iainr 24583 0.0 0.0 112656 960 pts/0 S+ 16:41 0:00 grep --color=auto glusterd
[forthea]root: gluster gluster> peer status Number of Peers: 6 Hostname: tatties Uuid: efb6684f-d516-4bc6-92ea-0bf687b8bd47 State: Peer in Cluster (Connected) Hostname: 129.215.18.94 Uuid: 70066537-d6e9-4d35-8fb8-dd5bb0280a4c State: Peer in Cluster (Connected) Other names: letha04 Hostname: 129.215.18.93 Uuid: 7b240054-5ca0-4d68-ae0a-059b283c71c1 State: Peer in Cluster (Connected) Other names: letha03.inf.ed.ac.uk Hostname: letha02 Uuid: 92757806-6409-4f31-a081-277447c53c0a State: Peer in Cluster (Connected) Hostname: letha05 Uuid: a0740a46-92a7-4d10-a4b4-505cc652c9c9 State: Peer in Cluster (Connected) Hostname: letha01 Uuid: 7324a5f0-8a84-4132-a988-04312cbbf01d State: Peer in Cluster (Connected) gluster>If this is showing any peers as lost or shutdown then they'll need restarted, you can restart the gluster daemon via:systemctl
[forthea]root: systemctl status glusterd
● glusterd.service - GlusterFS, a clustered file-system server
Loaded: loaded (/usr/lib/systemd/system/glusterd.service; disabled; vendor preset: enabled)
Active: active (running) since Thu 2017-06-29 10:28:56 BST; 6h ago
Main PID: 1039 (glusterd)
CGroup: /system.slice/glusterd.service
├─1039 /usr/sbin/glusterd -p /var/run/glusterd.pid --log-level INF...
├─1278 /usr/sbin/glusterfs -s localhost --volfile-id gluster/glust...
├─1284 /usr/sbin/glusterfsd -s forthea --volfile-id mscteach-gride...
├─1285 /usr/sbin/glusterfs -s localhost --volfile-id gluster/nfs -...
└─1329 /sbin/rpc.statd
Jun 29 10:28:57 forthea.inf.ed.ac.uk rpc.statd[1329]: Version 1.3.0 starting
Jun 29 10:28:57 forthea.inf.ed.ac.uk sm-notify[1330]: Version 1.3.0 starting
[forthea]root:
- "Stale file handles " are basically as per NFS, find the open copy of the file and kill the process or reboot the server
Gridengine
We've been requested to install gridengine, unfortunately gridengine has rotted somewhat since sun was bought up and oracle sold it off, we are currently using Son of gridengine which is an open source fork. Note that other than the above website there is no real definitive set of documentation for the version of gridengine we are running. Suns n6 docs should give a good overview. Gridengine is made up of three types of nodes, execution hosts which run the jobs, head nodes which provide a working environment for people to schedule jobs from and a scheduler node which runs the scheduler and manages the execution nodes. All configuration is in the shared gridengine-common filesystem which should be mounted as /opt/sge/default. configuration of the scheduler can be done via the qconf command or the qmoncommand. current jobs can be listed via qstat and the current state of hosts can be listed via qhost. some useful commands- qhost -list hosts
- qsub - sumbit jobs
- qstat - list info about jobs
- qconf - configure aspects about the cluster
- qmon (gui configuration utility)
common issues
- Deleting stuck jobs
[renown]iainr: qstat -u \* job-ID prior name user state submit/start at queue --------------------------------------------------------------------------------------- 17717 0.56000 scheduleex s0908078 r 06/28/2017 01:06:12 gpgpu@charles02.inf. 17715 0.56000 scheduleex s0908078 r 06/28/2017 01:04:42 gpgpu@charles17.inf. 17739 0.55750 TC_feedbac s1126151 r 06/28/2017 16:42:42 gpgpu@charles15.inf.3 17741 0.55750 fdgfd s1564225 r 06/28/2017 17:24:42 gpgpu@charles08.inf. 17745 0.55750 sdfds s1564225 r 06/28/2017 18:10:42 gpgpu@charles04.inf. 17740 0.55750 fdsfd s1564225 r 06/28/2017 17:17:12 gpgpu@charles07.inf. 17719 0.56000 scheduleex s0908078 r 06/28/2017 01:06:42 gpgpu@charles03.inf. 17714 0.55750 celeb_wgan s1473470 r 06/28/2017 00:40:42 gpgpu@charles15.inf. 17743 0.55750 fdsfd s1564225 r 06/28/2017 17:37:42 gpgpu@charles09.inf. 17738 0.55750 TC_feedbac s1126151 r 06/28/2017 16:40:57 gpgpu@charles14.inf.1 17738 0.55750 TC_feedbac s1126151 r 06/28/2017 16:40:57 gpgpu@charles18.inf.4 17738 0.55750 TC_feedbac s1126151 r 06/28/2017 16:40:57 gpgpu@charles12.inf.2 17784 0.55750 imagenet_w s1473470 r 06/29/2017 15:05:25 gpgpu@charles15.inf. 17787 0.55750 baseline_w s1473470 r 06/29/2017 15:50:10 gpgpu@charles12.inf. 17790 0.55750 relational s1473470 r 06/29/2017 15:54:40 gpgpu@charles12.inf. 16848 0.55100 test.sh iainr Eqw 06/14/2017 16:23:01 17739 0.00000 TC_feedbac s1126151 hqw 06/28/2017 16:42:39 4 [renown]iainr: qdel 16848 iainr has deleted job 16848 [renown]iainr: qstat -u \* job-ID prior name user state submit/start at queue --------------------------------------------------------------------------------------- 17717 0.56000 scheduleex s0908078 r 06/28/2017 01:06:12 gpgpu@charles02.inf. 17715 0.56000 scheduleex s0908078 r 06/28/2017 01:04:42 gpgpu@charles17.inf. 17739 0.55750 TC_feedbac s1126151 r 06/28/2017 16:42:42 gpgpu@charles15.inf.3 17741 0.55750 fdgfd s1564225 r 06/28/2017 17:24:42 gpgpu@charles08.inf. 17745 0.55750 sdfds s1564225 r 06/28/2017 18:10:42 gpgpu@charles04.inf. 17740 0.55750 fdsfd s1564225 r 06/28/2017 17:17:12 gpgpu@charles07.inf. 17719 0.56000 scheduleex s0908078 r 06/28/2017 01:06:42 gpgpu@charles03.inf. 17714 0.55750 celeb_wgan s1473470 r 06/28/2017 00:40:42 gpgpu@charles15.inf. 17743 0.55750 fdsfd s1564225 r 06/28/2017 17:37:42 gpgpu@charles09.inf. 17738 0.55750 TC_feedbac s1126151 r 06/28/2017 16:40:57 gpgpu@charles14.inf.1 17738 0.55750 TC_feedbac s1126151 r 06/28/2017 16:40:57 gpgpu@charles18.inf.4 17738 0.55750 TC_feedbac s1126151 r 06/28/2017 16:40:57 gpgpu@charles12.inf.2 17784 0.55750 imagenet_w s1473470 r 06/29/2017 15:05:25 gpgpu@charles15.inf. 17787 0.55750 baseline_w s1473470 r 06/29/2017 15:50:10 gpgpu@charles12.inf. 17790 0.55750 relational s1473470 r 06/29/2017 15:54:40 gpgpu@charles12.inf. 17739 0.00000 TC_feedbac s1126151 hqw 06/28/2017 16:42:39 4 [renown]iainr:
- host information: you can dumo information that the scheduler knwos about the hosts using the qhost command
[renown]iainr: qhost HOSTNAME ARCH NCPU NSOC NCOR NTHR LOAD MEMTOT MEMUSE SWAPTOS --------------------------------------------------------------------------------------- global - - - - - - - - -- charles01 lx-amd64 32 2 16 32 0.09 62.7G 5.2G 31.3G0 charles02 lx-amd64 32 2 16 32 1.11 62.7G 8.3G 31.3GM charles03 lx-amd64 32 2 16 32 0.06 62.7G 7.4G 31.3GM charles04 lx-amd64 32 2 16 32 0.01 62.7G 7.4G 31.3GM charles05 lx-amd64 32 2 16 32 0.03 62.7G 6.7G 31.3GM charles06 lx-amd64 32 2 16 32 0.03 62.7G 5.4G 31.3GM charles07 lx-amd64 32 2 16 32 0.01 62.7G 5.2G 31.3GM charles08 lx-amd64 32 2 16 32 1.01 62.7G 9.7G 31.3GG charles09 lx-amd64 32 2 16 32 0.02 62.7G 6.2G 31.3GG charles10 lx-amd64 32 2 16 32 0.04 62.7G 3.8G 31.3GM charles11 lx-amd64 24 2 12 24 0.04 62.8G 2.7G 31.4G0 charles12 lx-amd64 24 2 12 24 2.18 62.8G 41.6G 31.4GG charles13 lx-amd64 24 2 12 24 0.01 62.8G 1.6G 31.4GM charles14 lx-amd64 24 2 12 24 1.01 62.8G 26.1G 31.4GM charles15 lx-amd64 32 2 16 32 4.49 62.8G 43.6G 31.2GG charles16 lx-amd64 32 2 16 32 0.02 62.8G 5.4G 31.2G0 charles17 lx-amd64 32 2 16 32 1.14 62.8G 4.2G 31.2GM charles18 lx-amd64 32 2 16 32 2.04 62.8G 13.3G 31.2GG ...Note that if the load and memuse columns are sowing - then the execution daemon (sgeexecd) is not running on that node. If a host is showing all -'s then it has not been installed yet.There is also a "global" host that is used to hold some default configuration for all hosts. *restating sgeexecd
- Restarting qmaster: In the last couple of weeks systemd has had issues in restarting qmaster if the machine is rebooted, for the oment I'm started it by hand
export SGE_ND=1 /opt/sge/bin/lx-amd64/sge_qmaster
- To install an execution node
[forthea]iainr: cd /opt/sge [forthea]iainr: ls bin doc install_execd inst_sge man pvm util default examples install_qmaster lib mpi qmon utilbinmake sure that default is mounted
[forthea]iainr: ls default
common spool
[forthea]iainr:
</verbatim
install the exec node
<verbatim>[forthea]iainr: ./install_execd
Welcome to the Grid Engine execution host installation
------------------------------------------------------
If you haven't installed the Grid Engine qmaster host yet, you must execute
this step (with >install_qmaster<) prior the execution host installation.
For a successful installation you need a running Grid Engine qmaster. It is
also necessary that this host is an administrative host.
You can verify your current list of administrative hosts with
the command:
# qconf -sh
You can add an administrative host with the command:
# qconf -ah <hostname>
The execution host installation will take approximately 5 minutes.
Hit <RETURN> to continue >>
</verbatim>
The script should take configuration information from the common filesystem. You can install the qmaster node in a similar fashion.
---+++GPUs
Information about the gpus can be obtained via the nvidia-smi command
<verbatim>
[charles17]iainr: nvidia-smi
Fri Jun 30 14:53:13 2017
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 375.39 Driver Version: 375.39 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 TITAN X (Pascal) On | 0000:02:00.0 Off | N/A |
| 24% 35C P8 17W / 250W | 0MiB / 12189MiB | 0% E. Process |
+-------------------------------+----------------------+----------------------+
| 1 TITAN X (Pascal) On | 0000:03:00.0 Off | N/A |
| 29% 42C P8 17W / 250W | 0MiB / 12189MiB | 0% E. Process |
+-------------------------------+----------------------+----------------------+
| 2 TITAN X (Pascal) On | 0000:81:00.0 Off | N/A |
| 26% 38C P8 17W / 250W | 0MiB / 12189MiB | 0% E. Process |
+-------------------------------+----------------------+----------------------+
| 3 TITAN X (Pascal) On | 0000:82:00.0 Off | N/A |
| 25% 37C P8 16W / 250W | 0MiB / 12189MiB | 0% E. Process |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| No running processes found |
+-----------------------------------------------------------------------------+
</verbatim>
If thre are processes accessing the GPU then they will be listed
<verbatim>
nv[charles12]iainr: nvidia-smi
Fri Jun 30 14:57:54 2017
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 375.39 Driver Version: 375.39 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 TITAN X (Pascal) On | 0000:02:00.0 Off | N/A |
| 41% 69C P2 141W / 250W | 11705MiB / 12189MiB | 46% E. Process |
+-------------------------------+----------------------+----------------------+
| 1 TITAN X (Pascal) On | 0000:04:00.0 Off | N/A |
| 23% 31C P8 16W / 250W | 0MiB / 12189MiB | 0% E. Process |
+-------------------------------+----------------------+----------------------+
| 2 TITAN X (Pascal) On | 0000:83:00.0 Off | N/A |
| 72% 86C P2 254W / 250W | 11705MiB / 12189MiB | 74% E. Process |
+-------------------------------+----------------------+----------------------+
| 3 TITAN X (Pascal) On | 0000:84:00.0 Off | N/A |
| 34% 58C P2 83W / 250W | 11191MiB / 12189MiB | 91% E. Process |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 99508 C python 11703MiB |
| 2 99045 C python 11703MiB |
| 3 45132 C python 11189MiB |
+-----------------------------------------------------------------------------+
</verbatim>
there should be an associated process with each PID above
<verbatim>
s1473470 99508 116 18.8 45058704 12437588 ? Rl Jun29 1606:12 python train_celeb_wgan.py --experiment_title relational_wgan --relational_plus_discr True --batch_size 100
iainr 143110 0.0 0.0 112656 964 pts/0 S+ 14:59 0:00 grep --color=auto 99508
<./verbatim>
sometimes a user space process will die and zombify, in which case the GPU will fault
<verbatim>
[charles19]root: nvidia-smi
Fri Jun 30 15:01:18 2017
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 375.66 Driver Version: 375.66 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 TITAN X (Pascal) Off | 0000:02:00.0 Off | N/A |
| 23% 18C P8 14W / 250W | 0MiB / 12189MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 1 TITAN X (Pascal) Off | 0000:03:00.0 Off | N/A |
| 23% 24C P8 16W / 250W | 11621MiB / 12189MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 2 TITAN X (Pascal) Off | 0000:81:00.0 Off | N/A |
| 23% 21C P8 15W / 250W | 0MiB / 12189MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 3 TITAN X (Pascal) Off | 0000:82:00.0 Off | N/A |
| 23% 23C P8 16W / 250W | 0MiB / 12189MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 1 17235 C Unknown Error 11619MiB |
+-----------------------------------------------------------------------------+
[charles19]root: ps auxww|grep 17235
root 14869 0.0 0.0 112652 948 pts/0 S+ 15:01 0:00 grep 17235
s1473470 17235 0.0 0.0 0 0 ? Zl Jun17 0:42 [python] <defunct>
[charles19]root:
</verbatim>
The only solution we're aware o to fix this is to reboot the node. It's usually best to disable all the queue instances first and let other jobs finish.
-- Main.IainRae - 18 May 2016
</verbatim>
<nop>
Topic revision: r6 - 30 Jun 2017 - 14:19:03 - IainRae
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