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1. FAQ C NITS COMPUT AD gt X lt C CANTS Subject FAQ ndice de contenidos MEE e E A E E A E T E A E T 3 1 Whatiis COMPUTAEX sirsie seini ES AAA a aAa Ea a Eaa A sender 3 1 2What is C nitS 1 3Whatiis LUSITANIA iist a icavinesiedasudin tapai nas erand ae EA Tai aa a aE aee EESE 3 1 4Which are the goals of the Foundation COMPUTAEX GMG Gw sssssnseseseneeserene nere nerne reen renee nere renerne renere renerne enes 3 1 5What is a supercomp ut RS 2 LEE ED EET EDER ED acs dnicdegsdedeicisaeuncenvievh re A EE 3 1 6What is parallel computing oncnininnonnnsainaninn a a a are eden ellers 4 1 7Why p rallelj26 ipsnitnnunnnran m R i N ER nR R 4 1 8What is Shared MEMON menangna pnie A A T E 4 FOWhat isa gu SU ES SEE EU ERE a a aAa ara daana rE aa aa E Ea A R 4 1 410 What is a queue manager 2 rear Ea EEN havi E R 4 TA What is MPI SEE Ea ES Ea DEDE aiaia aa ise aaa ir a a iaae adia a Ea 5 112 What is OpenMP Z sa oe n a a A Ai ease ed 5 1 13How can i use LUSITANIA supercomputer resources 1 14What services does C nitS offer oe eee eesseeseesessecseeeeeseceeeeeeeeesaecaeenecseeseesaeeaeeaeesesaesseeaeeaesaesaesseseeseeeeaeeseaeeseeeeeae 5 1 15What is an example of computing capacity offered by LUSITANIA ee eeeeceeceeceeeeeseeneeeeeeeeeeeeeeeeetaeteeteeeneeeeneeeae 6 1 16What could compare LUSITANIA storage Capacity With eceeeesseeseeseeneceeeeeeeeseeeeaeeaesaeeeeseeteeeeeeeaeseteeeneeeeneeeeea2. 6 2 D E E E daneaweaude danas tenses BE ERE IEEE ERE seauwaayed E A A 7 2 1How do I stop a job in a queue manager isis ccsiccs ccccescdiccscesesacceesascnaeseesacesccscdsdenstesd szaussacsanesecngeeacsscvaseeiensdaeesiiavensaces 7 2 2How can view the output of a job that is rUNNING 0 eee eee seeeeeeeeceeeeeeeseeaeeeeeeeeeeeeeeeaeeaesaesaeeeseeseeeeaesaesaeeaesieeeeeeeaees 7 2 3Set environment variables for Intel Fortran Compiler 10 1 ccceseeeceeeeeeeeeeeeeseeeeeeeeceeeeeeeaesaeeaeeeeeseaeeeeaeeeneeeeeaees 7 2 4My software has defined storage requirements How can I request this Storage ceceseseteeeeeeeeeeeeeeeeeeeeneeeaees 7 2 51 filled out the resources request form and am making use of the supercomputer but need more storage than asked Winet SMOUIG dO anane aaa A Aa aR E ERA A A a Cen SE DENE NAR KOS KEN Aa TASG 7 2 6My jobs demand lots of I O operations Is there any type of storage to meet this NEC eee eeeeeeeeeeeeeteneeeeees 8 2 INNY doesnt my JOD HUN seen cnc ned ste Seere sa Ene ens ad Ones Ea ia adaa a eia rA AAE Tanaro R a e da AERA 8 2 8How can know what the job resources use ALO eeeeeceeeeseeeeeneeeeeeeeeseeaeeaeeaeeeeeeeeaecaeeaetaesaeseeseeeeeesaesaesaeeeeeeeseatensees 8 2 91 need to upload my source code to LUSITANIA supercomputer How must i proceed sssseerreersrerreree 8 2 10When connecting LUSITANIA a server authenticity message is shown What should d0 sssesceeseceeeecee 8 2
3. for platforms ranging from desktops to supercomputers In LUSITANIA supercomputer platform this API has the entire potential of the compute nodes since they are characterized by their large volume of shared memory 1 13 How can i use LUSITANIA supercomputer resources To make use of LUSITANIA supercomputer resources it must be filled the request resource form After reviewing your request C nitS will provide the neccesary information to access and use LUSITANIA supercomputer 1 14 What services does C nitS offer C nitS provides the infrastructure resources and technical support to carry out scientific technical and business projects where required High performance computing HPC o Shared memory system for high performance Large storage capacity o High availability http www mcs anl gov research projects mpi http openmp org wp Shttp www cenits es en formularios resource request form Pag 5 CENTS Subject FAQ o For critical applications o Backups Infrastructure and service settings o Requirements definition design and implementation o Definition of quality parameters QoS bandwidth fault tolerance o Definition and implementation of security policies Vulnerability Analysis DDefinition of firewall rules Consulting o Code parallelization o Simulation Emulation o Optimization o Cloud Grid Training Cooperation agreements Support for research develop
4. to other processes using the same shared memory 1 9 What is a queue A queue is a particular kind of collection in which the entities in the collection are kept and processed in incoming order The queue configuration priority resources runtime is applied to the entities in the collection 1 10 What is a queue manager A queue manager is a management system to plan and control task executions in the collection to optimize resources to minimize costs and maximize applications performance Pag 4 CENTS Subject FAQ 1 11 What is MPI MPI Message Passing Interface is a standard that defines the syntax and semantics of the functions contained in a message passing library designed to use it in programs that exploit the existence of multiple processors Message passing is a technique used in concurrent programming to provide synchronization between processes and to allow mutual exclusion Its main feature is that it does not require shared memory so it is very important in distributed systems programming In LUSITANIA supercomputer platform it can be used when a job runs on more than one node 1 12 What is OpenMP OpenMP Open Multi Processing is an application programming interface API for shared memory multiprocessing programming in multiple platforms It could also be defined as a portable and scalable programming model that gives developers a simple and flexible interface to develope parallel applications
5. tools for sustainable socioeconomic development encouraging the participation of civil society mobilising their resources and paying special attention to co operation between public and private research centres and the productive sector The Foundation s main objective is to create operate and manage the Supercomputing Centre of Extremadura 1 5 What is a supercomputer It is a computer with calculation capabilities far superior to the common depending on the season Today s supercomputers tend to become tomorrow s ordinary computers Pag 3 CENTS Subject FAQ 1 6 What is parallel computing Parallel computing is a form of computation in which many resources are carried out simultaneously to solve a problem Running on a computer with multiple CPUs The problem is divided into separate parts e Each part is running simultaneously 1 7 Why parallelize e Results are obtained in less time wall clock time e It is a solution to large complex problems It allows parametric scanning Study of different variants of the problem e Current processors are of n cores 1 8 What is shared memory Shared memory is one of the mechanisms listed under the name of Inter Process Comunication IPC along with semaphores and message queues FIFO Using shared memory as its name suggests we can create shared memory areas by several processes Thus process changes made to the values stored in shared memory are visible
6. 111 am experiencing performance issues in my job What is the problem s sssssissesssisiesisisinisieisiersinrieisinererinnres 9 P g 2 CENTS Subject FAQ 1 General 1 1 What is COMPUTAEX It is the Computing and Advanced Technologies Foundation of Extremadura hereafter referred to COMPUTAEX and willingly of the Junta de Extremadura as founding institution was established as an organization in nature non profit foundation Recorded in the Register of Foundations of Extremadura has legal personality and full capacity to act and can make therefore all necessary acts to fulfill the aims for which it was created 1 2 What is C nitS C nitS is the Extremadura Supercomputing Technological Innovation and Research Center aimed to promote and disseminate hpc services and advanced communications to the researcher communities of Extremadura or that company or institution that requests it and thus contribute through technological improvement and innovation improving the competitiveness of enterprises 1 3 What is LUSITANIA LUSITANIA is the name given to the supercomputer that C nitS houses whose distinguishing feature is its shared memory You can see all the technical features in detail in LUSITANIA technical features section 1 4 Which are the goals of the Foundation COMPUTAEX The Foundation s aim is to promote the development of information technologies the use of intensive computing and advanced communications as
7. are using message passing in a single node when it would be better shared memory Inappropriate storage use If high performance storage at scratch is not used you can experience an I O performance decrease Inappropriate network communication use If processes are running on both nodes and communications are needed between them ensure you have not specified the name of the nodes as cn001 and cn002 By default it uses the computing network so it is not necessary to indicate the nodes name to run in If needed it must be specify the name as cncp001 and cncp002 After checking the above if problems persist please contact the C nitS technical team Pag 9
8. following command e bjobs a W lt id trabajo gt The information displayed will refer to the name of the project cpu use memory swap the job s PID job start end time 2 9 I need to upload my source code to LUSITANIA supercomputer How must i proceed See section 2 4 of the user manual which details the process of uploading files 2 10 When connecting LUSITANIA a server authenticity message is shown What should I do Server authenticity message The authenticity of host ssh cenits es 193 144 255 13 can t be established RSA key fingerprint is fa 83 85 6c 88 2a 6b 31 74 7 8 39 98 a3 75 f0 Are you sure you want to continue connecting yes no This message is displayed the first time you try to connect to a ssh server Also it will be shown later if you delete the known_hosts file from your computer Pag 8 Cents Subject FAQ This message indicates that the public key of the server you are trying to access is not known and you are asked to trust the server It should be accepted to login 2 11 am experiencing performance issues in my job What is the problem Performance issues can be for different reasons e Misuse of the queue manager When the job is launched it must be specify the number of processes the job must use if the number is incorrect it can affect job performance and the other users too Improper implementation and processes execution on nodes For example it is possible that you
9. job If id job is skipped it will display the information on the lasted job 2 3 Set environment variables for Intel Fortran compiler 10 1 To work with the particular version of a compiler such as Fortran 10 1 you must set their environment variable running the following script opt intel fc 10 1 025 bin ifortvars sh 2 4 My software has defined storage requirements How can I request this storage The resources request form includes a section about resources for storage applications required by users 2 5 I filled out the resources request form and am making use of the supercomputer but I need more storage than asked What should do To request extra storage contact C nitS technical team by email solicitudes cenits es Pag 7 CENTS Subject FAQ 2 6 My jobs demand lots of I O operations Is there any type of storage to meet this need The two compute nodes have a scratch partition mounted on scratch to meet the high demand for I O in execution time for users jobs 2 7 Why doesn t my job run This may be because the resources are not yet available to run your job Check the status of the run queue with the following command bqueues The information displayed will refer to the total number of jobs submitted to the queue how many of them are running pending and were suspended 2 8 How can I know what the job resources use are To know job resources used check the state of it with the
10. ment and technological innovation If you want to request resources from our centre Resource request 1 15 What is an example of computing capacity offered by LUSITANIA LUSITANIA supercomputer has a maximum power calculating peak of 1850 GigaFLOPS The FLOPS Floating point Operations Per Second is used as a measure of computer performance especially in scientific calculations that require heavy use of floating point operations 1 16 What could compare LUSITANIA storage capacity with Supercomputer LUSITANIA storage capacity available could be divided into 2 TB of main memory e 276 68 TB of secundary memory in hard disks storage 11 68 for scratch 392 TB of secundary memory in tape storage It could be storage around a million and a half copies of Don Quixote and 435 dvd information in main memory It could be storage around 182 millions copies of Don Quixote and 60 280 dvd information in disk storage It could be storage around 257 millions copies of Don Quixote and 85 405 dvd information in tape storage http www cenits es en cenits resource request Pag 6 CENTS Subject FAQ 2 User 2 1 How do I stop a job in a queue manager If you want to stop a job because of an error or any other reason run the following command e bkill id job 2 2 How can I view the output of a job that is running The running job output can only be view with the next queue manager command e bpeek id
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