Differences

This shows you the differences between two versions of the page.

--- grid [2017/09/27 20:39]
popel [Advanced usage]
+++ grid [2017/09/29 18:20]
popel [Advanced usage]
@@ Line 120: / Line 120: @@
     * If your job needs more than one CPU (on a single machine) for most of the time, reserve the given number of CPU cores (and SGE slots) with <code>qsub -pe smp <number-of-CPU-cores></code> As you can see in [[#List of Machines]], the maximum is 32 cores. If your job needs e.g. up to 110% CPU most of the time and just occasionally 200%, it is OK to reserve just one core (so you don't waste). TODO: when using ''-pe smp -l mf=8G,amf=8G,h_vmem=12G'', which memory limits are per machine and which are per core?
     * If you are sure your job needs less than 1GB RAM, then you can skip this. Otherwise, if you need e.g. 8 GiB, you must always use ''qsub'' (or ''qrsh'') with ''-l mem_free=8G''. You should specify also ''act_mem_free'' with the same value and ''h_vmem'' with possibly a slightly bigger value. See [[#memory]] for details. TL;DR: <code>qsub -l mem_free=8G,act_mem_free=8G,h_vmem=12G</code>
-  * Be kind to your colleagues. If you are going to submit jobs that effectively occupy more than one fifth of our cluster for more than several hours, check if the cluster is free (with ''qstat -g c'' or ''qstat -u \*'') and/or ask your colleagues if they don't plan to use the cluster intensively in the near future. Note that if you allocate one slot (CPU core) on a machine, but (almost) all its RAM, you have effectively occupied the whole machine and all its cores.
+  * Be kind to your colleagues. If you are going to submit jobs that effectively occupy **more than one fifth of our cluster for more than several hours**, check if the cluster is free (with ''qstat -g c'' or ''qstat -u \*'') and/or ask your colleagues if they don't plan to use the cluster intensively in the near future. Note that if you allocate one slot (CPU core) on a machine, but (almost) all its RAM, you have effectively occupied the whole machine and all its cores. If you are submitting **more than 100 jobs**, consider using setting them a low priority (e.g. ''-p -1024'', see below) or use [[#qunhold]]. Don't submit more than ca 2000 jobs at once (this can overload the SGE).
@@ Line 135: / Line 135: @@
 ===== Advanced usage =====
+''qsub **-q** troja-all.q''
+This way your job is submitted to the Troja queue. The default is ''ms-all.q''. You can also use e.g.
+''-q '(troja*|ms*)''' to submit on any machine in those two queues (but **don't use ''-q '*'''** as this includes also [[:gpu|gpu.q]]),
+''-q '*@hector[14]''' to submit on hecor1 or hector4,
+''-q '[tm]*@!(hector*|iridium)''' to submit on any troja/ms machine except hectors and iridium.
+However, usually you should specify just the queue (troja-all.q vs. ms-all.q), not a particular machine, and instead use ''-l'' to specify the needed resources in a general way.
+''qsub **-l** ...''
+See ''man complex'' (run it on lrc or sol machines) for a list of possible resources you may require (in addition to ''mem_free'' etc. discussed above).
 ''qsub **-p** -100''
@@ Line 174: / Line 184: @@
 ''qsub **-soft** -l ... **-hard** -l ... -q ...''
 By default, all the resource requirements (specified with ''-l'') and queue requirements (specified with ''-q'') are //hard//, i.e. your job won't be scheduled unless they can be fulfilled. You can use ''-soft'' to mark all following requirements as nice-to-have. And with ''-hard'' you can switch back to hard requirements.
+''qsub **-sync** y''
+This causes qsub to wait for the job to complete before exiting (with the same exit code as the job). Useful in scripts.
 ''**qalter**''
 You can change some properties of already submitted jobs, which are still waiting in the queue (//pending//).
-''**man** qsub qstat qhold queue_conf sge_types complex''
+''**man** qsub qstat qalter qhold queue_conf sge_types complex''
 Find out all the gory details which are missing here. You'll have to do it one day anyway:-).
@@ Line 187: / Line 200: @@
 === qunhold ===
 ''~stepanek/bin/qunhold'' tries to keep the number of running SGE jobs under a given threshold: all jobs over the threshold are held. If the number of running jobs goes below the threshold (default: 100), 10 jobs (by default) are unheld. Beware: if your jobs submit new jobs, you can get far over the threshold!
+=== sshcwd ===
+This is useful not only when sshing to sol machines. Add the following lines to your ''~/.bashrc''.
+<code>
+function sshcwd () {
+  # save the current history so that it is available
+  # immediately on the remote machine
+  history -a;
+  # setup the working directory by setting WD
+  ssh -X -Y -C -t $@ "WD='$PWD' /bin/bash --login -i";
+}
+# use WD to setup the working directory
+if [ -n "$WD" ]; then
+  echo "Autochanging dir to $WD" >&2
+  cd $WD;
+fi
+alias sol1="sshcwd sol1.ufal.hide.ms.mff.cuni.cz"
+</code>
 === In-script options ===
@@ Line 202: / Line 236: @@
 === Array jobs ===
-If you have a set of tasks (of the same type) and want to run them on multiple machines,...
+If you have a set of tasks (of the same type) and want to run them on multiple machines, use ''qsub -t''...
 TODO
 ===== Monitorování úloh =====
@@ Line 243: / Line 278: @@
 Pokud chcete submittovaný program pouštět ve svém oblíbeném prostředí (např. nastavení ''PATH''), musíte v obalujícím skriptu příslušné ''.bash*'' načíst. Vždy je ale bezpečnější všude psát plné cesty, než spoléhat na PATH.
-==== Jiný shell ====
-Abych mohl poslat nějakou úlohu do fronty, musím pro ni vyrobit vlastní skript. Budiž, vyrobil jsem vlastní skript:
-<code>
-#!/bin/bash
-program > log.out 2> log.err
-</code>
-Když tento skript spustím, stane se očekávané. Přesměrují se výstupy z daného programu do souborů a je to.
-Když takový skript submitnu, program se **nespustí**. V logu zjistím, že (standardní chybový) výstup shellu, který pouštěl můj skript praví kryptickou zprávu "Ambiguous redirect".
-Nebudu vás napínat, zde je vysvětlení: SGE ignoruje první řádek skriptu (ve skutečnosti je pravda horší, hledá v něm nějaké parametry pro sebe) a spouští skript v ''csh''. Rozdíl mezi bashem a csh se v primitivních skriptech na první pohled nepozná, pozná se až v konstrukci if-then-else, a také v přesměrovávání. csh nerozumí přesměrování ''2>''
-Takto SGE přinutíte, aby použilo bash:
-<code>
-  qsub -S /bin/bash skript
-</code>
-Jinou možností je přesměrovat stderr a stdout pomocí syntaxe csh:
-<code>
-( command >stdout_file ) >&stderr_file
-</code>
 ==== bashrc a podobné nesmí nic vypisovat na konzoli ====
@@ Line 297: / Line 304: @@
 hard resource_list:         mem_free=16g
 hard resource_list:         mem_free=31g</code>
-==== Jak rezervovat více jader na stejném stroji pro 1 job ====
-<code>
-qsub -pe smp <pocet jader>
-</code>

[ Back to the navigation ] [ Back to the content ]

Institute of Formal and Applied Linguistics Wiki

Differences