LRC (Linguistic Research Cluster) is a name of ÚFAL's computational grid/cluster, which has (as of 2017/09) about 1600 CPU cores (115 servers + 2 submission heads), with a total 10 TiB of RAM. It uses (Sun/Oracle/Son of) Grid Engine software (SGE) for job scheduling etc. You can submit many computing tasks (jobs) at once, they will be placed in a queue and once a machine (slot) with the required capabilities (e.g. RAM, number of cores) is available, your job will be executed (scheduled) on this machine. This way we can maximize the usefulness of the computing resources and divide it among users in a fair way.

If you need GPU processing, see a special page about our GPU cluster called DLL (which is actually a subsystem of LRC with independent queue gpu.q).

Last update: 2017/09. All machines have Ubuntu 14.04.
Some machines are at Malá Strana (ground floor, new server room built from Lindat budget), some are at Troja (5 km north-east).
If you need to quickly distinguish which machine is located where, you can use your knowledge of Trojan war-related heroes, qhost -q, or the tables below.

The two lrc machines are so called heads of the cluster. No computation is allowed here, i.e. no CPU-intensive, disk-intensive nor RAM-intensive computation (very simple scripts are OK). You should just ssh to lrc1 or lrc2 and submit your jobs as described bellow.

Alternatively, you can ssh to one of the sol machines and submit jobs from here. It is allowed to compute here, which is useful e.g. when you have a script which submits your jobs, but it also collects statistics from the jobs outputs (and possibly submits new jobs conditioned on the statistics). However, the sol machines are relatively slow and may be occupied by your colleagues, so for bigger (longer) tasks, always prefer submission as separate jobs.

The pandora machines are in a special cluster (not accessible from lrc) and queue ms-guests.q available for our colleagues from KSVI and for students of Data intensive computing (see the 2016 handouts if you missed the course).

Add the following line into your '~/.bash_profile'.

source /net/projects/SGE/user/sge_profile

This detects if you are on one of the cluster machines (including lrc and sol) and sets env variables accordingly. It also prints a status message.
Usually, this is the first line of your '~/.bash_profile' and the second-and-last line is

[ -f ~/.bashrc ] && source ~/.bashrc

First, you need to ssh to the cluster head (lrc1 or lrc2) or to one of the sol machines. The full address is lrc1.ufal.hide.ms.mff.cuni.cz, but you can use just ssh lrc1 (“hide” means it is accessible only from the ÚFAL network, not from outside; if working from home/Eduroam, you need to login/VPN to the ÚFAL network first).

ssh lrc1
echo 'hostname; pwd; echo The second parameter is $2' > script.sh
  # prepare a shell script describing your task
qsub -cwd -j y script.sh Hello World
  # This submits your job to the default queue, which is currently ''ms-all.q''.
  # Usually, there is a free slot, so the job will be scheduled within few seconds.
  # We have used two handy qsub parameters:
  #  -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 (''script.sh.o*'')
  # We have also provided two parameters for our script "Hello" and "World".
  # The qsub prints something like
  #   Your job 121144 ("script.sh") has been submitted
qstat
  # This way we inspect all our jobs (both waiting in queue and scheduled, i.e. running).
qstat -u '*' | less
  # This shows jobs of all users.
qstat -j 121144
  # This shows detailed info about the job with this number (if it is still running).
less script.sh.o*
  # We can inspect the job's output (in our case stored in script.sh.o121144).
  # Hint: if the job is still running, press F in 'less' to simulate 'tail -f'.

The output of our job should look like:

LRC:ubuntu 14.04: 8.1.7a Son of Grid Engine variables set...
lucifer5
/home/popel/tmp
The second parameter is World
======= EPILOG: Tue Sep 26 19:49:05 CEST 2017
== Limits:   
== Usage:    cpu=00:00:00, mem=0.00000 GB s, io=0.00000 GB, vmem=N/A, maxvmem=N/A
== Duration: 00:00:02 (2 s)

Our admins configured the SGE to print some extra info on stderr: the first line and then the epilog.
The mem=XY GB s means gigabytes of RAM used times the duration of the job in seconds, so don't be afraid XY is usually a very high number (unlike in this toy example).
The maxvmem means the peak virtual memory consumption (which is useful for setting h_vmem, see below).

qdel 121144
  # This way you can delete ("kill") a job with a given number, or comma-or-space separated list of job numbers.
qdel \*
  # This way you can delete all your jobs. Don't be afraid - you cannot delete others jobs.

The purpose of these rules is to prevent your jobs to damage the work of your colleagues and to divide the resources among users in a fair way.

• Read about our network first (so you know that e.g. reading big data from your home in 200 parallel jobs is not a good idea, but regular cleanup of your data is a good idea). Ask your colleagues (possibly via devel) if you are not sure, esp. if you plan to submit jobs with unusual/extreme disk/mem/CPU requirements.
• While your jobs are running (or queued), check your jobs (esp. previously untested setups) and your email (esp. devel) regularly. If you really need to leave e.g. for two-week vacation offline, consult it first with it@ufal (whether they can kill your jobs if needed).
• You can ssh to any cluster machine, which can be useful e.g. to diagnose what's happening there (using htop etc.).
• However, never execute any computing manually on a cluster machine where you are sshed (i.e. not via qsub or qrsh). If you break this rule, your task will take CPU and memory, but the SGE will not know, so it may schedule other users' jobs on the same machine and their jobs may fail or run slowly. The sol machines are an exception from this rule.
• For interactive work, you can use qrsh, but please try to end the job (exit with Ctrl+D) once finished with your work, especially if you ask for a lot of memory or CPUs (see below). One semi-permanent qrsh job (with non-extreme CPU/mem requirements) per user is acceptable.
• Specify the memory and CPU requirements (if higher than the defaults) and don't exceed them.
  • 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

    qsub -pe smp <number-of-CPU-cores>

    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:

    qsub -l mem_free=8G,act_mem_free=8G,h_vmem=12G

• 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.

• There are three commonly used options for specifying memory requirements: mem_free, act_mem_free and h_vmem. Each has a different purpose.
• mem_free=1G means 1024×1024×1024 bytes, i.e. one GiB (gibibyte). mem_free=1g means 1000×1000×1000 bytes, i.e. one gigabyte. Similarly for the other options and other prefixes (k, K, m, M).
• mem_free (or mf) specifies a consumable resource tracked by SGE and it affects job scheduling. Each machine has an initial value assigned (slightly lower than the real total physical RAM capacity). When you specify qsub -l mem_free=4G, SGE finds a machine with mem_free >= 4GB, and subtracts 4GB from it. This limit is not enforced, so if a job exceeds this limit, it is not automatically killed and thus the SGE value of mem_free may not represent the real free memory. The default value is 1G. By not using this option and eating more than 1 GiB, you are breaking the rules.
• act_mem_free (or amf) is a ÚFAL-specific option, which specifies the real amount of free memory (at the time of scheduling). You can specify it when submitting a job and it will be scheduled to a machine with at least this amount of memory free. In an ideal world, where no jobs are exceeding their mem_free requirements, we would not need this options. However, in real world it is recommended to use this option with the same value as mem_free to protect your job from failing with out-of-memory error (because of naughty jobs of other users).
• h_vmem is equivalent to setting ulimit -v, i.e. it is a hard limit on the size of virtual memory (see RLIMIT_AS in man setrlimit). If your job exceeds this limit, memory allocation fails (i.e., malloc or mmap will return NULL), and your job will probably crash on SIGSEGV. TODO: according to man queue_conf, the job is killed with SIGKILL, not with SIGSEGV. Note that h_vmem specifies the maximal size of allocated_memory, not used_memory, in other words it is the VIRT column in top, not the RES column. SGE does not use this parameter in any other way. Notably, job scheduling is not affected by this parameter and therefore there is no guarantee that there will be this amount of memory on the chosen machine. The problem is that some programs (e.g. Java with the default setting) allocate much more (virtual) memory than they actually use in the end. If we want to be ultra conservative, we should set h_vmem to the same value as mem_free. If we want to be only moderately conservative, we should specify something like h_vmem=1.5*mem_free, because some jobs will not use the whole mem_free requested, but still our job will be killed if it allocated much more than declared. The default effectively means that your job has no limits.
• It is recommended to profile your task first, so you can estimate reasonable memory requirements before submitting many jobs with the same task (varying in parameters which do not affect memory consumption). So for the first time, declare mem_free with much more memory than expected and ssh to a given machine and check htop (sum all processes of your job) or (if the job is done quickly) check the epilog. When running other jobs of this type, set mem_free (and act_mem_free and h_vmem) so you are not wasting resources, but still have some reserve.
• s_vmem is similar to h_vmem, but instead of SIGSEGV/SIGKILL, the job is sent a SIGXCPU signal which can be caught by the job and exit gracefully before it is killed. So if you need it, set s_vmem to a lower value than h_vmem and implement SIGXCPU handling and cleanup.

• qsub -o LOG.stdout -e LOG.stderr

redirect std{out,err} to separate files with given names

qsub -S /bin/bash
  # Choose the interpreter of your script. I think ''/bin/bash'' is now (2017/09) the default (but it used to be ''csh'').
qsub -v PATH
  # export a given environment variable from the current shell to the job
qsub -V
  # export all environment variables
man qsub qstat qhold queue_conf sge_types complex
  # Find out all the gory details which are missing here. You'll have to do it one anyway:-).

• 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.
• If you often run (ad-hoc) bash commands via qsub, check two alternative qsub wrappers ~bojar/tools/shell/qsubmit or ~stepanek/bin/qcmd, which allow you to enter the command on command line without creating any temp script files. The wrappers have also other features (some qsub options have changed default values). qcmd is older, but unlike qsubmit it has POD documentation, correct time computation and you don't need to quote the command.

• qstat [-u user] – seznam úloh aktuálně běžících / ve frontě
• qhost – dostupné zdroje
• /SGE/REPORTER/LRC-UFAL/bin/lrc_users_real_mem_usage -u user -w – aktuální využití paměti uživatelem
• /SGE/REPORTER/LRC-UFAL/bin/lrc_users_limits_requested -w – nárokované požadavky uživatelů
• /SGE/REPORTER/LRC-UFAL/bin/lrc_nodes_meminfo – vypis vsech uzlu a stav vytiznosti pameti.
  • mem_total: celkova pamet uzlu
  • mem_free: tedy kolik je jeste volne pameti z pametove quoty uzlu
  • act_mem_free: kolik uzlu OPRAVDU zbyva volne pameti
  • mem_used: kolik je pameti skutecne pouzito
• /SGE/REPORTER/LRC-UFAL/bin/lrc_state_overview – celkový přehled o clusteru
  • celkovy pocet jader, pocet vyuzitych jader
  • celkova velikost RAM, kolik je ji fyzicky nepouzite, kolik je ji jeste nerezervovane
  • po jednotlivych uzivatelich (zrovna pocitajicich) – kolik jim bezi uloh, kolik jich maji ve fronte a kolik z nich je ve stavu hold
• cat /SGE/REPORTER/LRC-UFAL/stats/userlist.weight – seznam uživatelů clusteru seřazený podle dosavadní aktivity (počet odeslaných úloh × čas, který běžely), aktualizovaný každý den v noci
• Munin: graf vytíženosti clusteru podle uživatelů (viditelný pouze ze sítě ÚFAL)

Danovy starší zkušenosti s clusterem PBS (nikoli SGE) říkaly, že tohle nejde. Ale jde to, aspoň u nás. Příkazy qsub a spol. jsou kromě hlavy clusteru dostupné i na všech strojích clusteru, samozřejmě pokud váš soubor .bashrc, .cshrc apod. zajistí, že se i na nich provede inicializace prostředí SGE.

SGE spouští skripty v čistém prostředí. Nebuďte proto překvapeni, když vám skript na konzoli poběží dobře, ale po submitnutí fungovat nebude. Třeba nenašel potřebné programy v $PATH

Zatím nevím přesně, které ze souborů .login, .bashrc ap. SGE spouští, jestli vůbec nějaké. Naopak, experimentálně jsem ověřil, že qsub -S /bin/bash skript nenačte žádný z .bashrc, .bash_profile, .login, ani .profile.

Z toho například také vyplývá, že bez ošetření se jako Java používá

 java version "1.5.0"
 gij (GNU libgcj) version 4.1.2 20070502 (Red Hat 4.1.2-12)

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.

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 “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:

  qsub -S /bin/bash skript

Jinou možností je přesměrovat stderr a stdout pomocí syntaxe csh:

( command >stdout_file ) >&stderr_file

Opsáno z http://www.sara.nl/userinfo/lisa/usage/batch/index.html.

It is important, that the files that are sourced during a login such as .bash_profile .profile .bashrc .login .cshrc don't produce any output when a non-interactive login is done. If they do, changes are that your job will run, but that the batch system is unable to deliver to you the standard output and error files. In that case the status of your job will be 'E' after the job is finished. Here is an example how you can test in a .bash_profile or .bashrc if this is an interactive login:

unset INTERACTIVE
/usr/bin/tty > /dev/null 2>&1
/usr/bin/test $? = 0 && INTERACTIVE=yes
...
if [ "$INTERACTIVE" ]; then
  ... commands only for truly interactive sessions ...
fi

qstat -j 973884,982737,984029,984030,984031,984034,984036 | grep resource
hard resource_list:         mem_free=50g
hard resource_list:         mem_free=200g
hard resource_list:         mem_free=16g
hard resource_list:         mem_free=16g
hard resource_list:         mem_free=16g
hard resource_list:         mem_free=31g

qsub -pe smp <pocet jader>