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grid [2017/09/27 20:39] popel [Advanced usage] |
grid [2017/10/02 16:55] popel [Basic usage] |
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# We have used two handy qsub parameters: | # We have used two handy qsub parameters: | ||
# -cwd ... the script is executed in the current directory (the default is your home) | # -cwd ... the script is executed in the current directory (the default is your home) | ||
- | # -j y ... stdout and stderr outputs are merged and redirected to a file ('' | + | # -j y ... stdout and stderr outputs are merged and redirected to a file ('' |
# We have also provided two parameters for our script " | # We have also provided two parameters for our script " | ||
# The qsub prints something like | # The qsub prints something like | ||
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* 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 < | * 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 < | ||
* 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 '' | * 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 '' | ||
- | * 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 '' | + | * Be kind to your colleagues. If you are going to submit jobs that effectively occupy |
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===== Advanced usage ===== | ===== Advanced usage ===== | ||
+ | |||
+ | '' | ||
+ | This way your job is submitted to the Troja queue. The default is '' | ||
+ | '' | ||
+ | '' | ||
+ | '' | ||
+ | However, usually you should specify just the queue (troja-all.q vs. ms-all.q), not a particular machine, and instead use '' | ||
+ | |||
+ | '' | ||
+ | See '' | ||
'' | '' | ||
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'' | '' | ||
By default, all the resource requirements (specified with '' | By default, all the resource requirements (specified with '' | ||
+ | |||
+ | '' | ||
+ | This causes qsub to wait for the job to complete before exiting (with the same exit code as the job). Useful in scripts. | ||
'' | '' | ||
You can change some properties of already submitted jobs, which are still waiting in the queue (// | You can change some properties of already submitted jobs, which are still waiting in the queue (// | ||
- | '' | + | '' |
Find out all the gory details which are missing here. You'll have to do it one day anyway:-). | Find out all the gory details which are missing here. You'll have to do it one day anyway:-). | ||
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=== qunhold === | === qunhold === | ||
'' | '' | ||
+ | |||
+ | === sshcwd === | ||
+ | This is useful not only when sshing to sol machines. Add the following lines to your '' | ||
+ | |||
+ | < | ||
+ | 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 $@ " | ||
+ | } | ||
+ | |||
+ | # use WD to setup the working directory | ||
+ | if [ -n " | ||
+ | echo " | ||
+ | cd $WD; | ||
+ | fi | ||
+ | |||
+ | alias sol1=" | ||
+ | </ | ||
=== In-script options === | === In-script options === | ||
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=== Array jobs === | === 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, |
TODO | TODO | ||
+ | |||
===== Monitorování úloh ===== | ===== Monitorování úloh ===== | ||
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Pokud chcete submittovaný program pouštět ve svém oblíbeném prostředí (např. nastavení '' | Pokud chcete submittovaný program pouštět ve svém oblíbeném prostředí (např. nastavení '' | ||
- | |||
- | ==== Jiný shell ==== | ||
- | |||
- | Abych mohl poslat nějakou úlohu do fronty, musím pro ni vyrobit vlastní skript. Budiž, vyrobil jsem vlastní skript: | ||
- | |||
- | < | ||
- | #!/bin/bash | ||
- | program > log.out 2> log.err | ||
- | </ | ||
- | |||
- | 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 " | ||
- | |||
- | Nebudu vás napínat, zde je vysvětlení: | ||
- | |||
- | Takto SGE přinutíte, | ||
- | |||
- | < | ||
- | qsub -S /bin/bash skript | ||
- | </ | ||
- | |||
- | Jinou možností je přesměrovat stderr a stdout pomocí syntaxe csh: | ||
- | |||
- | < | ||
- | ( command > | ||
- | </ | ||
- | |||
==== bashrc a podobné nesmí nic vypisovat na konzoli ==== | ==== bashrc a podobné nesmí nic vypisovat na konzoli ==== | ||
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hard resource_list: | hard resource_list: | ||
hard resource_list: | hard resource_list: | ||
- | |||
- | ==== Jak rezervovat více jader na stejném stroji pro 1 job ==== | ||
- | |||
- | < | ||
- | qsub -pe smp <pocet jader> | ||
- | </ | ||