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PRACE User Support

925 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 =schedule of the HPCs are CPU hour based. This means that the available core hours are divided between users on a monthly basis. All UNIX users are connected to one or more account. This scheduler account is connected to an HPC project and a UNIX group. HPC jobs can only be sent by using one of the accounts. The core hours are calculated by the multiplication of wall time (time spent running the job) and the CPU cores requested.For example reserving 2 nodes (48 cpu cores) at the NIIFI SC for 30 minutes gives 48 * 30 =1440 core minutes = 24 core hours. Core hours are measured between the start and and the end of the jobs.
The most simple SGE command '''It is very important to be sure the display 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 cluster data: allocated time, no new jobs can be submitted until the beginning of the next accounting period. Account limits are regenerated the beginning of each month.'''
Information about an account can be listed with the following command:
<code>
qhostsbalance
</code>
A possible outcome of this command can be: {| class="wikitable" border="1" == Example ====|- |HOSTNAME|ARCH|NCPU|LOAD|MEMTOT|MEMUSE|SWAPTO|SWAPUS|-|global |<nowiki>-</nowiki>  |<nowiki>-</nowiki> |<nowiki>-</nowiki> |<nowiki>-</nowiki>  |<nowiki>-</nowiki>After executing the command, the 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).
|<nowikipre>Scheduler Account Balance---------- ----------- + ---------------- ----------- + ------------- --------</nowiki> |<nowiki>-</nowiki>|-|cn01 |linux-x64 |24 User Usage |5.00 Account Usage |62.9G Account Limit Available (CPU hrs)|8.6G |0.0 |0.0|-|cn02 |linux-x64 -------- ----------- + ---------------- ----------- + ------------- -----------|24 |alice 0.01 |62.9G |1.2G | foobar 0.0 | 0. 0|-|cn03 |linux-x64 |24 |bob * 0.03 |62.9G |1.5G |0. foobar 0 | 0. 0|}
The first two columns define the names and types of the computersbob * 7 | barfoo 7 | 1, which are in the cluster. The NCPU column shows the number of the available processor cores. LOAD shows the computer’s load for the moment (this value equals with the value demonstrated by the uptime UNIX command). The rest of the cells are: overall physical memory000 993alice 0 | barfoo 7 | 1, the actual used memory, the available swap-memory, and the used swap. The global line marks all the information in total regarding the cluster.000 993</pre>
We can === Estimating core time ===Before production runs, it is advised to have a look at the available queue-s with the core time estimate. The following commandcan be used for getting estimate:
<code>
qconf sestimate -sqlN NODES -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.
One probable outcome of '''It is important to provide the core time to be reserved most precisely, because the scheduler queue the jobs based on this value. Generally, a job with shorter core time will be run sooner. It is advised to check the time used to run the job after completion with <code>sacct</code> command: .'''
<code> parallel.q serial.q test.q </code>==== Example ====
To get more info about the state of the system use Alice 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
<code> qstat -fEstimated CPU hours: 2784</codepre>Unfortunately, she couldn't afford to run this job.
It shows which jobs run in which queues, and you can also get detailed info about the queues themselves (state, 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: === 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>
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 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) scontrol show job is to be found in the queue, it is directly next to the name of the row, like the recent "PI_SEQ_TES", which runs in the test.q row. The tasks waiting for the resources, because it is overwhelmed or the preliminary conditions are not prompt, appear behind the sum row, listed as pending jobs. For example: JOBID
<code>
queuename qtype resv/used/tot. load_avg arch states
---------------------------------------------------------------------------------
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
</code>
Each task is given All jobs will be inserted into an identifier, which is a number (a job ID, or j_id), this is followed by the job’s priority (0 in both cases), then the job’s name, and the user who posted the job, and the qw marks, that the job is waiting for the queueaccounting database. Finally the date The properties of the registration for the waiting queue is next When a job finishes running, completed jobs can be retrieved from this is created: jobnamedatabase.ojobnumber in our actual catalog, which contains the error messages and stapled outputs created Detailed statistics can be viewed by the program.. === Job submission === 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> using this 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 #$ sacct -N HOSTNAME /bin/hostname l -j JOBID
</code>
 Memory used can be posted with the following command: retrieved by using
<code>
qsub hostname.shsmemory JOBID
</code>
 The scripts Disk usage can be used for separating the different binariesretrieved by this command:  
<code>
#!/bin/sh case `uname` in SunOS) ./pi_sun FreeBSD) ./pi_bsd esacsdisk JOBID
</code>
With the following command, we can define the queue where the scheduler puts the job:==== Example ====
<code> qsub -q serialThere are 3 jobs in the queue.q rangeThe 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 short, informative names.sh</code>
<pre>
squeue -l
The command qsub can be issued with a number of different switches, which are gathered in the following tableWed Oct 16 08:30:07 2013 JOBID PARTITION NAME USER STATE TIME TIMELIMIT NODES NODELIST(REASON)591_[1-96] normal array alice PENDING 0:00 30:00 1 (None) 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>
{| class="wikitable" border="1"|This two-|Parameter|Possible example|Result|-| -N name| -N Flow|The node batch 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 had a restarttypical load of 10GB virtual, 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 ensuredand 6. (hour:minute:second)|-| -l| -l h_vmem=1G|Chooses a computer for the job where 1 GB 5GB RSS memory is available. In the case of parallel 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 computers.|-| -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 per 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 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 jobs will get higher priority.|}
<pre>
smemory 430
qsub command arguments can be added to the ~ MaxVMSize MaxVMSizeNode AveVMSize MaxRSS MaxRSSNode AveRSS---------- -------------- ---------- ---------- ---------- ----------10271792K cn06 10271792K 6544524K cn06 6544524K 10085152K cn07 10085152K 6538492K cn07 6534876K </.sge_request file. If this file exists then it will be added to the qsub arument list.pre>
Sometimes we want to delete a job before its running. For this you can use the ==== Checking jobs ====
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>
qdel job_idsjobcheck JOBID
</code>
command. ===== 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> qdel 903User</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.
The example deletes the job number 903<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, 0.0, 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, 0.0, 0.0] OFFcn05 24 ( 25/ 544) [ 25.11, 24.96, 20.97] [ 99.8, 0.0, 0.2, 0.0, 0.0] OFF</pre>
<code> qdel -f 903</code> It can delete the running jobs immediately.==== Checking licenses ====
For pending The used and then continuing jobs, use qmod {-s,-us}. available licenses can be retrieved with this command:
<code>
qmod -s 903 qmod -us 903 slicenses
</code>
==== Checking downtime ====
The previous one suspends In downtime periods, the running of number 903 (SIGSTOP)scheduler doesn't start new jobs, while the latter one allows (SIGCONT)but jobs can be sent.  If there is a need to change the features (resource requirements) of a job put into the waiting list, it The periods can be done with retrieved by using the following command: ''qalter''  
<code>
qalter -l h_cpu=0:12:0 903 sreservations
</code>
=== Running jobs ===
The previous command alternates Running applications in the hard-CPU requirements of HPC can be done in batch mode. This means all runs must have a job script containing the job number 903 (h_cpu) resources and changes it to 12 minutescommands needed. The switches parameters of the qalter command are mainly overlap scheduler (resource definitions) can be given with the ones <code>#SBATCH</code> directive. Comparison of the qsub commandschedulers, and 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:
<pre>
#!/bin/bash
#SBATCH -A ACCOUNT
#SBATCH --job-name=NAME
#SBATCH --time=TIME
</pre>
In a special case, we have where <code>ACCOUNT</code> is the name of the account to execute use (available accounts can be retrieved with the same task<code>sbalance</code> command), but on different data. These tasks are <code>NAME</code> is the short name of the array jobs. With SGE we can upload several jobs to job, <code>TIME</code> is the waitingmaximum walltime using <code>DD-HH:MM:SS</code> syntax. For example in the pi task shown in previous chapterAcceptable time formats include "minutes", "minutes:seconds", it can be posted multiple times"hours:minutes:seconds", with different parameters"days-hours", with the following script"days-hours:minutes" and "days-hours:minutes:''arrayseconds".sh''  
The following command submit jobs:
<code>
#!/bin/sbatch jobscript.sh #$ -N PI_ARRAY_TEST ./pi_gcc `expr $SGE_TASK_ID \* 100000`
</code>
The SGE_TASK_ID is an internal integer used by If the SGEsubmission was successful, which created values for each running job. The interval can be set up when posting the blockfollowing is outputted:   <codepre> qsub -t 1-7 array.sh Submitted batch job JOBID</codepre>  meaning that the array.sh program will run in seven issues, and the SGE_TASK_ID will have the value of 1, 2, ..., 7 in every running issue. The qstat -f shows how the block tasks are split:  <code>  <nowiki>--------------------------------------------------------------------------------- </nowiki>   parallel.q@cn30 BIP 0/0/24 0 linux-x64 <nowiki>--------------------------------------------------------------------------------- </nowiki>   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> It is clear, that behind the tasks there are their array index 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 command  where <code> qdel -f 907.5-7 JOBID</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: It can happen; that the task placed in the queue won’t start. This case the:  <code> qstat -j job_id </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 jobs. The scheduler will analyze the tasks in this order. Since it requires the reservation unique id of resources, it is not sure, that the tasks will run exactly the same order. If we wonder why a certain job won’t start, here’s how you can get information:  <code> qalter -w v job_id</code> One possible outcome  <code> Job 53505 cannot run in queue "parallel.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 queues</code> You can check with this command where the jobs are running:
The following commmand cancels the job:
<code>
qhost -j -qscancel JOBID
</code>
<code> HOSTNAME ARCH NCPU LOAD MEMTOT MEMUSE SWAPTO SWAPUS <nowiki>------------------------------------------------------------------------------- </nowiki> global - - - - - - - ==== Job queues ====
cn01 linux-x64 24 24.43 62.9G 3.0G 0.0 0.0 serial.q BI 0There are two separate queue (partition) available in the HPC, the <code>test</42code> queue and the <code>prod</48 120087 0code> queue.15501 runTha latter is for the production runs, the former is for testing purposes.sh roczei r 09In the test queue, 1 node can be allocated for the maximum of half hours, The default queue is <code>prod</23/2012 14:25:51 MASTER 22 120087 0.15501 runcode>.sh roczei r 09/23/2012 15Test partition can be chosen with the following directive:02:21 MASTER 78 120087 0.15501 run.sh roczei r 10/01/2012 07:58:21 MASTER 143 <pre> 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 ... #SBATCH --partition=test</codepre>
=== Queue types = Quality of Service (QoS) ====
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.
''parallel.q'' The following directive choses low priority:<pre>#SBATCH - for paralel jobs (jobs can run maximum 31 days)-qos=lowpri</pre>
==== Memory settings ====
''serial.q'' - 1000 MB memory is allocated for serial jobs (jobs 1 CPU core by default, more can run be allocated with the following directive:<pre>#SBATCH --mem-per-cpu=MEMORY</pre>where <code>MEMORY</code> is given in MB. The maximum 31 days)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.
''test==== 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.q'' - test queue, It is possible to seperate threads of the array job will be killed after 2 hoursby 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>
==== 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 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>).
Getting information on the waiting line’s status<pre>#!/bin/bash#SBATCH -A barfoo#SBATCH --job-name=mpi#SBATCH -N 2#SBATCH --ntasks-per-node=24#SBATCH --time=12:00:00#SBATCH -o slurm.outmpirun ./a.out</pre>
==== 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 ===== qstat -g c </code>In this case, MPI fills CPU cores by the order of threads (rank).
<pre>
Command to run: mpirun --bind-to-core --bycore
<code>[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 . . . . . . . . .][. . . . . . . . . . . .] CUSTER QUEUE CQLOAD USED RES AVAIL TOTAL aoACDS cdsuE [cn05:05493] MCW rank 3 bound to socket 0[core 3]: [. . . B . . . . . . . .][. . . . . . . . . . . .] <nowiki>-------------------------------------------------------------------------------- </nowikipre>
parallel.q 0.52 368 0 280 648 0 0 ===== Binding based on CPU socket ===== serial.q 0In this case, MPI threads are filling CPUs alternately.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 --bysocket
=== Running PVM job ===[cn05:05659] MCW rank 0 bound to socket 0[core 0]: [B . . . . . . . . . . .][. . . . . . . . . . . .][cn05:05659] MCW rank 1 bound to socket 1[core 0]: [. . . . . . . . . . . .][B . . . . . . . . . . .][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>
===== Binding by nodes =====
In this case, MPI threads are filling nodes alternately. At least 2 nodes needs to be allocated.
<pre>
Command to run: mpirun --bind-to-core --bynode
To run the previously shown and translated gexample application, we need the following task-describing ''gexample[cn05:05904] MCW rank 0 bound to socket 0[core 0]: [B .sh'' script. . . . . . . . . .][. . . . . . . . . . . .][cn05:05904] MCW rank 2 bound to socket 0[core 1]: [. B . . . . . . . . . .][. . . . . . . . . . . .] <code> #!/bin/sh #$ -N GEXAMPLE [cn06:05969] MCW rank 1 bound to socket 0[core 0]: [B . . . . . . . . . . .][. . . . . . . . . . . ./gexample << EOL ] 30 5 EOL </code> We can submit this with the following command[cn06:05969] MCW rank 3 bound to socket 0[core 1]:  <code> qsub -pe pvm 5 gexample[. B . . . . . . . . . .][. . . . . . . . . . . .sh ]</codepre> The -pe pvm 5 command will tell to the SGE to create a PVM parallel computer machine with 5 virtual processors, and run the application in this.
==== 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>
parallel.q@cn31 BIP 0/5/export OMP_NUM_THREADS=24 5.15 linux-x64 908 1.00000 GEXAMPLE stefan r 06/04/2011 13:05:14 5
</code>
Also note that after the running two output files were created: one containing an attached standard error and standard output (GEXAMPLE.o908), another describing ===== Example =====Alice user starts a 24 threaded OMP application for maximum 6 hours on the working method expenses of the (GEXAMLEfoobar account.po908)<pre>#!/bin/bash#SBATCH -A foobar#SBATCH --job-name=omp#SBATCH --time=06:00:00#SBATCH -N 1OMP_NUM_THREADS=24 . The latter one is mainly for finding errors/a.out</pre>
=== Running = Hybrid MPI -OMP jobs ====
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 process number is from 1 to the CPU socket number, OMP thread number is the number of CPU cores in a node, or the half or quarter of that (it depends on code). For the job script, the parameters of these two needs to be combined.
All computers are set up with several installations ===== Example =====Alice user sent a hybrid job on the expenses of the MPI system: vendor-specific MPI implementations'foobar' account for 8 hours, and MPICH system too2 nodes. The default setup 1 MPI process is running on one node using 24 OMP thread per node. For the vendor2 nodes, 2 MPI process is running, with 2x24 OMP threads<pre>#!/bin/bash#SBATCH -specific MPIA foobar#SBATCH --job-name=mpiomp#SBATCH -N 2#SBATCH --time=08:00:00#SBATCH --ntasks-per-node=1#SBATCH -o slurm.outexport OMP_NUM_THREADS=24mpirun ./a.out</pre>
Running in the MPI environment is similar ==== Maple Grid jobs ====Maple can be run - similarly to OMP jobs - on one node. Maple module need to the PVM environmentbe loaded for using it. Let’s have a look at the example shown A grid server needs to be started, because Maple is working in the previous chapter connectivityclient-server mode (<code>${MAPLE}/toolbox/Grid/bin/startserver</code>). A very simple task This application needs to use license, which tests have to be given in the MPI tasks’internal communicationjobscript (<code>#SBATCH --licenses=maplegrid:1</code>). Use the following connectivityStarting of a Maple job is done by using <code>${MAPLE}/toolbox/Grid/bin/joblauncher</code> code.sh script to run it:
===== Example =====Alice user is running a Maple Grid application for 6 hours on the expenses of 'foobar' account:<codepre> #!/bin/sh bash#SBATCH -A foobar #$ SBATCH --job-name=maple#SBATCH -N CONNECTIVITY 1</code>#SBATCH --ntasks-per-node=24#SBATCH --time=06:00:00#SBATCH -o slurm.out#SBATCH --licenses=maplegrid:1
<code> mpirun -np $NSLOTS ./connectivity </code>module load maple
Here, the $NLOTS variable indicates that how many processors should be used in the MPI environment. This equals with that number what we have reuired for the parallel environment{MAPLE}/toolbox/Grid/bin/startserver${MAPLE}/toolbox/Grid/bin/joblauncher ${MAPLE}/toolbox/Grid/samples/Simple. mpl</pre>
==== GPU compute nodes ====The Szeged site accomodates 2 GPU enabled compute nodes. Each GPU node has 6 Nvidia Tesla M2070 cards. The GPU nodes reside in a separate job can be submitted with queue (<code>--partition gpu</code>). To specify the following commandnumber of GPUs set <code>--gres gpu: #</code> directive.
===== Example =====Alice user submits to the foobar account a 4 GPU, 6 hour job.<codepre> qsub #!/bin/bash#SBATCH -A foobar#SBATCH --job-name=GPU#SBATCH --partition gpu#SBATCH -pe mpi 20 connectivity.sh -gres gpu:4</code>#SBATCH --time=06:00:00
With this command we instruct the scheduler to create a parallel MPI environment containing 20 processors, and reserve space for it in one of the queues. Once the space is available, the job starts:$PWD/gpu_burnout 3600</pre>
<code>
parallel.q@cn31 BIP 0/20/24 20.30 linux-x64
910 1.00000 CONNECTOVI stefan r 06/04/2011 14:03:14 20
</code>
Running the program will result in two files: == Extensions ==Extensions should be asked for at the first one Execution site (CONNECTIVITY.o910NIIF) 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 followat prace-up of the operation of the parallel environmentsupport@niif. If the running is successful, this file is emptyhu. The command -pe mpi 20 can All requests will be given in the script too with the directive #$ -pe mpi 20carefully reviewed and decided if eligable.
=== Running OpenMP jobs =Reporting after finishing project ==A report must be created after using PRACE resources. Please contact prace-support@niif.hu for further details.
There are applications that either use the solutions of the operation system for multi-threaded program execution, or use a special library designed for this, like OpenMP. These applications have to be instructed how many threads they can use. The matrix multiplication algorithm presented == Acknowledgement in the previous chapter can be described with the following ''omp_mm.sh'' script publications ==
<code> #!/bin/sh #$ -N OPENMP_MM </code> <code> ./omp_mm </code>PRACE
it can be submitted with this command which will use 6 threads  <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/2655...4499”

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