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PRACE User Support

851 bájt törölve, 2019. október 29., 15:56
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→‎Acknowledgement in publications
 
 
== User Guide to obtain a digital certificate ==
<code>
gsissh -p 2222 prace-login.budapest.hpcsc.niif.hu
</code>
<code>
globus-url-copy file://task/myfile.c gsiftp://prace-login.budapestsc.hpcniif.hu/home/taskprace/pr1hrocz/myfile.c
</code>
* -stripe Use this parameter to initiate a “striped” GridFTP transfer that uses more than one node at the source and destination. As multiple nodes contribute to the transfer, each using its own network interface, a larger amount of the network bandwidth can be consumed than with a single system. Thus, at least for “big” (> 100 MB) files, striping can considerably improve performance.
==Usage of the Sun Grid Engine SLURM scheduler ==  Basically the SGE is a scheduler, which divides the resources, computers into resource partitions. These are called queues. A queue can’t be larger than a physical resource; it can’t expand its borders. SGE registers a waiting list for the resources managed by itself, to which the posted computing tasks are directed. The scheduler searches for the resource defined by the description of the task and starts it. The task-resource coupling depends on the ability of the resources and the parameters of the tasks. In case the resources are overloaded, the tasks have to wait while the requested processor and memory becomes available.  The detailed documentation of the SGE can be found [Website: http://docsslurm.oracleschedmd.com/cd/E24901_01/doc.62/e21976.pdf here].  SGE version on all HPC sites: [http://gridscheduler.sourceforge.net/documentation.html Open Grid Scheduler (OGS/GE 2011.11p1)]  === The most simple commands ===  The most simple SGE command is the display of the cluster data:  <code> qhost</code> A possible outcome of this command can be: {| class="wikitable" border="1" |- |HOSTNAME|ARCH|NCPU|LOAD|MEMTOT|MEMUSE|SWAPTO|SWAPUS|-|global |<nowiki>-</nowiki>  |<nowiki>-</nowiki> |<nowiki>-</nowiki> |<nowiki>-</nowiki>
|<nowiki>-</nowiki> |<nowiki>-</nowiki> |<nowiki>-</nowiki>|-|cn01 |linux-x64 |24 |5The schedule of the HPCs are CPU hour based.00 |62This means that the available core hours are divided between users on a monthly basis.9G |8All UNIX users are connected to one or more account.6G |0This scheduler account is connected to an HPC project and a UNIX group.0 |0.0|-|cn02 |linux-x64 |24 |0.01 |62.9G |1.2G |0.0 |0.0|-|cn03 |linux-x64 |24 |0.03 |62.9G |1.5G |0.0 |0.0|} The first two columns define the names and types HPC jobs can only be sent by using one of the computers, which are in the clusteraccounts. The NCPU column shows core hours are calculated by the number multiplication of wall time (time spent running the job) and the available processor CPU coresrequested. LOAD shows For example reserving 2 nodes (48 cpu cores) at the computer’s load NIIFI SC for the moment (this value equals with the value demonstrated by the uptime UNIX command)30 minutes gives 48 * 30 = 1440 core minutes = 24 core hours. The rest of the cells Core hours are: overall physical memory, measured between the actual used memory, the available swap-memory, start and and the used swap. The global line marks all end of the information in total regarding the clusterjobs. We can have a look at the available queue-s with the following command:  <code> qconf -sql</code>
One probable outcome '''It is very important to be sure the application maximally uses the allocated resources. An empty or non-optimal job will consume allocated core time very fast. If the account run out of the allocated time, no new jobs can be submitted until the beginning of the command: next accounting period. Account limits are regenerated the beginning of each month.'''
Information about an account can be listed with the following command:
<code>
parallel.q serial.q test.q sbalance
</code>
To get more info about ==== Example ====After executing the state of command, the system use following table shows up for Bob. The user can access, and run jobs by using two different accounts (foobar, barfoo). He can see his name marked with * in the table. He shares both accounts with alice (Account column). The consumed core hours for the users are displayed in the second row (Usage), and the consumption for the jobs ran as the account is displayed in the 4th row. The last two row defines the allocated maximum time (Account limit), and the time available for the machine (Available).
<codepre> Scheduler Account Balance---------- ----------- + ---------------- ----------- + ------------- -----------User Usage | Account Usage | Account Limit Available (CPU hrs) qstat -f--------- ----------- + ---------------- ----------- + ------------- -----------alice 0 | foobar 0 | 0 0</code>bob * 0 | foobar 0 | 0 0
It shows which jobs run in which queuesbob * 7 | barfoo 7 | 1, and you can also get detailed info about the queues themselves (state000 993alice 0 | barfoo 7 | 1, environment). The command can be used without the -f switch too, but it is less informative, since in this case only the jobs’ states will appear. The command’s outcome: 000 993</pre>
<code> queuename qtype resv/used/tot. load_avg arch states -------------------------------------------------------------------------------- test.q@cn.32 BIP 0/3/24 3.15 linux-x64 905 1.00000 PI_SEQ_TES stefan r 06/04/2011 09:12:14 1 </code> The first column of this table shows the name of the row, the second column marks the type (B-batch, I-interactive, C-checkpointing, P-parallel environment, E-error state). The third part of the column shows how many jobs can be run at the same === Estimating core time in the row. All in all, these values fit to the number of overall processor cores in the system. The second item of the column shows the free compartments at the moment.=== If a running (scheduled) job is to be found in the queueBefore production runs, it is directly next advised to the name of the row, like the recent "PI_SEQ_TES", which runs in the test.q rowhave a core time estimate. The tasks waiting following command can be used for the resources, because it is overwhelmed or the preliminary conditions are not prompt, appear behind the sum row, listed as pending jobs. For examplegetting estimate:
<code>
queuename qtype resv/used/tot. load_avg arch states sestimate -N NODES -------------------------------------------------------------------------------- parallel.q@cn31 BIP 0/24/24 22.3 linux-x64 --------------------------------------------------------------------------------- test.q@cn32 BIP 0/24/24 23.5 linux-x64 ############################################################################ - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS ############################################################################ 905 0.00000 PI_SEQ_TES stefan qw 06/04/2011 09:12:04 1 t WALLTIME
</code>
where <code>NODES</code> are the number of nodes to be reserved, <code>WALLTIME</code> is the maximal time spent running the job.
Each task '''It is given an identifier, which is a number (a job ID, or j_id)important to provide the core time to be reserved most precisely, this is followed by because the job’s priority (0 in both cases), then scheduler queue the job’s namejobs based on this value. Generally, and the user who posted the a job, and with shorter core time will be run sooner. It is advised to check the qw marks, that time used to run the job is waiting for the queueafter completion with <code>sacct</code> command. Finally the date of the registration for the waiting queue is next'''
When a job finishes running, this is created: jobname.ojobnumber in our actual catalog, which contains the error messages and stapled outputs created by the program.. === Job submission = Example ====Back then, the SGE scheduler was designed to be able to operate different types of architectures. That’s why you can’t post binary files directly, only scripts, like the  <code> qsub script.sh</code> command. The script describes the task, the main parameters of it, and its running. For example in the following script, the described ''hostname.sh'' task:  <code> #!/bin/sh #$ -N HOSTNAME /bin/hostname </code>
can be posted with the following commandAlice want to reserve 2 days 10 hours and 2 nodes, she checks, if she have enough time on her account.<pre>sestimate -N 2 -t 2-10: 00:00
Estimated CPU hours: 2784<code/pre> qsub hostnameUnfortunately, she couldn't afford to run this job.sh</code>
The scripts can be used for separating the different binaries: === Status information ===
Jobs in the queue can be listed with <code>squeue</code> command, the status of the cluster can be retrieved with the <code>sinfo</code> command. All jobs sent will get a JOBID. The properties of a job can be retrieved by using this id. Status of a running or waiting job:
<code>
#!/bin/sh case `uname` in SunOS) ./pi_sun FreeBSD) ./pi_bsd esac</code>scontrol show job JOBID
With the following command, we can define the queue where the scheduler puts the job:
 
<code>
qsub -q serial.q range.sh
</code>
The command qsub can be issued with a number of different switches, which are gathered in the following table: {| class="wikitable" border="1"|-|Parameter|Possible example|Result|-| -N name| -N Flow|The job will appear under this name in the queue.|-| -cwd| -cwd|The output and the error files will appear in this actual catalog.|-| -S shell| -S /bin/tcsh|The shell in which the scripts run.|-| -j {y,n}| -j y|Joining the error and the output in one file.|-| -r {y,n}| -r y|After a restart, should the job restart too (from the beginning).|-| -M e-mail| -M stefan@niif.hu|Scheduler information will be sent to this address about the job.|-| -l| -l h_cpu=0:15:0|Chooses a queue for the job where 15 minutes of CPU time could be ensured. (hour:minute:second)|-| -l| -l h_vmem=1G|Chooses a computer for the job where 1 GB memory is available. In the case of parallel All jobs its value is extended with the required number of slots. If this parameter is not given, the default setting will be the number of the maximum memory cores set up in the computersinserted into an accounting database.|-| -l| -l in|Consuming resources, complex request. (This will be defined in the documentation written for the system administrators)|-| -binding| -binding linear:4|Chooses 4 CPU cores on the worker node-on and assignes in a fix way. Further information: [http://docs.oracle.com/cd/E24901_01/doc.62/e21976/chapter2.htm#autoId75 here].|-| -l| -l exclusive=true|Demand The properties of exclusive task execution (another job will not be scheduled on the chosen computers). |-| -P| -P niifi|Chooses a HPC project. This command will list the available HPC projects: ''qconf -sprjl''|-| -R | -R y|Resource reservation. This will cause that bigger parallel completed jobs will get higher priority.|} qsub command arguments can be added to the ~/retrieved from this database.sge_request file. If this file exists then it will Detailed statistics can be added to the qsub arument list. Sometimes we want to delete a job before its running. For viewed by using this you can use the command:
<code>
qdel job_idsacct -l -j JOBID
</code>
command. Memory used can be retrieved by using
<code>
qdel 903smemory JOBID
</code>
The example deletes the job number 903. Disk usage can be retrieved by this command:
<code>
qdel -f 903sdisk JOBID
</code>
It can delete the running jobs immediately.==== Example ====
For pending and then continuing There are 3 jobsin the queue. The first is an array job which is waiting for resources (PENDING). The second is an MPI job running on 4 nodes for 25 minutes now. The third is an OMP run running on one node, just started. The NAME of the jobs can be freely given, it is advised to use qmod {-sshort,-us}informative names.
<codepre> qmod squeue -s 903 qmod -us 903 </code>l
The previous one suspends the running of number 903 Wed Oct 16 08:30:07 2013 JOBID PARTITION NAME USER STATE TIME TIMELIMIT NODES NODELIST(SIGSTOPREASON), while the latter one allows 591_[1-96] normal array alice PENDING 0:00 30:00 1 (SIGCONTNone). 589 normal mpi bob RUNNING 25:55 2:00:00 4 cn[05-08] 590 normal omp alice RUNNING 0:25 1:00:00 1 cn09</pre>
If there is This two-node batch job had a need to change the features (resource requirements) typical load of a job put into the waiting list10GB virtual, it can be done with the command: ''qalter'' and 6.5GB RSS memory per node.
<codepre> qalter -l h_cpu=0:12:0 903 </code>smemory 430
The previous command alternates the hard MaxVMSize MaxVMSizeNode AveVMSize MaxRSS MaxRSSNode AveRSS-CPU requirements of the job number 903 (h_cpu) and changes it to 12 minutes. The switches of the qalter command are mainly overlap the ones of the qsub command.--------- -------------- ---------- ---------- ---------- ----------10271792K cn06 10271792K 6544524K cn06 6544524K 10085152K cn07 10085152K 6538492K cn07 6534876K </pre>
In a special case, we have to execute the same task, but on different data. These tasks are the array ==== Checking jobs. With SGE we can upload several jobs to the waiting. For example in the pi task shown in previous chapter, it can be posted multiple times, with different parameters, with the following script:''array.sh'' ====
It is important to be sure the application fully uses the core time reserved. A running application can be monitored with the following command:
<code>
#!/bin/sh #$ -N PI_ARRAY_TEST ./pi_gcc `expr $SGE_TASK_ID \* 100000` sjobcheck JOBID
</code>
The SGE_TASK_ID is an internal integer used by the SGE, which created values for each running job. The interval can be set up when posting the block: ===== Example =====
This job runs on 4 nodes. The LOAD group provides information about the general load of the machine, this is more or less equal to the number of cores. The CPU group gives you information about the exact usage. Ideally, values of the <code> qsub -t 1-7 array.sh User</code>column are over 90. If the value is below that, there is a problem with the application, or it is not optimal, and the run should be ended. This example job fully using ("maxing out") the available resources.
meaning that the array<pre>Hostname LOAD CPU Gexec CPUs (Procs/Total) [ 1, 5, 15min] [ User, Nice, System, Idle, Wio]cn08 24 ( 25/ 529) [ 24.83, 24.84, 20.98] [ 99.8, 0.sh program will run in seven issues0, and the SGE_TASK_ID will have the value of 0.2, 0.0, 0.0] OFFcn07 24 ( 25/ 529) [ 24.93, 24.88, 20.98] [ 99.8, 0.0, 0.2, 0.0, 0.0] OFFcn06 24 ( 25/ 529) [ 25.00, 24.90, 20.97] [ 99.9, 0.0, 0.1, 2 0.0, 0.0] OFFcn05 24 ( 25/ 544) [ 25.11, 24.96, 20.97] [ 99.8, 0.0, 0.2, 0.0, 7 in every running issue 0. The qstat -f shows how the block tasks are split: 0] OFF</pre>
<code> --------------------------------------------------------------------------------- parallel.q@cn30 BIP 0/0/24 0 linux-x64 --------------------------------------------------------------------------------- test.q@cn32 BIP 0/7/24 7.15 linux-x64 907 1.00000 PI_ARRAY_T stefan r 06/04/2011 10:34:14 1 1 907 0.50000 PI_ARRAY_T stefan t 06/04/2011 10:34:14 1 2 907 0.33333 PI_ARRAY_T stefan t 06/04/2011 10:34:14 1 3 907 0.25000 PI_ARRAY_T stefan t 06/04/2011 10:34:14 1 4 907 0.20000 PI_ARRAY_T stefan t 06/04/2011 10:34:14 1 5 907 0.16667 PI_ARRAY_T stefan t 06/04/2011 10:34:14 1 6 907 0.14286 PI_ARRAY_T stefan t 06/04/2011 10:34:14 1 7 </code>==== Checking licenses ====
It is clear, that behind the tasks there are their array index The used and available licenses can be retrieved with which we can refer to the components to the task. For example, in the case of block tasks, there is a possibility to delete particular parts of the block. If we want to delete the subtasks from 5-7 of the previous task, the this command :
<code>
qdel -f 907.5-7 slicenses
</code>
will delete chosen components, but leaves the tasks 907.1-4 intact.The result of the running is seven individual files, with seven different running solutions:==== Checking downtime ====
It can happen; that the task placed in In downtime periods, the queue won’t scheduler doesn't startnew jobs, but jobs can be sent. This case The periods can be retrieved by using thefollowing command:
<code>
qstat -j job_id sreservations
</code>
command will show the detailed scheduling information, containing which running parameters are unfulfilled by the task. The priority of the different tasks only means the gradiation listed in the pending === Running jobs. The scheduler will analyze the tasks in this order. Since it requires the reservation of resources, it is not sure, that the tasks will run exactly the same order.===
If we wonder why Running applications in the HPC can be done in batch mode. This means all runs must have a certain job won’t startscript containing the resources and commands needed. The parameters of the scheduler (resource definitions) can be given with the <code>#SBATCH</code> directive. Comparison of the schedulers, here’s how you can get informationand the directives available at slurm are available at this [http: //slurm.schedmd.com/rosetta.pdf table].
==== Obligatory parameters ====The following parameters are obligatory to provide:<codepre> qalter #!/bin/bash#SBATCH -A ACCOUNT#SBATCH --job-name=NAME#SBATCH --w v job_idtime=TIME</codepre>
One possible outcome where <code>ACCOUNT</code> is the name of the account to use (available accounts can be retrieved with the <code>sbalance</code> command), <code>NAME</code> is the short name of the job, <code>TIME</code> is the maximum walltime using <code>DD-HH:MM:SS</code> syntax. Acceptable time formats include "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds".
The following command submit jobs:
<code>
Job 53505 cannot run in queue "parallelsbatch jobscript.q" because it is not contained in its hard queue list (-q) Job 53505 (-l NONE) cannot run in queue "cn30.budapest.hpc.niif.hu" because exclusive resource (exclusive) is already in use Job 53505 (-l NONE) cannot run in queue "cn31.budapest.hpc.niif.hu" because exclusive resource (exclusive) is already in use Job 53505 cannot run in PE "mpi" because it only offers 0 slots verification: no suitable queuessh
</code>
You can check with this command where If the submission was successful, the jobs are runningfollowing is outputted: <pre>Submitted batch job JOBID</pre>where <code> qhost -j -qJOBID</code>is the unique id of the job
The following commmand cancels the job:
<code>
HOSTNAME ARCH NCPU LOAD MEMTOT MEMUSE SWAPTO SWAPUS ------------------------------------------------------------------------------- global - - - - - - - cn01 linux-x64 24 24.43 62.9G 3.0G 0.0 0.0 serial.q BI 0/42/48 120087 0.15501 run.sh roczei r 09/23/2012 14:25:51 MASTER 22 120087 0.15501 run.sh roczei r 09/23/2012 15:02:21 MASTER 78 120087 0.15501 run.sh roczei r 10/01/2012 07:58:21 MASTER 143 120087 0.15501 run.sh roczei r 10/01/2012 08:28:51 MASTER 144 120087 0.15501 run.sh roczei r 10/04/2012 17:41:51 MASTER 158 120340 0.13970 pwhg.sh roczei r 09/24/2012 23:24:51 MASTER 3 120340 0.13970 pwhg.sh roczei r 09/24/2012 23:24:51 MASTER 5 120340 0.13970 pwhg.sh roczei r 09/24/2012 23:24:51 MASTER 19 120340 0.13970 pwhg.sh roczei r 09/24/2012 23:24:51 MASTER 23 120340 0.13970 pwhg.sh roczei r 09/24/2012 23:24:51 MASTER 31 120340 0.13970 pwhg.sh roczei r 09/24/2012 23:24:51 MASTER 33 120340 0.13970 pwhg.sh roczei r 09/26/2012 13:42:51 MASTER 113 120340 0.13970 pwhg.sh roczei r 10/01/2012 07:43:06 MASTER 186 120340 0.13970 pwhg.sh roczei r 10/01/2012 07:58:36 MASTER 187 ... scancel JOBID
</code>
=== Queue types = Job queues ====
There are two separate queue (partition) available in the HPC, the <code>test</code> queue and the <code>prod</code> queue. Tha latter is for the production runs, the former is for testing purposes. In the test queue, 1 node can be allocated for the maximum of half hours, The default queue is <code>prod</code>. Test partition can be chosen with the following directive:
<pre>
#SBATCH --partition=test
</pre>
''parallel.q'' - for paralel jobs ==== Quality of Service (jobs can run maximum 31 daysQoS)====
There is an option for submitting low priority jobs. These jobs can be interrupted by any normal priority job at any time, but only the half of the time is billed to the account. Interrupted jobs will be automatically queued again. Therefore it is important to only run jobs that can be interrupted at any time, periodically saves their states (checkpoint) and can restart quickly.
The default QoS is <code>normal</code>, non-interruptable.
''serial.q'' The following directive choses low priority:<pre>#SBATCH - for serial jobs (jobs can run maximum 31 days)-qos=lowpri</pre>
==== Memory settings ====
''test.q'' - test queue1000 MB memory is allocated for 1 CPU core by default, more can be allocated with the job will be killed after 2 hoursfollowing directive:<pre>#SBATCH --mem-per-cpu=MEMORY</pre>where <code>MEMORY</code> is given in MB. The maximum memory/core at NIIFI SC is 2600 MB.
==== Email notification ====
Sending mail when the status of the job change (start, stop, error):
<pre>
#SBATCH --mail-type=ALL
#SBATCH --mail-user=EMAIL
</pre>
where <code>EMAIL</code> is the e-mail to notify.
==== Array jobs ====
Array jobs are needed, when multiple one threaded (serial) jobs are to be sent (with different data). Slurm stores unique id of the instances in the <code>SLURM_ARRAY_TASK_ID</code> enviromnemt variable. It is possible to seperate threads of the array job by retrieving these ids. Output of the threads are written into <code>slurm-SLURM_ARRAY_JOB_ID-SLURM_ARRAY_TASK_ID.out</code> files. The scheduler uploads outputs tightly. It is useful to use multiply threads for a CPU core. [http://slurm.schedmd.com/job_array.html More on this topic]
===== Example =====
Alice user submits 96 serial job for a maximum of 24 hour run.
on the expenses of 'foobar' account. The <code>#SBATCH --array=1-96</code> directive indicates, that it is an array job. The application
can be run with the <code>srun</code> command. This is a shell script in this example.
<pre>
#!/bin/bash
#SBATCH -A foobar
#SBATCH --time=24:00:00
#SBATCH --job-name=array
#SBATCH --array=1-96
srun envtest.sh
</pre>
Getting information ==== MPI jobs ====Using MPI jobs, the number of MPI processes running on a node is to be given (<code>#SBATCH --ntasks-per-node=</code>). The most frequent case is to provide the waiting line’s status:number of CPU cores. Parallel programs should be started by using <code>mpirun</code> command.
===== Example =====
Bob user allocates 2 nodes, 12 hour for an MPI job, billing 'barfoo' account. 24 MPI thread will be started on each node. The stdout output is piped to <code>slurm.out</code> file (<code>#SBATCH -o</code>).
<codepre> qstat #!/bin/bash#SBATCH -A barfoo#SBATCH -g c -job-name=mpi#SBATCH -N 2#SBATCH --ntasks-per-node=24#SBATCH --time=12:00:00#SBATCH -o slurm.outmpirun ./a.out</codepre>
==== CPU binding ====
Generally, the performance of MPI application can be optimized with CPU core binding. In this case, the threads of the paralel program won't be scheduled by the OS between the CPU cores, and the memory localization can be made better (less cache miss). It is advised to use memory binding. Tests can be run to define, what binding strategy gives the best performance for our application. The following settings are valid for OpenMPI environment. Further information on binding can be retrieved with <code>--report-bindings</code> MPI option. Along with the running commands, few lines of the detailed binding information are shown. It is important, that one should not use task_binding of the scheduler!
<code>===== Binding per CPU core ===== CUSTER QUEUE CQLOAD USED RES AVAIL TOTAL aoACDS cdsuE <nowiki>-------------------------------------------------------------------------------- </nowiki>In this case, MPI fills CPU cores by the order of threads (rank).
parallel.q 0.52 368 0 280 648 0 0 serial.q 0.05 5 0 91 96 0 0 test.q 0.00 0 0 24 24 0 0</codepre>Command to run: mpirun --bind-to-core --bycore
=== Running PVM job ===[cn05:05493] MCW rank 0 bound to socket 0[core 0]: [B . . . . . . . . . . .][. . . . . . . . . . . .][cn05:05493] MCW rank 1 bound to socket 0[core 1]: [. B . . . . . . . . . .][. . . . . . . . . . . .][cn05:05493] MCW rank 2 bound to socket 0[core 2]: [. . B . . . . . . . . .][. . . . . . . . . . . .][cn05:05493] MCW rank 3 bound to socket 0[core 3]: [. . . B . . . . . . . .][. . . . . . . . . . . .]</pre>
===== Binding based on CPU socket =====
In this case, MPI threads are filling CPUs alternately.
<pre>
Command to run: mpirun --bind-to-core --bysocket
To run the previously shown and translated gexample application, we need the following task-describing ''gexample[cn05:05659] MCW rank 0 bound to socket 0[core 0]: [B . . . . . . . . . . .][. . . . . . . . . . . .][cn05:05659] MCW rank 1 bound to socket 1[core 0]: [. . . . . . . . . . . .][B . . . . . . . . . . .sh'' script][cn05:05659] MCW rank 2 bound to socket 0[core 1]: [. B . . . . . . . . . .][. . . . . . . . . . . .][cn05:05659] MCW rank 3 bound to socket 1[core 1]: [. . . . . . . . . . . .][. B . . . . . . . . . .]</pre>
<code> ===== Binding by nodes ===== #!/bin/sh #$ -N GEXAMPLE In this case, MPI threads are filling nodes alternately. At least 2 nodes needs to be allocated./gexample << EOL 30 5 EOL </codepre>Command to run: mpirun --bind-to-core --bynode
We can submit this with the following command[cn05: 05904] MCW rank 0 bound to socket 0[core 0]: [B . . . . . . . . . . .][. . . . . . . . . . . .][cn05:05904] MCW rank 2 bound to socket 0[core 1]: [. B . . . . . . . . . .][. . . . . . . . . . . .][cn06:05969] MCW rank 1 bound to socket 0[core 0]: [B . . . . . . . . . . .][. . . . . . . . . . . .][cn06:05969] MCW rank 3 bound to socket 0[core 1]: [. B . . . . . . . . . .][. . . . . . . . . . . .]</pre>
==== OpenMP (OMP) jobs ====
For OpenMP paralell applications, 1 node needs to be allocated, and the number of OMP threads needs to be provided with the <code>OMP_NUM_THREADS</code> environment variable. The variable needs to be written before the application (see example), or needs to be exported before executing the command:
<code>
qsub -pe pvm 5 gexample.sh export OMP_NUM_THREADS=24
</code>
The -pe pvm 5 command will tell to the SGE to create ===== Example =====Alice user starts a PVM parallel computer machine with 5 virtual processors, and run 24 threaded OMP application for maximum 6 hours on the application in thisexpenses of foobar account.  <codepre> parallel.q@cn31 BIP 0#!/5bin/24 5.15 linuxbash#SBATCH -A foobar#SBATCH --job-x64 name=omp 908 1.00000 GEXAMPLE stefan r #SBATCH --time=06/04/2011 13:0500:14 5 00</code>#SBATCH -N 1 Also note that after the running two output files were created: one containing an attached standard error and standard output (GEXAMPLEOMP_NUM_THREADS=24 .o908), another describing the working method of the (GEXAMLE.po908). The latter one is mainly for finding errors/a.out === Running MPI jobs ===</pre>
All computers are set up with several installations of the ==== Hybrid MPI system: vendor-specific MPI implementations, and MPICH system too. The default setup is the vendor-specific MPI.OMP jobs ====
Running When an application uses MPI and OMP it is running in hybrid MPI-OMP mode. Good to know that Intel MKL linked applications MKL calls are OpenMP capable. Generally, the following distribution suggested: MPI environment process number is similar from 1 to the PVM environment. Let’s have a look at CPU socket number, OMP thread number is the example shown number of CPU cores in a node, or the previous chapter connectivityhalf or quarter of that (it depends on code). A very simple task which tests For the MPI tasks’internal communication. Use job script, the following connectivityparameters of these two needs to be combined.sh script to run it:
===== Example =====Alice user sent a hybrid job on the expenses of the 'foobar' account for 8 hours, and 2 nodes. 1 MPI process is running on one node using 24 OMP thread per node. For the 2 nodes, 2 MPI process is running, with 2x24 OMP threads<codepre> #!/bin/sh bash #$ SBATCH -A foobar#SBATCH --job-name=mpiomp#SBATCH -N CONNECTIVITY 2#SBATCH --time=08:00:00#SBATCH --ntasks-per-node=1#SBATCH -o slurm.outexport OMP_NUM_THREADS=24mpirun ./a.out</codepre>
==== Maple Grid jobs ====Maple can be run - similarly to OMP jobs - on one node. Maple module need to be loaded for using it. A grid server needs to be started, because Maple is working in client-server mode (<code> mpirun -np $NSLOTS {MAPLE}/toolbox/Grid/bin/startserver</code>).This application needs to use license, which have to be given in the jobscript (<code>#SBATCH --licenses=maplegrid:1</connectivity code>). Starting of a Maple job is done by using <code>${MAPLE}/toolbox/Grid/bin/joblauncher</code>code.
Here, the $NLOTS variable indicates that how many processors should be used in the MPI environment. This equals with that number what we have reuired ===== Example =====Alice user is running a Maple Grid application for 6 hours on the parallel environmentexpenses of 'foobar' account:<pre>#!/bin/bash#SBATCH -A foobar#SBATCH --job-name=maple#SBATCH -N 1#SBATCH --ntasks-per-node=24#SBATCH --time=06:00:00#SBATCH -o slurm. out#SBATCH --licenses=maplegrid:1
The job can be submitted with the following command: module load maple
<code>${MAPLE}/toolbox/Grid/bin/startserver qsub -pe mpi 20 connectivity${MAPLE}/toolbox/Grid/bin/joblauncher ${MAPLE}/toolbox/Grid/samples/Simple.sh mpl</codepre>
With this command we instruct the scheduler to create ==== GPU compute nodes ====The Szeged site accomodates 2 GPU enabled compute nodes. Each GPU node has 6 Nvidia Tesla M2070 cards. The GPU nodes reside in a parallel MPI environment containing 20 processors, and reserve space for it in one of the queuesseparate job queue (<code>--partition gpu</code>). Once To specify the space is available, the job startsnumber of GPUs set <code>--gres gpu:#</code> directive.
===== Example =====Alice user submits to the foobar account a 4 GPU, 6 hour job.<codepre> parallel.q@cn31 BIP 0#!/20bin/24 20.30 linuxbash#SBATCH -A foobar#SBATCH --job-name=GPU#SBATCH --partition gpu#SBATCH --x64 gres gpu:4 910 1.00000 CONNECTOVI stefan r #SBATCH --time=06/04/2011 14:0300:14 20 </code>00
Running the program will result in two files: the first one (CONNECTIVITY.o910) is the overlap of the result of the already run program standard output and standard error, while the second one (CONNECTIVITY.po910) is for the follow-up of the operation of the parallel environment. If the running is successful, this file is empty. The command -pe mpi 20 can be given in the script too with the directive #$ -pe mpi 20PWD/gpu_burnout 3600</pre>
=== Running OpenMP jobs ===
There are applications that either use the solutions of == Extensions ==Extensions should be asked for at the operation system for multiExecution site (NIIF) at prace-threaded program execution, or use a special library designed for this, like OpenMPsupport@niif. These applications have to be instructed how many threads they can usehu. The matrix multiplication algorithm presented in the previous chapter can All requests will be described with the following ''omp_mmcarefully reviewed and decided if eligable.sh'' script
<code>== Reporting after finishing project == #!/bin/sh #$ A report must be created after using PRACE resources. Please contact prace-N OPENMP_MM </code>support@niif.hu for further details.
<code> ./omp_mm </code>== Acknowledgement in publications ==
it can be submitted with this command which will use 6 threads PRACE
<code> qsub -pe openmp 6 omp_mm'''We acknowledge [PRACE/KIFÜ] for awarding us access to resource based in Hungary at [Budapest/Debrecen/Pécs/Szeged].sh</code>'''
KIFÜ
=== Checkpointing support ==='''We acknowledge KIFÜ for awarding us access to resource based in Hungary at [Budapest/Debrecen/Pécs/Szeged].'''
Where technical support has been received the following additional text should also be used:
'''The support of [name of person/people] from KIFÜ, Hungary to the technical work is gratefully acknowledged.'''
At the moment the system doesn’t support any automatic checkpointing/restarting mechanism. If it is need, the application has to take care of it.[[Category: HPC]]
A lap eredeti címe: „https://wiki.niif.hu/index.php?title=Speciális:MobileDiff/2656...4499”

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