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| == Introduction == The '''GridUI''' (Grid User Interface) cluster is the interactive gateway to the [[http://grid.ifca.es|Advanced Computing and e-Science]] resources at IFCA. This cluster is comprised of a pool of Scientific Linux machines reachable through a single entry point. The connections to the internal machines are managed by a director node that tries to ensure that proper balancing is made across the available nodes at a given moment. |
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| == Introduction == The '''GRIDUI''' (Grid User Interface) cluster is the interactive gateway to the [[http://grid.ifca.es|Advanced Computing and e-Science]] resources at IFCA. This cluster is formed by several identical Scientific Linux 5 hosts, that can be reached through a single entry point. The connections to the internal machines are managed by a director node that tries to ensure that proper balancing is made across the available nodes at a given moment. Nevertheless, direct access to a particular node can be obtained. Please note that this cluster is not intended for the execution of CPU intensive tasks, for this purpose use any of the available computing resources. |
Please note that this cluster is ''not intended for the execution of CPU intensive tasks'', for this purpose use any of the available computing resources. Every process spawned are limited to a maximum CPU time of 2 hours. |
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| {{{#!wiki warning '''Direct node access''' |
== Authentication == |
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| Note that even though is possible to bypass the director accessing a node directly this is ''not recommended nor advisable''. Fair usage of the resources and proper balancing of the connections cannot be guaranteed if any user commits any abuse of this feature. Please note also that the GRIDUI machines have exactly the same hardware and software. }}} {{{#!wiki warning '''Scientific Linux 4 cluster''' Note that from 3rd November 2010 no Scientific Linux Cern 4 version is available. }}} {{{#!rhtml <table border="1" cellpadding="2" cellspacing="0" align="center"> <tr align=center bgcolor=#A0A0A0><td>Hostname</td><td>Port</td><td>Gives access to</td><td>Distribution and Architecture</td></tr> <tr> <td><strong>gridui.ifca.es</strong></td> <td rowspan="2">22, 22000</td> <td rowspan="2">Balanced GRIDUI Cluster</td> <td rowspan="2" align="center">Scientific Linux CERN SLC release 5.5 (Boron), x86_64</td> </tr> <tr> <td><strong>griduisl5.ifca.es</strong></td> </tr> <tr> <td><strong>gridui.ifca.es</strong></td> <td rowspan="2">22001</td> <td rowspan="2">gridui01.ifca.es</td> <td rowspan="2" align="center">Scientific Linux CERN SLC release 5.5 (Boron), x86_64</td> </tr> <tr> <td><strong>griduisl5.ifca.es</strong></td> </tr> <tr> <td><strong>gridui.ifca.es</strong></td> <td rowspan="2">22002</td> <td rowspan="2">gridui02.ifca.es</td> <td rowspan="2" align="center">Scientific Linux CERN SLC release 5.5 (Boron), x86_64</td> </tr> <tr> <td><strong>griduisl5.ifca.es</strong></td> </tr> <tr> <td><strong>gridui.ifca.es</strong></td> <td rowspan="2">22003</td> <td rowspan="2">gridui03.ifca.es</td> <td rowspan="2" align="center">Scientific Linux CERN SLC release 5.5 (Boron), x86_64</td> </tr> <tr> <td><strong>griduisl5.ifca.es</strong></td> </tr> <tr> <td><strong>gridui.ifca.es</strong></td> <td rowspan="2">22004</td> <td rowspan="2">gridui04.ifca.es</td> <td rowspan="2" align="center">Scientific Linux CERN SLC release 5.5 (Boron), x86_64</td> </tr> <tr> <td><strong>griduisl5.ifca.es</strong></td> </tr> <tr> <td><strong>gridui.ifca.es</strong></td> <td rowspan="2">22005</td> <td rowspan="2">gridui05.ifca.es</td> <td rowspan="2" align="center">Scientific Linux CERN SLC release 5.5 (Boron), x86_64</td> </tr> <tr> <td><strong>griduisl5.ifca.es</strong></td> </tr> <tr> <td><strong>gridui.ifca.es</strong></td> <td rowspan="2">22006</td> <td rowspan="2">gridui06.ifca.es</td> <td rowspan="2" align="center">Scientific Linux CERN SLC release 5.5 (Boron), x86_64</td> </tr> <tr> <td><strong>griduisl5.ifca.es</strong></td> </tr> </table> }}} == Authentication == Authentication is centralized via secured LDAP. All the changes made to a user account in one node take immediate effect in the whole cluster. There is also a secured web interface, that allows a user to change his/her details, available at https://cerbero.ifca.es/. If you need to reset your account password, please contact the system administrators. With this username you should be able to access also the ticketing system at http://support.ifca.es/ |
See [[Cluster/SSO]]. |
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| As the cluster is based on several Grid User Interfaces it allows users to access either EGEE-III, int.eu.grid, [[http://www.euforia-project.eu/EUFORIA/|EUFORIA]], [[https://web.lip.pt/wiki-IBERGRID/|IBERGRID]] and [[http://grid.csic.es|GRID-CSIC]] infrastructures. To set up the correct environment variables, please `source` any of the environment scripts located under `/gpfs/csic_projects/grid/etc/env/`. For example, to use the I2G infrastructure: | As the several virtual organizations supported use its own set of resources, it is commonly required to set up the correct environment variables in order to use the grid tools. Environment scripts are located under `/nfs4/usr/etc/env/`: |
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| $ source /gpfs/csic_projects/grid/etc/env/i2g-env.sh | $ source /nfs4/usr/etc/env/ibergrid-env.sh |
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| The available enviroments are: {{{#!rhtml <table border="1" cellpadding="2" cellspacing="0" align="center"> <tr align=center bgcolor=#A0A0A0> <td>Filename</td> <td>Allows access to</td> </tr> <tr> <td>euforia-env.{csh,sh}</td> <td>EUFORIA</td> </tr> <tr> <td>ibergrid-env.{csh,sh}</td> <td>IBERGRID and EGI</td> </tr> <tr> <td>ngi-env.{csh,sh}</td> <td>EGI and IBERGRID NGI</td> </tr> </table> }}} More information on seting up the Grid UI is available locally at the [[DUS: Setting up the User Interface account|corresponding DUS page]]. == PBS Cluster == PBS cluster was '''decommissioned''' in December 2009. Please use the new [[#SGE_Cluster|SGE Cluster]] instead. |
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| Local submission is allowed for certain projects. As stated below, there are some shared areas that can be accessed from the computing nodes. The underlying batch system is [[http://wikis.sun.com/display/GridEngine|Sun Grid Engine]] 6.2u5. Please note that the syntax for job submission (`qsub`) and monitoring (`qstat`) is similar to the one you might be accustomed to from PBS, but there are important differences. Refer to the following sources for information: | Local submission is allowed for certain projects. As stated below, there are some shared areas that can be accessed from the computing nodes. The underlying batch system is [[https://arc.liv.ac.uk/trac/SGE|Son of Grid Engine]] 8.0.0d. Refer to the following sources for information: |
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| * Using Grid Engine [[http://wikis.sun.com/display/GridEngine/Using+Sun+Grid+Engine|official documentation]]. | * Using [[/GridEngine]]. |
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| * SGE [[http://arc.liv.ac.uk/SGE/howto/basic_usage.html|basic usage]]. | * SGE [[http://grid.ifca.es/wiki/Cluster/SGE/howto/basic_usage.html|basic usage]]. |
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| For the shake of clarity, in the following examples we will only show the options relevant to that example. However, you should take into account that there are some options that are mandatory (for example, the project submission). | {{{#!wiki important '''IFCA Gridengine documentation has moved''' |
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| === Job submission and projects === Users should submit their jobs directly to their project by using `qsub -P <project>`. {{{#!highlight console numbers=disable $ qsub -P <project> <jobfile> }}} {{{#!wiki warning '''Job submission witout project''' '''Job submission without specifying a project is not allowed'''. Although you should already know to which project you should submit, you can check the list of projects you are allowed to use by issuing `/gpfs/csic_projects/utils/bin/rep-sge-prjs.py`. However, you should contact your supervisor if you are unsure about your project. }}} A scratch area is defined for every job as the environment variable `$TMPDIR`. This area is cleared after the job has exited. === Specifying resources === In order to get your submitted jobs executed fast, you should tweak some of the resouces that your job is requested. The more accurate you are to your job bounds, the faster your job will run (the default values are quite high in order to prevent jobs to be killed by the batch system, thus they penalize a lot the job execution). Some of these limits are defined in the `$SGE_ROOT/default/common/sge_request` file. If your application is always expected to use the same values, you can override that file by creating a `$HOME/.sge_request` file. For further details, please check the `sge_request` manual page. ==== Wall Clock time ==== A default wall clock time of 72 hours is enforced by default in all jobs submitted to the cluster. Should you require a higher value, please set it by yourself by requesting a new `h_rt` value in the form `hours:minutes:seconds`. Please note that requesting a high value may impact negatively in your job scheduling and execution. Please try to be as accurate as possible when setting this required value. For example, a job requiring 22h, with a couple of "safety" one extra hours should be sent as follows: {{{#!highlight console numbers=disable $ qsub -l h_rt=24:00:00 <jobfile> }}} ==== Memory management ==== When requesting memory for a job you must take into account that per-job memory is limited in the default queues to a [[http://en.wikipedia.org/wiki/Resident_set_size|Resident Set Size]] (h_rss) of 5 GB. If you need to use more memory, you should request the special resource `highmem`. Please notice that your group may not be able to request that flag by default. If you need to do so, please [[http://grid.ifca.es/wiki/Cluster/Usage#Support|open a ticket]] requesting it. Also, notice that these nodes might be overloaded by other users requesting the same flag, so use it wisely. It is '''highly recommended''' that you tune your memory requirements to some realistic values. Special emphasis is made in the following resources: * `h_rss` * `mem_free` ===== h_rss ===== This limit refers to the '''hard resident set size limit'''. The batch system will make sure a given job does not consume more memory than the value assigned to that variable. This means that '''any job above the requested `h_rss` limit will be killed (SIGKILL) by the batch system'''. It is recommended to request this resource as a top limit for your application. If you expect your job to consume no more than a peak value of 3GB you should request those 3GB as its resident set size limit. This request '''shall not produce a penalty''' on the scheduling of your jobs. ===== mem_free ===== This refers to the free RAM necessary for the job to run. The batch system will allow jobs to run only if sufficient memory (as requested by `mem_free`) is available for them on a given node. It will subtract that amount of memory from the available resources, once the job is running. This ensures that a node with 16 GB of memory will not run jobs totalling more than 16 GB. The default value is 1.8 GB per slot. Please note that breaking the `mem_free` limit will not automatically kill your job. Its aim is just to try to ensure that your job has available the memory you requested. Also note that this value is not intended to be use to reflect the memory peaks of your job. This request will impact the scheduling of your jobs, so it is highly recommended to tune it to fit your actual application memory usage. ===== Memory usage above 5G ===== For serial jobs requiring more than 5 GB of memory, submission requesting the '''''highmem''''' flag is necessary. Using this flag, the `h_rss` limit will be unset, but the requirement tuning described above still applies. If your group is allowed to request it, and your job needs 20GB of memory, you can request it as follows: {{{#!highlight console numbers=disable $ qsub -l highmem,mem_free=20G <jobfile> }}} * A job that might reach 30 GB and needs 20GB will be submitted as: {{{#!highlight console numbers=disable $ qsub -l highmem,h_rss=30G,mem_free=20G <jobfile> }}} For jobs needing more than these 5G using MPI, please refer to the [[#Parallel_jobs|Parallel job submission]] section. ===== Examples ===== * A job that needs to have 4 GB of memory assigned to it: {{{#!highlight console numbers=disable $ qsub -l mem_free=4G <jobfile> }}} * A job that might peak at 4 GB, but in its execution normally needs 3 GB: {{{#!highlight console numbers=disable $ qsub -l h_rss=4G,mem_free=3G <jobfile> }}} * A job that might reach 4 GB, and also needs 4 GB: {{{#!highlight console numbers=disable $ qsub -l h_rss=4G,mem_free=4G <jobfile> }}} ==== Infiniband ==== If you are executing MPI parallel jobs you may benefit from the Infiniband interconnection available on the nodes. In order to do so, you must request the special resource `infiniband`: {{{#!highlight console numbers=disable $ qsub -l infiniband <jobfile> }}} ##==== Scratch space ==== ## ##The scratch area for the jobs submitted to the cluster is located under `/tmp/` and is pointed by the `$TMPDIR` variable. ## ##By default, jobs request a 2GB scratch area. Should you need more space, please use the `scract_space` in your resource requiremens: ## ## $ qsub -l scratch_space=20G ## ##Please note that this space is dynamic. To check the current disk usage in the nodes you can issue: ## ## $ qhost -F scratch_space ##--> === Parallel jobs === Parallel jobs can be submitted to the parallel environment `mpi`, specifying the number of slots required. SGE will try to spread them over the available resources. {{{#!highlight console numbers=disable $ qsub -pe mpi 8 <jobfile> }}} Please note that parallel jobs will be routed to queue ''parallel'' (see [[#Memory_management|previous section]]). Also note that access to that queue is restricted to groups having requested it beforehand. The following parallel environments are available: {{{#!rhtml <table border="1" cellpadding="2" cellspacing="0" align="center"> <tr align=center bgcolor=#A0A0A0> <td>PE Name</td> <td>Node distribution</td> </tr> <tr> <td>smp</td> <td>All slots in just 1 node</td> </tr> <tr> <td>mpi</td> <td>All slots spread across available nodes.</td> </tr> <tr> <td>8mpi</td> <td>All slots spread across available nodes, 8 slots on each node. The number of slots requested must be multiple of 8.</td> </tr> </table> |
The specific documentation for IFCA has been moved [[/GridEngine|to a separate section]]. |
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| === Interactive jobs === Interactive, short lived and high priority jobs can be sent if your project has permission to do so (see the `qsub` and `qrsh`manual pages). This kind of jobs can only request a '''maximum of 1h of WALL clock time'''. === Pseudo-Interactive jobs === A special resource, called `immediate` is available for some users, that need fast scheduling for their short-lived batch jobs. This kind of jobs can only request a '''maximum of 1h of WALL clock time'''. {{{#!highlight console numbers=disable $ qsub -l immediate <jobfile> }}} Please note that you might not have access to these resources. === Resource quotas === Some limits may be enforced by the administrators in a user/group/project basis. To check the current resource quotas, the following command must be issued: {{{#!highlight console numbers=disable $ qconf -srqs }}} In order to know the current usage of the quotas defined above, the comand `qquota` must be used: {{{#!highlight console numbers=disable $ qquota -P <project> }}} === Advanced reservation === Some users and/or projects might request a reservation of a set of resources in advance. This is called an "Advanced Reservation (AR). If your project needs such a reservation you should make a petition using the [[http://support.ifca.es/|support helpdesk]]. You need to specify the following: * Start datetime, and end datetime (or duration) of the reservation. * Duration of your job(s) (i.e. `h_rt` for the individual jobs). * Computational resources needed (mem_free, number of slots). Once the request has been made, the system administrators will give you the ID(s) of the AR created. You can submit your jobs whenever you want by issuing: {{{#!highlight console numbers=disable $ qsub -ar <reservation_id> <other_job_options> }}} You can submit your job(s) before the AR starts and also once it is started. However, you should take care of the duration of the reservation and your job' duration. If your job execution exceeds either the `h_rt` that it has requested or the duration of the AR it will be killed by the batch system. You should also take into account that your reservation might not be created in the date and time that you requested if there are no resources available. In this case, it will be created whenever it is possible. To avoid this, please request your reservations well in advance. Since the requested and reserved resources cannot be used for other jobs, those requested resources will be used for accounting purposes as if they were resources used by normal jobs (even in the case that the AR is unused). '''Please request only the resources that you need'''. If you want to query the existing advance reservations, you can use the `qrstat` command. To query about an specific advance reservation, you can issue: {{{#!highlight console numbers=disable $ qrstat -ar ''<reservation_id>'' }}} |
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| If you wish to check your quota at a later time, you can use the commands `mmlsquota gpfs_csic` (for user quotas) and `mmlsquota -g `id -g` gpfs_projects` (for group quotas). A script reporting both quotas is located on `/gpfs/csic_projects/utils/bin/rep-user-quotas.py`. A sample output of the latter could be: | If you wish to check your quota at a later time, you can use the commands `mmlsquota gpfs_csic` (for user quotas) and `mmlsquota -g `id -g` gpfs_projects` (for group quotas). A script reporting both quotas is located on `/nfs4/usr/bin/rep-user-quotas.py`. A sample output of the latter could be: |
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| == Extra utils == Some extra packages as [[http://python.org|Python 2.6]] and [[http://software.intel.com/en-us/articles/non-commercial-software-development/|Intel Non-Commercial Compilers]] can be found on `/gpfs/csic_projects/utils/`. |
== Extra utils/Software == Some extra packages as latest [[http://python.org|Python]] versions and [[http://software.intel.com/en-us/articles/non-commercial-software-development/|Intel Non-Commercial Compilers]] can be found at `/nfs4/opt/`. Here also is the preferred location for some other piece of software commonly used like: * Matlab's like `octave` language for numerical anaylisis. * Data plotting `gnuplot` program. * Profiling and debugging `valgrind` tools. |
IFCA Datacenter usage guidelines
Contents
If you find any information that is out-dated, incorrect or incomplete, do not hesitate to Open a ticket.
1. Introduction
The GridUI (Grid User Interface) cluster is the interactive gateway to the Advanced Computing and e-Science resources at IFCA. This cluster is comprised of a pool of Scientific Linux machines reachable through a single entry point. The connections to the internal machines are managed by a director node that tries to ensure that proper balancing is made across the available nodes at a given moment.
Please note that this cluster is not intended for the execution of CPU intensive tasks, for this purpose use any of the available computing resources. Every process spawned are limited to a maximum CPU time of 2 hours.
Login on these machines is provided via Secure Shell. The RSA key fingerprint of them is 46:85:91:c1:eb:61:55:34:25:2c:d6:0a:08:22:1f:77.
Outgoing SSH connections are not allowed by default from this cluster. Inactive SSH sessions will be closed after 12h.
2. Authentication
See Cluster/SSO.
3. Grid resources
As the several virtual organizations supported use its own set of resources, it is commonly required to set up the correct environment variables in order to use the grid tools. Environment scripts are located under /nfs4/usr/etc/env/:
$ source /nfs4/usr/etc/env/ibergrid-env.sh
4. SGE Cluster
The SGE Cluster is based on Scientific Linux CERN SLC release 5.5 machines, running on x86_64. The exact number or resources available is shown on the monitorization page.
Local submission is allowed for certain projects. As stated below, there are some shared areas that can be accessed from the computing nodes. The underlying batch system is Son of Grid Engine 8.0.0d. Refer to the following sources for information:
Using /GridEngine.
Some useful HOWTOS.
SGE basic usage.
IFCA Gridengine documentation has moved
The specific documentation for IFCA has been moved to a separate section.
5. Shared areas
The $HOME directories (/home/$USER) are shared between the UIs and the computing nodes. There is a projects shared area (located at /gpfs/csic_projects/), also accessible from the UI and the computing nodes. If your group does not have this area, please open an Incidence ticket.
5.1. Usage
The shared directories are not intended for scratch, use the temporal areas of the local filesystems instead. In other words, instruct every job you send to copy the input from the shared directory to the local scratch ($TMPDIR), execute all operations there, then copy the output back to some shared area where you will be able to retrieve it comfortably from the UI.
As mentioned above, the contents of $TMPDIR are removed after job execution.
5.2. Disk quotas
Disk quotas are enabled on both user and projects filesystems. A message with this information should be shown upon login. If you need more quota on your user space (not in the project shared area), please contact the system administrators explaining your reasons.
If you wish to check your quota at a later time, you can use the commands mmlsquota gpfs_csic (for user quotas) and mmlsquota -g id -g gpfs_projects (for group quotas). A script reporting both quotas is located on /nfs4/usr/bin/rep-user-quotas.py. A sample output of the latter could be:
**********************************************************************
INFORMATION ABOUT YOUR CURRENT DISK USAGE
USER Used Soft Hard Doubt Grace
Space (GB): 3.41 20.00 0.00 0.06 none
Files (x1000): 64 0 0 0 none
GROUP Used Soft Hard Doubt Grace
Space (GB): 0.00 1000.00 1500.00 0.00 none
Files (x1000): 0 0 0 0 none
**********************************************************************For a basic interpretation of this output, note that the "Used" column will tell you about how much disk space you are using, whereas "Soft" denotes the limit this "Used" amount should not exceed. The "Hard" column is the value of the limit "Used" plus "Doubt" should not cross. A healthy disk space management would require that you periodically delete unused files in your $HOME directory, keeping its usage below the limits at all times. In the event that the user exceeds a limit, a grace period will be shown in the "Grace" column. If the user does not correct the situation within the grace period, she will be banned from writing to the disk.
For further information you can read the mmlsquota command manual page.
6. Extra utils/Software
Some extra packages as latest Python versions and Intel Non-Commercial Compilers can be found at /nfs4/opt/. Here also is the preferred location for some other piece of software commonly used like:
Matlab's like octave language for numerical anaylisis.
Data plotting gnuplot program.
Profiling and debugging valgrind tools.
Please note that these packages are provided as-is, without further support from IFCA staff.
7. Support
Before opening a new incidence, please check the Frequently Asked Questions page
Questions, support and/or feedback should be directed through the use the Helpdesk.