National Supercomputer Center in Tianjin - Acad · National SuperComputer Center in TianJin TH-1A...

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1 National Supercomputer Center in Tianjin TH-1A System Manual June, 2011

Transcript of National Supercomputer Center in Tianjin - Acad · National SuperComputer Center in TianJin TH-1A...

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National Supercomputer Center in Tianjin

TH-1A System Manual

June, 2011

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Contents

1 TH-1A System Environment ............................................................................................................. 1

1.1 Hardware................................................................................................................................. 1

1.1.1 Login node ................................................................................................................... 1

1.1.2 Computing nodes [0-7167] .......................................................................................... 1

1.1.3 Interconnection System................................................................................................ 1

1.2 System environment................................................................................................................ 2

1.3 Compiling environment .......................................................................................................... 2

1.3.1 Intel compiler ............................................................................................................... 2

1.3.2 GCC compiler .............................................................................................................. 4

1.3.3 mpi compiler environment........................................................................................... 4

1.3.4 CUDA compiler environment..................................................................................... 5

1.3.5 Other compilation (Python etc)................................................................................... 5

2 TH-1A Usage ..................................................................................................................................... 6

2.1 Requirements .......................................................................................................................... 6

2.2 Login and transfer data ........................................................................................................... 6

2.2.1 Login VPN ................................................................................................................... 6

2.2.2 Login the server ......................................................................................................... 12

2.2.3 File Transfer............................................................................................................... 14

2.3 Environment variables setting............................................................................................... 15

2.4 Exit system............................................................................................................................ 16

2.5 Change account and password .............................................................................................. 16

3 Job submission ................................................................................................................................. 16

3.1 Usage limitation .................................................................................................................... 17

3.2 Commands for viewing status............................................................................................... 18

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3.2.1 yhinfo or yhi (Viewing node).................................................................................... 18

3.2.2 yhqueue(viewing job status) ...................................................................................... 18

3.3 Job submission ...................................................................................................................... 19

3.3.1 Interactive submission (yhrun)................................................................................... 19

3.3.2 Batch submission ( yhbatch)............................................................................................... 23

3.3.3 Distributive submission ( yhalloc) .............................................................................. 25

3.4 Job aborted ( yhcancel) .......................................................................................................... 26

Appendix A Common command of Unix............................................................................................ 29

A1 Basic commands .............................................................................................................. 29

A2 Directory operation .............................................................................................................. 29

A3 Create, copy and delete file.................................................................................................. 29

A4 File attributes........................................................................................................................ 29

A5 show and link ....................................................................................................................... 30

A6 Find and compare file........................................................................................................... 30

A7 Compresion and backup....................................................................................................... 30

A8 Redirection of I/O ................................................................................................................ 30

Appendix B Common command for vi .............................................................................................. 31

B1 Enter and exit vi ................................................................................................................... 31

B2 Move the cursor.................................................................................................................... 31

B3 Input, delete, substitution, restoration and find .................................................................... 31

B4 Edit line ................................................................................................................................ 32

Appendix C Common commands for GDB......................................................................................... 33

C1 Initiate gdb............................................................................................................................ 33

Quit gdb ...................................................................................................................................... 33

Control execution of program..................................................................................................... 33

Break point and watch point ....................................................................................................... 33

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Stack............................................................................................................................................ 34

Data display ................................................................................................................................ 34

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1 TH-1A System Environment

1.1 Hardware

TH-1A public system is composed of 7168 computing nodes, 3 login nodes and store nodes. All nodes and I/O nodes are connected by “Tianhe high-speed interconnection network”.

Computing nodes: two Intel Xeon X5670 CPUs (total 12 cores) and one Tesla M2050 GPU with 3GB GDDR5 memory on board.

Three login nodes: 8-way 8cores SMP server (total 64 cores).

1.1.1 Login node

LN1-3 login nodes are mainly used for login, program development and submission. LN1-3 is composed as follow: 8 Intel Xeon X7550 CPU which is 64 cores and basic frequency 2GB; 256GB memory; 600GB SAS disk capacity.

1.1.2 Computing nodes [0-7167]

Computing nodes are used for executing serial and parallel tasks; every computing node is a multi-core SMP server.

Computing node environment: two Intel Xeon 5670 CPU with frequency 2.93GHz and 24GB memory.

Resources for parallel tasks running on TH-1A are allocated according to cores of CPU, so TH-1A system can support maximum 86016(12*7168) parallel tasks with MPI parallel processes.

1.1.3 Interconnection System

In TH-1A system,all of computing nodes are connected by Tianhe high speed interconnection system which is characteristic of high communication efficiency and low communication latency. It is designed to support communication among parallel tasks and data exchange.

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1.2 System environment

Login nodes are equipped with Kylin version 3.1 operating system with customized secure strategy. In TH-1A system, RedHat Enterprise Linux 5.3 x86_64 is installed on every computation node, abiding by POSIX, LSB, providing development and runtime environment for 64 bits program. User path is /vol-th/home.

1.3 Compiling environment

Two sets of compilation system have been installed on LN1-3 of TH-1A system: Intel compiling system and GCC compiling system. User can choose different compiling system according to objective program. Because TH-1A takes Intel CPU as main CPU, we recommend users to use Intel compiling system.

1.3.1 Intel compiler

Two compilers have been installed on TH-1A, which are v10.1.018 and v11.1. V11.1 is chosen for default compiler. Both compilers support C, C++, Fortran 77 and Fortran 90 program.

Intel compiler v10.1.018 is installed in /opt/intel. This compiler includes three parts: cce (used for C, C++), fce (used for fortran), mkl library (Intel core math library) and parallel version of mkl library( cmkl).

Installation path:/opt/intel/

cce is installed in the directory of /opt/intel/cce/10.1.018, bin of cce directory includes icc (c program compiler), icpc (c++ program compiler); lib of cce directory includes corresponding dynamic link library.

fce is installed in the directory of /opt/intel/fce/10.1.018, bin of fce directory includes ifort (fortran program compiler); lib of fce directory includes corresponding dynamic link library.

mkl library is installed in /opt/intel/mkl/. There are 3 different versions: 10.0.5.025, 10.2.1.017, 10.2.5.035. Each version includes corresponding dynamic link library of 32-bit,64-bit and em64t. User can choose what they want.

Intel compiler v11.1 is installed in /opt/intel/Compiler/11.1/059, all of c, c++ and Fortran 77/90 compilers are installed in /opt/intel/Compiler/11.1/059/bin/intel64/, the command for compilation is icc, icpc and ifort.

In /vol-th/lib, users can find where their lib is. If users need these, it need import environment variables just as follow. Note that TH-1A has import LD_LIBRARY_PATH for users by default.

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export LD_LIBRARY_PATH=/vol-th/lib:$LD_LIBRARY_PATH mkl library of Intel 11.1 is instal led in /opt/intel/Compiler/11.1/059/mkl, users

can use mkl library from lib/em64t. Before using mkl library, users need set corresponding environment variable

(LD_LIBRARY_PATH) just as follow:

export LD_LIBRARY_PATH=/vol-th/lib/mklem64t/:$LD_LIBRARY_PATH Note: 1. Default environment variable (PATH) for users has already included /opt /intel/ Compiler/11.1/059/bin/intel64/, users can directly select icc or icpc or ifort to compile program.

2. LN1-3 as login and compiling nodes, have complete operating system. Considering efficiency of computing nodes, compact operating system is installed on each of them. The dynamic link library must be pointed to vol-th/lib. LD_LIBRARY_PATH has been set to include dynamic link library of intel compiler as default, just as shown:

export LD_LIBRARY_PATH=/vol-th/lib:$LD_LIBRARY_PATH

Common compiling option as shown: (1) Optimization options

-O0: Prohibit optimization -O1: Optimize the code size and code locality. -O2 (default): Optimized code speed (recommended) -O3: -O2+ Radical optimization (loop, storage access conversion, prefetch).

note: -O3 is not applicable for all of programs. -fast: open-O3, -ipo, -static, -no –prec -div and –xP -ipo: Interprocedural Optimization

(2)Output and debugging options -c: Only generate object file -S: Only generate assembly file -g: Debugging options -o <file>: Generated specific output file name

(3) Floating-point option -mp: Maintain floating point precision (prohibit certain optimization) -mp1: Improve floating-point precision. Compared to –mp, -mp1 have less

impact on performance. (4) Link Options

-L<dir>: Specify search path while linking the library -l<string>: Link a specific library -static: Statically linking -shared: Generate the shared library

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1.3.2 GCC compiler

GCC version 4.1.2 is installed on TH-1A. Relevant compilation command can be found in /usr/bin.

Currently, GCC 4.6.1 is installed on TH-1A. The installation path is /vol-th/software/gcc-4.6.1,before using it, users must set as follow:

export PATH=/vol-th/software/gcc-4.6.1/bin:$PATH

1.3.3 mpi compiler environment

Because two sets of compilation system (Intel compiler and gcc compiler) have been installed on TH-1A, there are two different versions of mpi for different users. TH-1A takes proprietary high-speed interconnect network, MPI automatically selects corresponding compilation environment according to Intel and GCC compiler.

Version of mpi based on Intel:

Installation directory is /usr/loca/mpi, to pursue better efficiency, this version uses Intel compiler to compile.

Recommend to use /usr/local/mpi, for which can provide better efficiency.

Version of mpi based on GCC:

There are two versions of mpi based on GCC environment on TH-1A, they are gcc4.1.2 and gcc4.6.1.

GCC 4.1.2 compiler is installed in /usr/local/mpi-gcc, which is suitable for mpi application based on GCC, such as CUDA+MPI, NAMD etc.

GCC 4.6.1 is installed in /usr/local/mpi-gcc46, it is suitable for higher version of mpi application based on GCC.

Parallel mpi compilation notes: 1. There are two compilers of mpi on TH-1A, we recommend mpi from

/usr/local/mpi without specific purpose, this mpi is static library, so users don not need to worry about problems of dynamic link library.

2. If users need to use gcc, users could choose mpi from /usr/local/mpi-gcc or /usr/local/mpi-gcc46 according to special purpose, this mpi is also static library , so users don not need to worry about problems of dynamic link library neither.

3. TH-1A is connected by proprietary high speed interconnection network, also provide MPI service. If users need to use other versions of mpi, such as openmpi1.4.8, mpich2-1.3.1 etc, they can deploy those individually, then use them to compile mpi applications with proprietary high speed interconnection network. However, performance

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will not be satisfactory than MPI which has already been installed on TH-1A. Location of standard head file is automatically included in MPI compilation

commands, and these commands automatically link necessary MPI interface without specifying parameters in command lines for users.

If users use makefile or autoconf to compile MPI parallel applications, set CC, CXX, F77, F90 of makefile to mpicc, mpicxx, mpif77, mpif90, or set CC, CXX, F77 and F90 before conFiguration of autoconf to mpicc, mpicxx, mpif77 and mpif90.

1.3.4 CUDA compiler environment

One M2050 GPU is installed in each computing node, so TH-1A provides CUDA compiler in the LN1-3.

CUDA compiler environment is composed of three parts: compiler, SDK and hardware driver. CUDA has been updated to v4.0 for compiling and driver.

CUDA compiler is installed in /usr/local/cuda. Please select cuda-4.0 as compiler. cuda-4.0 means CUDA4.0 compiler.

Besides V4.0, there are other versions of CUDA compilers; They are earlier CUDA compilers: 3.0, 3.1 and 3.2:

To meet requirements for computing node, corresponding library of compiler need to be copied to shared directory, so directory of /vol-th includes cudalib, namely /vol-th/cudalib includes many corresponding dynamic link library of cuda compiler for users.

CUDA SDK is also deployed in the shared directory, /vol-th/cudasdk

Users could select one of many versions of sdk in this directory to compile program.

Note: Because CUDA has been updated to V4.0,recommend users to select V4.0 and corresponding dynamic link library to compile and run programs.

1.3.5 Other compilation (Python etc)

Currently, other compilers like Python are also installed on TH-1A. The version of python is 2.7 and the path is /vol-th/software/python2.7. If users want to use it, users need to conFigure as follow:

export PATH=/vol-th/sottware/python2.7/bin:$PATH

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2 TH-1A Usage NSCC has adjusted network architecture to protect users’ data, so there are some

necessary measures to follow:

2.1 Requirements

Users need to follow:

1. Fill related files and abide by protocol after NSCC check out users’ requirement. 2. Own an account of VPN (If users do not get it and email shown successfully pass

censor after relevant procedures, please contact + 86-022-65375500 to tell us, we will solve the problem).

3. Own an account and password connecting to TH-1A. (Likewise, if users do not have it, please contact +86-022-65375500).

Now, users can try to connect TH-1A. The procedures and relevant software are stated as follow.

2.2 Login and transfer data

Currently, TH-1A is connected to internet through two ISPs(internet service provider) which are China Unicom and China telecom, users can choose different URL to login VPN according to local ISP.

If you are user of China Unicom, type following URL in your browser

https://vpn.nscc-tj.cn If you are user of China Telecom, type following URL in your browser

https://vpn1.nscc-tj.cn We take users’ operation of china Unicom as example, because all of operation is the

same except URL. If you are user of china telecom, just change https://vpn.nscc-tj.cn to https://vpn1.nscc-tj.cn

2.2.1 Login VPN

For the safety of users’ data, users need to login VPN before using TH-1A. NSCC just allows users to login VPN through browser in order to consider flexibility,

no need to install any client software. We recommend users to use IE browser or some other browsers such as Maxthon, 360 based on IE core.

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VPN procedures as follow: 1. Find “tools” of IE explorer——“Internet options”——“security”—“trusted site” ,

add https://vpn1.nscc-tj.cn” (if you are user of china telecom, replace it with https://vpn1.nscc-tj.cn), shown as follow:

Fig 2-1 trusted site

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Fig 2-2 Add VPN site

2. Click customized “trusted site”, make sure if ActivX is activated, shown as follow:

Fig 2-3 Customization

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Fig 2-4 ActiveX activated or not

3. Access https://vpn1.nscc-tj.cn, user may see following phenomenon, then click yes button.

Fig 2-5 Warning alert 1

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Fig 2-6 Warning alert 2

4. Click red circle, then enter following page:

Fig 2-7 VPN homepage

5. Type your ID, password and verification code, user will see following hint:

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Fig 2-8 Control Installation

6. Please install corresponding controls, then login the page, you will see following page.

Fig 2-9 login the page

As shown above, TCP is resources the users can use. TH-1A provides TH-1A-LN1,

TH-1A-LN2 and TH-1A-LN3 for users to use TCP (marked with red circle). They are three login nodes (LN1-LN3) for users.

Now users have completed VPN login.

VPN login notes:

1. Users can find login button in the upper right corner from our homepage www.nscc-tj.gov.cn, users can also login the vpn from homepage.

2. Allow of operations above is aimed for users of IE or IE core browsers, so we recommend users to use IE browser for convenience. If users tend to use firefox or Chrome which is not developed based on IE core, please these users search and install IE-tab control from internet before login.

3. If users are using some anti-virus software, click or make sure VPN can work normally through software setting.

4. VPN just allows 5 VPN users maximally using one account (only one VPN user from one pc). If user asks for special needs such as more users, please notify us of your

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requirement. Because VPN account allow many users to login ,changing password is forbidden, if users need to change it, contact us and let us change it for you.

5. Users compile and submit tasks with client software after login, do not exit browser or VPN, otherwise connection will be broken.

6. If users do nothing after login 30 minutes, connection will be broken. (If users login with SSH and do nothing, connection will also be broken).

7. Users can exit VPN by click “exit” button on the page, so no need to shut the browser. (There is still 5 minutes for users to use VPN since the browser is shut down, if users do nothing within 5 minutes, the connection will be shut down).

8. If users meet some other problems, please contact us with telephone or email (relevant info is in the appendix).

2.2.2 Login the server

To further ensure the security of users’ data, NSCC prohibits users to use telnet etc, SSH is the only way that users use TH-1A.Users can find many SSH client software from the internet and they are free, such as SSH Secure Shell, Client, SecureCRT, Putty etc.

NSCC provide TCP service for users as shown in Fig 2-9. After successfully login the VPN, the user can see what can be used. TH-1A provides TH-1A-LN0, TH-1A-LN1, TH-1A-LN2 for TCP service.

When login the VPN, fill Host Name with TH-1A-LN0. We will respectively take Secure Shell Client, SecureCRT and Putty as example to show how to login:

SSH Secure Shell Client is shown in Fig 2-10:

Fig 2-10 SSH Secure Shell Client login page

SecureCRT is shown in Fig 2-11:

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Fig 2-11 SecureCRT login page

Putty is shown in Fig 2-12:

Fig 2-12 Putty login page Type corresponding id and its password after login the VPN, users can use TH-1A

through LN0 node.

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User will see following info after login LN0:

1. Welcome to TH-1A System of NSCC-TJ.

2. If you have any problem, you can send mail to [email protected] After this message, users can compile and submit program.

Attention: LN1-3 of TH-1A are login nodes, they are only responsible for login and compilation

and submission for users, other operations are not allowed on LN1-3 by TH-1A. Owing to part of users of TH-1A is also users of TH-1, NSCC set access

permissions that users can login TH-1 through LN2 of TH-1A, it means users can login LN2 of TH-1 through TH-1A-LN2 with the help of SSH. Described as follows:

ssh fengjh@TH-1-LN2 or copy data of TH-1 to TH-1A through scp.

2.2.3 File Transfer

User can upload local files to TH-1A through sftp client software, such as SSH Secure Shell Client etc, shown in Fig 2-13:

Fig 2-13 SSH Secure Shell Client transferring page

Another way is transferring local file through sftp of WinScp (it is free and accessible from internet, it also support breakpoint continuingly), login page is shown in

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Fig 2-14:

Fig 2-14 WinSCP login page

These client software on the top can help users to transfer files. We recommend users to use WinSCP, which have interruption resuming capability.

2.3 Environment variables setting

The setting may be different because of different shell which users use. Suppose we want to add a variable MYENV which represents string “/usr/local/bin”, setting as follows:(Bash is default environment variable of TH-1A)

1) Bash setting export MYENV=/usr/local/bin If users need to automatically set it after login the system, users can add upper

command to file .bashrc (in the folder $HOME). 2) sh setting MYENV=/usr/local/bin export MYENV

If users need to automatically set it after login the system, users can add upper command to file .bash_profile (in the folder $HOME)

3) csh setting

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setenv MYENV /usr/local/bin If users need to automatically set it after login the system, users can add upper

command to file .cshrc (in the folder $HOME)

2.4 Exit system

Execute command “exit” or press “ctrl-d”.

2.5 Change account and password

Currently LDAP has been applied to system to manage users, corresponding directory is created when new user login the LN2 first time. Users can change the password with the command passwd, take user ncps as example:

[ncps@ln2 ~]$ passwd Changing password for user ncps. Enter login(LDAP) password:New password: Re-enter new password: LDAP password information changed for ncps passwd:all authentication tokens updated successfully. Firstly, type the password which NSCC provides for users at the first time, then

type new password and type it again, users will see successful prompt. Special tips: NSCC adopts many measures and a lot of technology to protect data

security of users, however, user itself must assure the password is not compromised and change the password usually (better once every two months).

If users need to change the password of VPN, please contact technical personnel and let us change it for you.

3 Job submission In the TH-1A, serial or parallel programs are run on every computation node, so

there is resources management system to be responsible for job mission. Resources management system constructs a queue which is made up with tasks submitted, then determine where the tasks are allocated according to TH-1A operation status. No need to worry about resources conflict. Certainly user can manage and monitor status of program through resources management system.

However, NSCC confines some operations for higher efficiency, faster response

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and better stability, list as follows:

3.1 Usage limitation

1. Partition restraint

Currently, it is total 3 partitions in TH-1A, as shown in the following table:

Table 3-1 Partition restraint

Restraint Name Implication Most

used Most coresTime for

submission(min) gpu_test GPU test partition 32 384 2*24 TH_NET Common users 256 3072 2*24

TH_NEW Users of long queue 64 768 7*24

Users can see it according users’ user rights, command yhi –l is for checking the corresponding partition information.

PARTITION means disk partition. TIMELIMIT means time limitation of this partition. NODES means the number of nodes. STATE means the status of the current node (Down means inactivation. Idle means node is idle and can be used. Allocated means one or more tasks are run on this node). NODELIST means node-list.

Corresponding user queue can be made in every partition. TH_NET is open to all of users. gpu_test is for testing relevant GPU applications, and single task is only allowed to use 32 nodes maximally, total 384 cores in this partition. If users can not see corresponding resources, that means the user does not have the right to use this partition.

Attention: 1. Due to failure rate sometimes happens on large-scale system, in every partition

NSCC set the limit of running time of one task to protect the stability. We recommend users to set “breakpoint” for program in case the program can be resumed when some unexpected error happens.

If there is no way to resume your program and running time exceeds 2*24 hours, please contact technical personnel.

2. User restraint Beside the partition restraint above, some other user restraint exists. This restraint is

mainly based on contract between NSCC and user, including the maximum number of

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nodes used, the maximum number of cores used, the maximum number of cores single-task uses etc.

While using TH-1A users can apply for more resources which are beyond the contract, NSCC will modify the contract after NSCC censors what user need.

For the consideration of security of users’ data and system, the common user can not link computing nodes through SSH without applying for resources.

3.2 Commands for viewing status

Viewing the usage of resources is recommended before submitting job, because users can choose what should do in the next step. For example, users can use gpu_test partition if just debugging, you can choose corresponding computing nodes based on commands for viewing status.

3.2.1 yhinfo or yhi (Viewing node)

yhi is abbreviated to yhinfo, users can use yhi or yhinfo to check the statue of nodes, then determine what to do after yhi or yhinfo.

The results of yhi:PARTITION means partitions that have the right to be used; TIMELIMIT means time limitation of this partition; NODES means the number of nodes, STATE means the status of the current nodes (down means inactivation, idle means nodes are idle after commence; allocated means one or more tasks are run on those nodes; NODELIST means node-list.

3.2.2 yhqueue(viewing job status)

yhqueue or yhq is used for checking running status of every node, shown in Fig 3-1:

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Fig 3-1 Statue of node

JOBID means job ID; Name means name of the job; USER is user’s name; TIME is elapsed time; NODES is the number of nodes being used; NODELIST is nodes which job is running. JOBID will be used in the command yhcancel.

Users can view jobs which are submitted of one’s own through yhq. Detail of viewing jobs: User can check detail of jobs which have been submitted of one’s own.

yhcontrol show jobs jobid In this command, jobid means id of job which should be inputted according to

users’ demands. The detailed info will be listed after this command.

3.3 Job submission

Currently, there are three submission ways: interactive submission (yhrun), batch submission (yhbatch) and distributive submission (yhalloc). Terminate job through yhcancel; get jobid through yhq as described above.

To simplify operation and be convenient for users, relevant commands are only introduced simply in the manual. Users can type “—help” after the command to get more info.

3.3.1 Interactive submission (yhrun)

There are two steps for running job: resources allocation and task loading. Use

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yhbatch to submit job script for batch submission. The job script is carried at the first node after dispatching through command yhrun. For interactive tasks, resources allocation and task loading are both carried by command yhrun. After login the shell while executing yhrun, yhrun firstly asks system for resources allocation and waits for it, then loads the task at the nodes allocated.

yhrun is explained as follow: yhrun [options] program yhrun has many options. Common parameters are as follow:

-n, --ntasks=ntasks Specify the number of process. Ask yhrun for allocating and loading ntasks processes.

Every CPU runs one process by default. However, -c will changed this default parameter.

-N, --nodes=minnodes[-maxnodes] Ask for allocating minimum minnodes nodes for this task. The scheduler may decide

to start task at the more nodes of which the number is more than minnodes. Users can specify maximum nodes by maxnodes (for example “-- nodes=2-4”). If –N is not set, system will allocate enough nodes to meet requirement by default.

-p, --partition=partition Asking for resources from partition. If not specified, set default partition by default.

-t, --time=minutes Set the limitation of running time. It is partition’s limit time by default. When the time

exceeds limitation, task is killed by signal of SIGTERM and SIGKILL.

-D, --chdir=path Change current directory to path. It is current directory by default.

-l, --label Add job id before standard output/standard error output at every line. Usually the

remote output is transferred to output of yhrun through buffer.

-J, --job-name=jobname Specify the name of job. The executable program is the default name.

-W, --wait=seconds Specify the waiting time after exiting the first job and before exiting the rest jobs. 0

means infinite time (an alert is sent every 60 seconds).

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-w, --nodelist=nodelist|filename Require nodes which are in the specified list. These nodes are minimum nodes which

are allocated for job. nodelist can be expression which is shown like this :cn[1-5,7,12]. If “/” appears, nodelist will be considered as a file name which includes required nodes.

-x, --execlude=nodelist|filename Exclude nodes out of list. These nodes will not be allocated.

--checkpoint-path=path Specify directory for saving which checking the job. Current directory is set as

default. --checkpoint-period=number[h|m]

Set regular checking operation for job. If number is not followed by time, it means hour.

--restart-path=path Specify path for restoring since last check point. Path is the path of checkpoint image

file.

--exclusive Make sure this job does not share the nodes with other jobs. If use this option, it

means this job needs exclusive nodes. If there are not enough idle nodes, the job will wait.

In the upper parameters, –N, -n, -p, -w, -x are most used, -N specifies the number of node, -n specifies the number of process, -p specifies the name of partition, -w specifies the list of node, -x specified nodes list which are not allocated (used for excluding nodes which users think has problems).

Non-preemptive dispatching is deployed on TH-1, which means if the job does not take all of nodes and other jobs need them, these idle nodes can be allocated to other jobs. For example, if one job takes 4 cores of one node and a new job also needs 4 cores of one node, the new job will be run on this node.

For example: 1) In the partition TH_NEW, hostname is running on the cn [4-16]

$ yhrun -w cn[4-16] –p TH_NEW hostname yhrun:XXXXX:use ‘-t’ option to set time limit of job. defaults to 5 (minutes) yhrun:job 4385 queued and waiting for resources yhrun:job 4385 has been allocated resources

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cn4 cn7 ... cn14

2) cg.C.4 which is a MPI program with 4 tasks is running in the gpu_test partition, one MPI process on one node. Nodes are allocated to run it including cn[4-5]; the running time is no more than 20 minutes; checking info as shown below:

$ yhrun -w cn[1-2] -n 4 -N 4 -t 20 –p gpu_test cg.C.4

NAS Parallel Benchmarks 3.2 --CG Benchmark

Size:150000 Iterations:75 Number of active processes:4 Number of nonzeroes per row:15 Eigenvalue shift:.110E+03

iteration ||r|| zeta

1 0.15244429457374E-12 109.9994423237398 2 0.45529118072694E-15 27.3920437146522 3 0.45039339889198E-15 28.0339761840269 4 0.44936453849220E-15 28.4191507551292

yhrun:interrupt (one more within 1 sec to abort) yhrun:task[0-4]:running 5 0.44884028024712E-15 28.6471670038895 6 0.44551302644602E-15 28.7812969418413

Attention:

1. yhrun can be used as mpirun. Especially, users can use yhrun instead of mpirun to submit MPI program when the program is compiled by compiler under path /usr/local/mpi or /usr/local/mpi-gcc.

2. yhrun is an interactive submission command. If users need to interact with program, directly select yhrun to submit jobs. Choose batch submission command yhbatch if no need to interact.

3. The task will be shut down after close client software, if the task is submitted by yhrun and input and output is not redirected. So please redirect input and output when using yhrun to submit task if no special requirement. Keep the corresponding logfile which is provided to technical personnel of NSCC in case error happens.

Example of redirection:

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yhrun –p test –N 16 –n 128 ./a.out >log 2>&1 & > is symbol of redirection. 2>&1 means redirecting standard error output to standard

output. The last symbol “&” means the background submission way, which can guarantee that the connection will not be broken after exiting client software.

4. Note again: To assure the stability of task, please use the batch submission(yhbatch) if no special requirement.

3.3.2 Batch submission ( yhbatch)

When need interactive requirements, use directly yhrun to submit job. If no need to interact or could not directly use yhrun to submit job, please use batch submission.

Batch submission is a job script in which specifies restraint and can be submitted as a job. Batch submission command is yhbatch. The command is executed once submitted, and then return to the command line window then the job will be under queue. When resources are available and nodes are allocated, the script will be executed.

Users can also use yhrun to load job in writing a script. At this time yhrun gets resources through sensing environment variables, so directly creates a new job without resubmitting the job.

The script of batch is a text file. The first line starts with “#!” and the script makes corresponding script interpreters, such as sh, bash, rsh, csh etc.

This submission is suitable for jobs which specify resources requirements or jobs which have own executing commands. The jobs which need continuously execute more tasks are also suitable. Users could submit many tasks by a script. The system will run it one by one.

As described below, there are two steps of running a script: resources allocation and task loading. Batch submission uses yhbatch to submit script, yhbatch is responsible for allocation. After yhbatch get resources, the submitted script is carried at the first node which is one of available nodes.

For example: The user’s script mybash.sh shown as follow: #! /bin/bash yhrun –n 16 –p TH_NET hostname

According to this srcipt, hostname which is made up with 16 processes need to be

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run on the TH_NET. Users’ batch submission is shown as follow: yhbatch –n 16 –p TH_NET ./mybash.sh Pay attention: using chmod to change the executable permission. Command is

chmod +x filename (filename is file name which needs to be changed). After computation, one output file whose name starts with “slurm” and extension

name is “.out” is created in the current work directory. yhbatch has many parameters which are similar to ones of yhrun, no elaboration for

this command. Users can use yhbatch --help to get more detail. Example 2 yhrun can be added to the script submitted by yhbatch. This script also supports

mpirun etc. For example, a.out is created by program which uses compiler from /vol5/mpi-gcc/openmpi-1.4.3, cn12-cn27 are allocated for this program, total 16 nodes and 128 processes. hostlist includes cn12-cn27 as shown:

cn12:8 cn13:8 cn14:8 cn15:8 cn16:8 cn17:8 cn18:8 cn19:8 cn20:8 cn21:8 cn22:8 cn23:8 cn24:8 cn25:8 cn26:8 cn27:8 sub.sh is shown as follows:

#!/bin/bash /vol5/mpi-gcc/openmpi-1.4.3/bin/mpirun –hostfile hostlist –np 128 ./a.out

Using following command to submit (after make sure sub.sh is executable):

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yhbatch –N 16 –p test –w cn[12-27] ./sub.sh

Special note: Batch submission is suitable in many cases. Limited to length of this manual, we can not explain more details. If you have any problem, please contact us.

3.3.3 Distributive submission ( yhalloc)

Distributive submission is similar to the integration of interactive and batch submission. Users need to specify demand conditions, and then ask resource manager for resources allocation. Submitted jobs will queue until the resources are available for task, the command is executed at the nodes where task is submitted. The allocated resources are released after command is finished.

If yhalloc is not followed by corresponding script or executable file, it choose /bin/sh to get suitable shell environment by default.

The main difference between yhalloc and yhbatch is that for yhalloc corresponding command is directly executed at all computing nodes where the task is submitted when the resources are available, while for yhbatch corresponding command is executed at the first node which is one of the allocated nodes when the resources are available.

After the resources for yhalloc are allocated, the task will be executed. This submission way is suitable for specifying nodes and other restraint such as ansys or models of other simulation software. Taking lsdyna of ansys as an example, corresponding memory and node-list are specified in parallel computer system under the circumstances of lsdyna12.1. Because it needs to specify corresponding node-list, yhalloc is a perfect choice.

For example: one user of ansys needs 8 nodes, 32 processes, 4 cores at every node. Using yhalloc, two submission ways are considered.

One is firstly asking for resources, command shown as follows: yhalloc –N 8 –n 32 Get jobID 163 through yhq, nodes are cn[60-67], user uses following command to

switch to cn60: ssh cn60 After it: lsdyna121 pr=dyna -dis memory=250m i=test.k o=test.out -machines

cn60:4:cn61:4:62:4:63:4:64:4:65:4:66:4:67:4

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lsdyna can be run correctly. The second submission way: Firstly check idle nodes through yhi, assure the number of idle nodes is 8 such as

cn[64-71], write following script lsdyna.sh: #!/bin/bash lsdyna121 pr=dyna -dis memory=250m i=test.k o=test.out -machines

cn64:4:cn65:4:66:4:67:4:68:4:69:4:70:4:71:4

Then typing following command: yhalloc –N 8 –n 32 –w cn[64-71] ./lsdyna.sh

Attention: granting executable rights to script through chmod +x lsdyna.sh yhalloc has a lot of parameters, most of which are similar to yhrun. Users can get

more info through yhalloc –help.

Particular notice: 1. Usage of yhalloc and yhbatch are almost the same. Main difference is loading

points: corresponding command is directly executed at the nodes where the task is submitted when the resources is available for yhalloc, while corresponding command is executed at the first node which is one of the allocated nodes when the resources is available for yhbatch.

2. For tasks submitted through command yhalloc, input and output need to be redirected and tasks should better use background submission way after exiting the client. Refer to 3.3.1 attention 3 for more info about background submission.

3.4 Job aborted ( yhcancel)

yhcancel is used to cancel the task, which is shown below:

Start a new SSH connection and abort it by yhcancel. Results are shown in Fig 3-3:

Fig 3-3 usage of yhcancel

After yhcancel is executed, info is shown as Fig 3-4:

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Fig 3-4 info after abortion

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Remarks: notes and contact

Limited to length of the manual, just some usual contents is introduced. If users need special requirements, please contact technical personnel of NSCC.

Remote graphic interface can be used after installing Exceed, VNC, Xmanager etc. NSCC can support for it.

Important note: Do not run executable files at login nodes (greatly impact on usage for other users). Please use batch submission if no special requirement. When the problem happens, contact us and provide us your log file for solving problem better.

Contact:

E-mail: [email protected]

Telephone: +86 022-65375500/022-65375501

For support users better, NSCC has asked technical personnel to respond to problems within 24 hours.

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Appendix A Common command of Unix A1 Basic commands

date: show current date and time, format: $date. who: inquire about current users’ info, format: $who. w: inquire about current users’ behavior, format: $w. write: sent message directly to another terminal, format:

$write username Hello: We have a meeting at Room 412.

End input message through typing Ctrl-D, info can be seen in the terminal of username.

mesg: choose to accept from write or not, format: $mesg n reject info from write; $mesg y allow other users to send message; $mesg report if allow others to send message to your terminal.

ps: used for viewing active processes, format: $ps [options]. kill: terminate specific process, format: $kill [-signal] pid.

A2 Directory operation

mkdir: create directory, format: $mkdir directory .... rmdir: remove directory, format: $rmdir directory .... pwd: show current working directory, format: $pwd. ls: show contents of directioy, format: $ls [options] [names]. cd: change the working directory, format: $cd [directory].

A3 Create, copy and delete file

touch: create a file with nothing, format: $touch name of file. rm: delete a file or directory, format: $rm [-r] [-f] [-i] file .... cp: copy a file or a directory, format: $cp [-i] [-r] file1 [file2...] target

-r: if file is a directory, cp will copy it and its all files. mv: move or rename file, format: $mv file1 target.

A4 File attributes

chmod: change rights to read or write or execute, format: $chmod [who] operator [permission] file-list.

chown: change the owner of file, format: $chown [-R] [-h] owne file….

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chgrp: change the group owner of file, format: $chgrp [-R] [-h] group file…

A5 show and link

cat: used to show and link file, format: $cat file1 file2 show content of file1and file2; $cat file1 file2 > file3 combine file1 and file2 to file3.

more: show content of file, format: $more name of file. head: show previous lines of file, format: $head [-n] [file…]. tail: show all of content in the screen from specific position:

$tail [+n] [lbc] file start to show lines from the beginning adds n:lines $tail [-n] [lbc] file start to show lines from the end subtracts n lines $tail –f file show new content circularly every one second

ln: make link for specific file, format: $ln [-s] [-f] [-n] file target

A6 Find and compare file

grep: search string, format: $grep pattern files. find: starting from specific directory, search recursively matching files from sub-directory, format: $find dirname option-list. diff: distinguish two files, format: diff [options] file1 file2.

A7 Compresion and backup compress: compress the file, format: $compress [-cfv] filename. uncompress: decompress the file, format: $uncompress [-cfv] filename. tar: make an archive for file (backup for system), format:

$tar c|t|x [bvf] [tarfile] [bsize] [file_list].

A8 Redirection of I/O

<: redirection of input, format: $command < file. >: redirection of output and update specific file, format: $command > file. >>: redirection of output and append the result to specific file, format:

$command >> file.

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Appendix B Common command for vi

B1 Enter and exit vi

Enter vi: $ vi filename vi Some ways that getting out of vi: :q exit. If file is updated, hint will be shown at the bottom of screen. :q! forced to exit. :w rewrite file without quitting. :wq rewrite file and quit. :x the same as wq.

B2 Move the cursor

↑ or k move the cursor up one line and remain the position of row ↓ or j move the cursor down one line and remain the position of row → or l move the cursor right one character ← or h move the cursor left one character $ move the cursor to the end of current line ^ move the cursor to the start of current line w move the cursor to initial of next word in current line b move the cursor to initial of last word in current line e move the cursor to last character of current word in current line ^F move forward a full screen ^D move downward half screen ^B move backward a full screen ^U move up half screen When using k, j, l and h, add a number before these buttons in order to move cursor

many times without pressing button several times.

B3 Input, delete, substitution, restoration and find

a insert main text from cursor a insert main text from beginning in current line I insert main text in the front of cursor I Insert main text at end of current line o Insert main text from beginning in next line O Insert main text from beginning in last line Esc Quit entry mode. Backspace Delete character in entry mode x Delete current character which cursor points to

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nx Delete n characters from where cursor stay dw Delete word where cursor stays ndw Delete n words from where cursor stay dd Delete line where cursor stays ndd Delete n lines from where cursor stay rx Substitute character where cursor stays with x nrx Substitute n characters where cursor stays with x u Abolish recent commands U Restore to status which is before modification /pattern Search string “pattern” down from buffer ?pattern Search string “pattern” up from buffer n re-search N re-search in opposite direction

B4 Edit line

:set nu Show line number :set nonu Cancel line number :1, $p Show all of buffer :r wqb wqb is sent to read-buffer and inserted at current cursor :1, 5w clh Content which is located from line 1 to 5 is written to clh :2, 5d Delete from line 2 to 5 :2, 5t8 Copy content which is located from line 2 to 5 behind line 8 :! ls Quit vi temporarily, execute command ls. :sh Quit vi temporarily, execute shell command, type ^D or exit to return main text.

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Appendix C Common commands for GDB Initiate gdb

gdb Initiate gdb without specifying objective gdb program Begin to debug objective program gdb program [arglist] core Debug the coredump created by objective program gdb --help Get help info

Quit gdb

quit Execute program: run arglist Using parameter arglist to start program run Using current parameter to start program set args arglist Set parameters for next run command set args Clear the parameter list show args Show the parameter list show env Show all of environment variables show env var Show specified environment variables set env var string Set the environment variables unset env var Delete specific variables from list

Control execution of program

continue Resume the program step Execute the program step by step until next line si Execute the program step by step until next instruct next Execute next line code including function call nexti Execute next line machine instruct until [location] Run until it gets to the location finish Run until current stack returns return Skip(do not execute)specified stack

Break point and watch point

break [file:] line Set break point in the line-th line of [file] break [file:] func Set break point at where func is located in the [file] break *addr Set break point at where addr is located break Set break point for next instruct

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break … if expr If the result of expression expr is nonzero, break point will work watch expr Set break point for expression expr(stop when value chages) info break Show break point info info watch Show watch point info clear Delete break point of next instruct clear [file:] func Delete break point of entry of func clear [file:] line Delete break point which is located in line delete [n] Delete n-th break point disable [n] Disable n-th breakpoint enable [n] Enable n-th break point ignore n count Ignore cout times of n-th break point

Stack

backtrace View current stack frame n Select n-th stack up n Move n stacks up down n Move n stacks down info args View parameter list of current stack info locals View local variable of current stack

Data display

print expr Show the result of expression expr x [/Nuf] expr View memory address in specified format, parameters

explained as following: N specify the number of specified data unit u unit size:

b, single byte h, half word(2 bytes) w, word(4 bytes) g, 8 bytes

f Format for showing data: x, Hexadecimal d, Decimal u, Unsigned decimal o, Octal t, Binary a, Address or relative address c, Character f, floating-point