Changes for page Slurm

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1		-XWiki 2.1
	1	+MediaWiki 1.6

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3	3	Slurm is fully integrated in our system. You do not need set any environment variables.
4	4
5	5
	6	+== Partitions ==
6	6
7		-{{toc/}}
8		-
9		-== Partitions ==
10		-
11	11	A partition is a subset of the cluster, a bundle of compute nodes with the same characteristics.
12	12
13	13	Based on access restrictions our cluster is divided in different partitions. 'sinfo' will only show partitions you are allowed to use. Using 'sinfo -a' shows all partitons.
...	...	@@ -14,28 +14,114 @@
14	14
15	15	A partition is selected by '-p PARTITIONNAME'.
16	16
17		-|=**Partition** |=**No. Nodes** |=**Cores/M** |=**Tot. Cores**|=**RAM/GB** |=**CPU** |=**Remark/Restriction**
18		-|itp |10|20 |200|64 |Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz|Common Usage
19		-|dfg-big|3|32|96|128|8-Core AMD Opteron(tm) Processor 6128|Group Valenti
20		-|dfg-big|3|48|144|128/256|12-Core AMD Opteron(tm) Processor 6168|Group Valenti
21		-|dfg-big|4|64|256|128/256|16-Core AMD Opteron(tm) Processor 6272|Group Valenti
22		-|dfg-big|4|48|192|128/256|12-Core AMD Opteron(tm) Processor 6344|Group Valenti
23		-|fplo|2|12|24|256|Intel(R) Xeon(R) CPU E5-2630 v2 @ 2.60GHz|Group Valenti
24		-|fplo|4|16|32|256|Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz|Group Valenti
25		-|dfg-xeon|5|16|32|128|Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz|Group Valenti
26		-|dfg-xeon|7|20|140|128|Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz|Group Valenti
27		-|iboga|34|20|880|64|Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz|Group Rezzolla
28		-|dreama|1|40|40|1024|Intel(R) Xeon(R) CPU E7-4820 v3 @ 1.90GHz|Group Rezzolla
29		-|barcelona|8|40|320|192|Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz|(((
30		-Group Valenti
31		-)))
32		-|barcelona|1|40|40|512| |Group Valenti
33		-|mallorca|4|48|192|256|AMD EPYC 7352 24-Core Processor|Group Valenti
34		-|calea|36|64|2304|256|Intel(R) Xeon(R) Platinum 8358 CPU @ 2.60GHz|(((
35		-Group Rezzolla
36		-)))
37		-|majortom|1|64|64|256|AMD EPYC 7513 32-Core Processor|Group Bleicher
	14	+{| border="1" align="center"
	15	+|-
	16	+! scope="col" | '''Partition'''
	17	+! scope="col" | '''No. Nodes'''
	18	+! scope="col" | '''Cores/M'''
	19	+! scope="col" | '''Tot. Cores'''
	20	+! scope="col" | '''RAM/GB'''
	21	+! scope="col" | '''CPU'''
	22	+! scope="col" | '''Remark/Restriction'''
	23	+|-
	24	+| itp
	25	+| 10
	26	+| 20
	27	+| 200
	28	+| 64
	29	+| Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
	30	+| Common Usage
	31	+|-
	32	+| dfg-big
	33	+| 3
	34	+| 32
	35	+| 96
	36	+| 128
	37	+| 8-Core AMD Opteron(tm) Processor 6128
	38	+| Group Valenti
	39	+|-
	40	+| dfg-big
	41	+| 3
	42	+| 48
	43	+| 144
	44	+| 128/256
	45	+| 12-Core AMD Opteron(tm) Processor 6168
	46	+| Group Valenti
	47	+|-
	48	+| dfg-big
	49	+| 4
	50	+| 64
	51	+| 256
	52	+| 128/256
	53	+| 16-Core AMD Opteron(tm) Processor 6272
	54	+| Group Valenti
	55	+|-
	56	+| dfg-big
	57	+| 4
	58	+| 48
	59	+| 192
	60	+| 128/256
	61	+| 12-Core AMD Opteron(tm) Processor 6344
	62	+| Group Valenti
	63	+|-
	64	+| fplo
	65	+| 2
	66	+| 12
	67	+| 24
	68	+| 256
	69	+| Intel(R) Xeon(R) CPU E5-2630 v2 @ 2.60GHz
	70	+| Group Valenti
	71	+|-
	72	+| fplo
	73	+| 4
	74	+| 16
	75	+| 32
	76	+| 256
	77	+| Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
	78	+| Group Valenti
	79	+|-
	80	+| dfg-xeon
	81	+| 5
	82	+| 16
	83	+| 32
	84	+| 128
	85	+| Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
	86	+| Group Valenti
	87	+|-
	88	+| dfg-xeon
	89	+| 7
	90	+| 20
	91	+| 140
	92	+| 128
	93	+| Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
	94	+| Group Valenti
	95	+|-
	96	+| iboga
	97	+| 44
	98	+| 20
	99	+| 880
	100	+| 64
	101	+| Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
	102	+| Group Rezzolla
	103	+|-
	104	+| dreama
	105	+| 1
	106	+| 40
	107	+| 40
	108	+| 1024
	109	+| Intel(R) Xeon(R) CPU E7-4820 v3 @ 1.90GHz
	110	+| Group Rezzolla
	111	+|-
	112	+| barcelona
	113	+| 8
	114	+| 40
	115	+| 320
	116	+| 192
	117	+| Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
	118	+| Group Valenti
38	38
	120	+|}
	121	+
39	39	Most nodes are for exclusive use by their corresponding owners. The itp nodes are for common usage. Except for 'fplo' and 'dfg-big' nodes, all machines are connected with Infiniband for all traffic (IP and internode communitcation - MPI)
40	40
41	41	== Submitting Jobs ==
...	...	@@ -44,36 +44,34 @@
44	44
45	45	This is very simple for serial (1 CPU) jobs:
46	46
47		-{{{ sbatch -p PARTITION jobscript.sh}}}
	130	+ sbatch -p PARTITION jobscript.sh
48	48
49	49	where jobscript.sh is a shell script with your job commands.
50	50
51		-Running **openMPI** jobs is not much more complictated:
	134	+Running '''openMPI''' jobs is not much more complictated:
52	52
53		-{{{ sbatch -p PARTITION -n X jobscript.sh}}}
	136	+ sbatch -p PARTITION -n X jobscript.sh
54	54
55	55	where X is the number of desired MPI processes. Launch the job in the jobscript with:
56	56
57		-{{{ mpirun YOUREXECUTABLE}}}
	140	+ mpirun YOUREXECUTABLE
58	58
59	59	You don't have to worry about the number of processes or specific nodes. Both slurm and openmpi know
60	60	about each other.
61	61
62		-If you want **infiniband** for your MPI job (which is usually a good idea, if not running on the same node), you have to request the feature infiniband:
	145	+If you want '''infiniband''' for your MPI job (which is usually a good idea, if not running on the same node), you have to request the feature infiniband:
63	63
64		-{{{ sbatch -p dfg -C infiniband -n X jobscript.sh}}}
	147	+ sbatch -p dfg -C infiniband -n X jobscript.sh
65	65
66	66	Note: Infiniband is not available for 'fplo' and 'dfg-big'.
67	67
68		-Running **SMP jobs** (multiple threads, not necessary mpi). Running MPI jobs on a single node is recommended for the
	151	+Running '''SMP jobs''' (multiple threads, not necessary mpi). Running MPI jobs on a single node is recommended for the
69	69	dfg-big nodes. This are big host with up to 64 cpu's per node, but 'slow' gigabit network connection. Launch SMP jobs with
70	70
71		-{{{ sbatch -p PARTITION -N 1 -n X jobscript.sh}}}
	154	+ sbatch -p PARTITION -N 1 -n X jobscript.sh
72	72
73	73	=== Differences in network the network connection ===
74		-
75		-
76		-
	157	+
77	77	The new v3 dfg-xeon nodes are equipped with 10 GB network. This is faster (trough put) and has lower latency then gigabit ethernet, but is not is not as fast as the DDR infinband network. The 10 GB network is used for MPI and I/O. Infiniband is only use for MPI.
78	78
79	79	== Defining Resource limits ==
...	...	@@ -80,13 +80,13 @@
80	80
81	81	By default each job allocates 2 GB memory and a run time of 3 days. More resources can be requested by
82	82
83		-{{{ --mem-per-cpu=<MB>}}}
	164	+ --mem-per-cpu=<MB>
84	84
85	85	where <MB> is the memory in megabytes. The virtual memory limit is 2.5 times of the requested real memory limit.
86	86
87	87	The memory limit is not a hard limit. When exceeding the limit, your memory will be swapped out. Only when using more the 150% of the limit your job will be killed. So be conservative, to keep enough room for other jobs. Requested memory is blocked from the use by other jobs.
88	88
89		-{{{ -t or --time=<time>}}}
	170	+ -t or --time=<time>
90	90
91	91	where time can be set in the format "days-hours". See man page for more formats.
92	92
...	...	@@ -98,17 +98,16 @@
98	98
99	99	sbatch arguments can be written in the jobfile:
100	100
101		-{{{#! /bin/bash
	182	+<pre>
	183	+#! /bin/bash
102	102	#
103	103	# Choosing a partition:
104	104	#SBATCH -p housewives
105	105
106		-YOUR JOB COMMANDS....}}}
	188	+YOUR JOB COMMANDS....
	189	+</pre>
107	107
108		-
109		-
110	110	= Links =
111	111
	193	+* SLURM-Homepage [http://slurm.schedmd.com/slurm.html]
112	112
113		-
114		-* SLURM-Homepage [[url:http://slurm.schedmd.com/slurm.html]]