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Huawei Cluster User's Guide

Huawei Cluster User's Guide

Table of Contents

  1. Introduction
  2. System Overview
    1. Login Nodes
    2. Password Management
  3. File Systems
    1. GPFS Filesystem
    2. Active Archive - HSM (Tape Layer)
    3. Local Hard Drive
    4. Root Filesystem
    5. Quotas
  4. Data management
    1. Transferring files
    2. Active Archive Management
    3. Repository management (GIT/SVN)
  5. Running Jobs
    1. Queues
    2. Submitting jobs
    3. Interactive Sessions
    4. Job directives
    5. Examples
    6. Interpreting job status and reason codes
    7. Resource usage and job priorities
  6. Software Environment
    1. OpenHPC
    2. Compilation for the architecture
    3. C Compilers
    4. FORTRAN Compilers
    5. Modules Environment
    6. BSC Commands
  7. Getting help
  8. Frequently Asked Questions (FAQ)
  9. Appendices
    1. SSH
    2. Transferring files on Windows
    3. Using X11
    4. Requesting and installing a .X509 user certificate

Introduction ↩

This user’s guide for the Huawei cluster is intended to provide the minimum amount of information needed by a new user of this system. As such, it assumes that the user is familiar with many of the standard features of supercomputing as the Unix operating system.

Here you can find most of the information you need to use our computing resources and the technical documentation about the machine. Please read carefully this document and if any doubt arises do not hesitate to contact us (Getting help).

Please note that this documentation could have some changes and revisions in the near future. The cluster is still in the early stages of deployment and some settings may be prone to some further tuning.

System Overview ↩

The Huawei cluser is a supercomputer based on Kunpeng 920 processors, which are based on the ARMv8.1 architecture. It is a system using a Mellanox high performance network interconnect and running CentOS 7.6 as operating system.

The computing elements of this cluster are split into 3 different blocks:

General purpose computing block, which has 16 nodes with the following characteristics:

Dedicated node for AI Training:

Dedicated node for AI Inference:

Remember that the BIOS and kernel reserves memory, so the actual total usable RAM that commands like “free” or “lstopo” report will be slighlty lower than the total theoretical amount.

Login Nodes ↩

You can connect to the Huawei cluster using the follwing public login node. Please note that only incoming connections are allowed in the whole cluster. The login hostname is:

hualogin1.bsc.es

Password Management ↩

In order to change the password, you have to login to a different machine (dt01.bsc.es). This connection must be established from your local machine.

    % ssh -l username dt01.bsc.es

    username@dtransfer1:~> passwd
    Changing password for username.
    Old Password: 
    New Password: 
    Reenter New Password: 
    Password changed.

Mind that the password change takes about 10 minutes to be effective.

File Systems ↩

IMPORTANT: It is your responsibility as a user of our facilities to backup all your critical data. We only guarantee a daily backup of user data under /gpfs/home. Any other backup should only be done exceptionally under demand of the interested user.

Each user has several areas of disk space for storing files. These areas may have size or time limits, please read carefully all this section to know about the policy of usage of each of these filesystems. There are 3 different types of storage available inside a node:

GPFS Filesystem ↩

The IBM General Parallel File System (GPFS) is a high-performance shared-disk file system providing fast, reliable data access from all nodes of the cluster to a global filesystem. GPFS allows parallel applications simultaneous access to a set of files (even a single file) from any node that has the GPFS file system mounted while providing a high level of control over all file system operations. In addition, GPFS can read or write large blocks of data in a single I/O operation, thereby minimizing overhead.

An incremental backup will be performed daily only for /gpfs/home.

These are the GPFS filesystems available in the machine from all nodes:

Active Archive - HSM (Tape Layer) ↩

Active Archive (AA) is a mid-long term storage filesystem that provides 15 PB of total space. You can access AA from the Data Transfer Machine (dt01.bsc.es and dt02.bsc.es) under /gpfs/archive/hpc/your_group.

NOTE: There is no backup of this filesystem. The user is responsible for adequately managing the data stored in it.

Hierarchical Storage Management (HSM) is a data storage technique that automatically moves data between high-cost and low-cost storage media. At BSC, the filesystem using HSM is the one mounted at /gpfs/archive/hpc, and the two types of storage are GPFS (high-cost, low latency) and Tapes (low-cost, high latency).

HSM System Overview

Hardware

Software

Functioning policy and expected behaviour

In general, this automatic process is transparent for the user and you can only notice it when you need to access or modify a file that has been migrated. If the file has been migrated, any access to it will be delayed until its content is retrieved from tape.

Only the files with a size between 1GB and 12TB will be moved (migrated) to tapes from the GPFS disk when no data access and modification have been done for a period of 30 days.

    /gpfs/archive/hpc

From the user point of view, the deletion will be transparent and have the same behaviour. On the other hand, it is not possible to modify a migrated file; in that case, you will have to wait for the system to retrieve the file and put it back on disk.

If there is not enough space to recover a given file from tape, the retrieve will fail and everything will remain in the same state as before, that is, you will continue to see the file on tape (in the “migrated” state).

You can use the hsmFileState script to check if the file is resident on disk or has been migrated to tape..

Examples of use cases

    $ hsmFileState file_1MB.dat
    resident -rw-rw-r-- 1 user group 1048576 mar 12 13:45 file_1MB.dat

    $ hsmFileState file_10GB.dat
    migrated -rw-rw-r-- 1 user group 10737418240 feb 12 11:37 file_10GB.dat

Local Hard Drive ↩

Every node has a local (or several) hard drive that can be used as a local scratch space to store temporary files during executions of one of your jobs. This space is mounted over /scratch/tmp/$JOBID directory and pointed out by $TMPDIR environment variable. If the node also has NVME drives available, that extra space can be accessed through the path pointed by the $NVMEDIR variable (/nvme).

The amount of space within the /scratch filesystem depends on which node you are using. Here are the specifications for each type of node:

All data stored in these local drives at the compute nodes will not be available from the login nodes. You should use the directory referred to by $TMPDIR (or $NVMEDIR if it applies) to save your temporary files during job executions. This directory will automatically be cleaned after the job finishes.

Root Filesystem ↩

The root file system, where the operating system is stored doesn’t reside in the node, this is a NFS filesystem mounted from one of the servers.

As this is a remote filesystem only data from the operating system has to reside in this filesystem. It is NOT permitted the use of /tmp for temporary user data. The local hard drive can be used for this purpose as you could read in Local Hard Drive.

Quotas ↩

The quotas are the amount of storage available for a user or a groups’ users. You can picture it as a small disk readily available to you. A default value is applied to all users and groups and cannot be outgrown.

You can inspect your quota anytime you want using the following command from inside each filesystem. 

     % bsc_quota

Please note that this command is not directly available from the cluster, you will have to launch it from the Data Transfer Machine (dt01.bsc.es / dt02.bsc.es).

The command provides a readable output for the quota. Check BSC Commands for more information.

If you need more disk space in this filesystem or in any other of the GPFS filesystems, the responsible for your project has to make a request for the extra space needed, specifying the requested space and the reasons why it is needed. For more information or requests you can Contact Us.

Data management ↩

Transferring files ↩

There are several ways to copy files from/to the Cluster:

Direct copy to the login nodes.

As said before no connections are allowed from inside the cluster to the outside world, so all scp and sftp commands have to be executed from your local machines and never from the cluster. The usage examples are in the next section.

On a Windows system, most of the secure shell clients come with a tool to make secure copies or secure ftp’s. There are several tools that accomplish the requirements, please refer to the Appendices, where you will find the most common ones and examples of use.

Data Transfer Machine

We provide special machines for file transfer (required for large amounts of data). These machines are dedicated to Data Transfer and are accessible through ssh with the same account credentials as the cluster. They are:

These machines share the GPFS filesystem with all other BSC HPC machines. Besides scp and sftp, they allow some other useful transfer protocols:

    localsystem$ scp localfile username@dt01.bsc.es:
    username's password:

    localsystem$ scp username@dt01.bsc.es:remotefile localdir
    username's password:

    localsystem$ rsync -avzP localfile_or_localdir username@dt01.bsc.es:
    username's password:

    localsystem$ rsync -avzP username@dt01.bsc.es:remotefile_or_remotedir localdir
    username's password:

    localsystem$ sftp username@dt01.bsc.es
    username's password:
    sftp> get remotefile

    localsystem$ sftp username@dt01.bsc.es
    username's password:
    sftp> put localfile

    bbcp -V -z <USER>@dt01.bsc.es:<FILE> <DEST>
    bbcp -V <ORIG>  <USER>@dt01.bsc.es:<DEST>

    globus-url-copy -help
    globus-url-copy -tcp-bs 16M -bs 16M -v -vb your_file sshftp://your_user@dt01.bsc.es/~/

Setting up sshfs - Option 1: Linux

        sshfs -o workaround=rename <yourHPCUser>@dt01.bsc.es: <localDirectory>

Setting up sshfs - Option 2: Windows

In order to set up sshfs in a Windows system, we suggest two options:

  1. sshfs-win

    • Follow the installation steps from their official repository.

    • Open File Explorer and right-click over the “This PC” icon in the left panel, then select “Map Network Drive”.

    Menu selection
    Menu selection
    • In the new window that pops up, fill the “Folder” field with this route:
        \\sshfs\<your-username>@dt01.bsc.es
    Example
    Example
    • After clicking “Finish”, it will ask you for your credentials and then you will see your remote folder as a part of your filesystem.
    Done!
    Done!

  2. win-sshfs

    • Install Dokan 1.0.5 (is the version that works best for us)

    • Install the latest version of win-sshfs. Even though the installer seems to do nothing, if you reboot your computer the direct access to the application will show up.

    • The configuration fields are: 

    % Drive name: whatever you want
% Host: dt01.bsc.es
% Port: 22
% Username: <your-username>
% Password: <your-password>
% Directory: directory you want to mount
% Drive letter: preferred
% Mount at login: preferred
% Mount folder: only necessary if you want to mount it over a directory, otherwise, empty
% Proxy: none
% KeepAlive: preferred
    Example
    Example
    • After clicking “Mount” you should be able to access to your remote directory as a part of your filesystem.
    Done!
    Done!

Active Archive Management ↩

To move or copy from/to AA you have to use our special commands, available in dt01.bsc.es and dt02.bsc.es or any other machine by loading “transfer” module:

These commands submit a job into a special class performing the selected command. Their syntax is the same than the shell command without ‘dt’ prefix (cp, mv, rsync, tar).

    dtq

dtq shows all the transfer jobs that belong to you, it works like squeue in SLURM.

    dtcancel <job_id>

dtcancel cancels the transfer job with the job id given as parameter, it works like scancel in SLURM.

    % dttar -cvf  /gpfs/archive/hpc/group01/outputs.tar ~/OUTPUTS 

    # Example: Copying data from /gpfs to /gpfs/archive/hpc    
    % dtcp -r  ~/OUTPUTS /gpfs/archive/hpc/group01/

    # Example: Copying data from /gpfs/archive/hpc to /gpfs
    % dtcp -r  /gpfs/archive/hpc/group01/OUTPUTS ~/

    # Example: Copying data from /gpfs to /gpfs/archive/hpc    
    % dtrsync -avP  ~/OUTPUTS /gpfs/archive/hpc/group01/

    # Example: Copying data from /gpfs/archive/hpc to /gpfs
    % dtrsync -avP  /gpfs/archive/hpc/group01/OUTPUTS ~/

    # Example: Copying data from group01 to group02
    % dtsgrsync group02 /gpfs/projects/group01/OUTPUTS /gpfs/projects/group02/

    # Example: Moving data from /gpfs to /gpfs/archive/hpc    
    % dtmv ~/OUTPUTS /gpfs/archive/hpc/group01/

    # Example: Moving data from /gpfs/archive/hpc to /gpfs
    % dtmv /gpfs/archive/hpc/group01/OUTPUTS ~/

Additionally, these commands accept the following options:

--blocking: Block any process from reading file at final destination until transfer completed.

--time: Set up new maximum transfer time (Default is 18h).

It is important to note that these kind of jobs can be submitted from both the ‘login’ nodes (automatic file management within a production job) and ‘dt01.bsc.es’ machine. AA is only mounted in Data Transfer Machine. Therefore if you wish to navigate through AA directory tree you have to login into dt01.bsc.es

Repository management (GIT/SVN) ↩

There’s no outgoing internet connection from the cluster, which prevents the use of external repositories directly from our machines. To circumvent that, you can use the “sshfs” command in your local machine, as explained in the previous [Setting up sshfs (Linux)] and [Setting up sshfs (Windows)] sections.

Doing that, you can mount a desired directory from our GPFS filesystem in your local machine. That way, you can operate your GPFS files as if they were stored in your local computer. That includes the use of git, so you can clone, push or pull any desired repositories inside that mount point and the changes will transfer over to GPFS.

Running Jobs ↩

Slurm is the utility used for batch processing support, so all jobs must be run through it. This section provides information for getting started with job execution at the Cluster.

Important notices:

You can check this limit with bsc_queues.

Queues ↩

There are several queues present in the machines and different users may access different queues. All queues have different limits in amount of cores for the jobs and duration. You can check anytime all queues you have access to and their limits using:

    % bsc_queues

The standard configuration and limits of the queues are the following

Queue Maximum numer of nodes (cores) Maximum wallclock
debug 4 (512) 2 h
normal 8 (1024) 3 days
interactive 1 (128) 2 h
xlarge 16 (2048) 72 h
xlong 8 (1024) 10 days

For longer and/or larger executions special queues (xlarge and xlong) are available upon request and will require proof of scalability and application performance. To solicit access to these special queues please contact us.

Special nodes

One of the main appeals of this cluster is the inclusion of two specialized nodes: one node for AI training and another one for AI inference. In order to request one of those nodes, you will have to add some specific options to your jobscript. Please note that the specialized resources inside those nodes are not managed through "#SBATCH --gres" parameters, so you should allocate the full node.

To request one of those nodes, you should add one of these directives in you jobscript:

    #SBATCH --constraint=Ascend910A
    or
    #SBATCH --constraint=Ascend310

The first constraint is used to define that you specifically need the AI Training node. The second one is used when the AI Inference node is needed. Note: it is highly recommended to request the full node, either explicitly requesting all the cores or using the "#SBATCH --exclusive" parameter. Keep in mind that there is only one node of each type in the whole cluster!

Submitting jobs ↩

The method for submitting jobs is to use the SLURM sbatch directives directly.

A job is the execution unit for SLURM. A job is defined by a text file containing a set of directives describing the job’s requirements, and the commands to execute.

In order to ensure the proper scheduling of jobs, there are execution limitations in the number of nodes and cores that can be used at the same time by a group. You may check those limits using command ‘bsc_queues’. If you need to run an execution bigger than the limits already granted, you may [Contact Us]

SBATCH commands

These are the basic directives to submit jobs with sbatch:

    sbatch <job_script>

submits a “job script” to the queue system (see Job directives).

    squeue

shows all the submitted jobs.

    scancel <job_id>

remove the job from the queue system, canceling the execution of the processes, if they were still running.

Interactive Sessions ↩

Allocation of an interactive session in the interactive partition has to be done through SLURM:

    salloc --partition=interactive
    or
    salloc -p interactive

Job directives ↩

A job must contain a series of directives to inform the batch system about the characteristics of the job. These directives appear as comments in the job script and have to conform to either the sbatch syntaxes.

sbatch syxtax is of the form:

     #SBATCH --directive=value

Additionally, the job script may contain a set of commands to execute. If not, an external script may be provided with the ‘executable’ directive. Here you may find the most common directives for both syntaxes:

     #SBATCH --qos=debug

To request the queue for the job. If it is not specified, Slurm will use the user’s default queue. The debug queue is only intended for small test.

     #SBATCH --time=DD-HH:MM:SS

The limit of wall clock time. This is a mandatory field and you must set it to a value greater than real execution time for your application and smaller than the time limits granted to the user. Notice that your job will be killed after the time has passed.

     #SBATCH --workdir=pathname

The working directory of your job (i.e. where the job will run). If not specified, it is the current working directory at the time the job was submitted.

    #SBATCH --error=file

The name of the file to collect the standard error output (stderr) of the job.

    #SBATCH --output=file

The name of the file to collect the standard output (stdout) of the job.

    #SBATCH --nodes=number
    or
    #SBATCH -N number

The number of requested nodes.

Note: Please keep in mind that this parameter will enforce the exclusivity of the nodes in case you request more than one. For example, let’s say that we specify just one node with this parameter, but we only want to use two tasks that use only one core each:

    #SBATCH -N 1
    #SBATCH -n 2
    #SBATCH -c 1

This will only request the use of the total resources, which are just two cores. The remaining resources of the used node will be left available for other users. If we request more than one node (and we leave the other parameters untouched) like this:

    #SBATCH -N 2
    #SBATCH -n 2
    #SBATCH -c 1

It will request the exclusivity of both nodes. This means that it will request the full resources of both nodes and they won’t be shared between other users. It’s important to be aware of this behavior, as it will charge the CPU time of all those resources to your computation time budget (in case you have one), even if you specified the use of only two cores. With this being said, we can continue with the description of the remaining SLURM parameters.

    #SBATCH --ntasks=number

The number of processes to start.

Optionally, you can specify how many threads each process would open with the directive:

    #SBATCH --cpus-per-task=number

The number of cores assigned to the job will be the total_tasks number * cpus_per_task number.

    #SBATCH --tasks-per-node=number

The number of tasks assigned to a node.

    #SBATCH --ntasks-per-socket=number

The number of tasks assigned to a socket.

    #SBATCH --reservation=reservation_name

The reservation where your jobs will be allocated (assuming that your account has access to that reservation). In some ocasions, node reservations can be granted for executions where only a set of accounts can run jobs. Useful for courses.

    #SBATCH --array=<indexes>

Submit a job array, multiple jobs to be executed with identical parameters. The indexes specification identifies what array index values should be used. Multiple values may be specified using a comma separated list and/or a range of values with a “-” separator. Job arrays will have two additional environment variable set. SLURM_ARRAY_JOB_ID will be set to the first job ID of the array. SLURM_ARRAY_TASK_ID will be set to the job array index value. For example:

    sbatch --array=1-3 job.cmd
    Submitted batch job 36

Will generate a job array containing three jobs and then the environment variables will be set as follows:

    # Job 1
    SLURM_JOB_ID=36
    SLURM_ARRAY_JOB_ID=36
    SLURM_ARRAY_TASK_ID=1

    # Job 2
    SLURM_JOB_ID=37
    SLURM_ARRAY_JOB_ID=36
    SLURM_ARRAY_TASK_ID=2

    # Job 3
    SLURM_JOB_ID=38
    SLURM_ARRAY_JOB_ID=36
    SLURM_ARRAY_TASK_ID=3

Note: the maximum number of elements that a job array can contain is 1000 jobs. Any number higher than that will result in an error when trying to submit the job.

    #SBATCH --exclusive

To request an exclusive use of a compute node without sharing the resources with other users. This only applies to jobs requesting less than one full node. All jobs with more cores than a full node will automatically use all requested nodes in exclusive mode.

Variable Meaning
SLURM_JOBID Specifies the job ID of the executing job
SLURM_NPROCS Specifies the total number of processes in the job
SLURM_NNODES Is the actual number of nodes assigned to run your job
SLURM_PROCID Specifies the MPI rank (or relative process ID) for the current process. The range is from 0-(SLURM_NPROCS–1)
SLURM_NODEID Specifies relative node ID of the current job. The range is from 0-(SLURM_NNODES–1)
SLURM_LOCALID Specifies the node-local task ID for the process within a job

For more information:

    man sbatch
    man srun
    man salloc

Examples ↩

sbatch examples

Example for a sequential job:

    #!/bin/bash
    #SBATCH --job-name="test_serial"
    #SBATCH --workdir=.
    #SBATCH --output=serial_%j.out
    #SBATCH --error=serial_%j.err
    #SBATCH --ntasks=1
    #SBATCH --time=00:02:00
    ./serial_binary> serial.out

The job would be submitted using:

    > sbatch ptest.cmd

Examples for a parallel job:

    #!/bin/bash
    #SBATCH --job-name=omp
    #SBATCH --workdir=.
    #SBATCH --output=omp_%j.out
    #SBATCH --error=omp_%j.err
    #SBATCH --cpus-per-task=128
    #SBATCH --ntasks=1
    #SBATCH --time=00:10:00
    #SBATCH --qos=debug
    ./openmp_binary

    #!/bin/bash
    #SBATCH --job-name=mpi
    #SBATCH --output=mpi_%j.out
    #SBATCH --error=mpi_%j.err
    #SBATCH --ntasks=256
    srun ./mpi_binary

    #!/bin/bash
    #SBATCH --job-name=test_parallel
    #SBATCH --workdir=.
    #SBATCH --output=mpi_%j.out
    #SBATCH --error=mpi_%j.err
    #SBATCH --ntasks=16
    #SBATCH --cpus-per-task=16
    #SBATCH --tasks-per-node=8
    #SBATCH --time=00:02:00
    srun ./parallel_binary> parallel.output

    #!/bin/bash
    #SBATCH --job-name=test_parallel
    #SBATCH --workdir=.
    #SBATCH --output=mpi_%j.out
    #SBATCH --error=mpi_%j.err
    #SBATCH --ntasks=1
    #SBATCH --cpus-per-task=192
    #SBATCH --tasks-per-node=1
    #SBATCH --time=00:02:00
    #SBATCH --constraint=Ascend910A
    srun ./parallel_binary> parallel.output

Interpreting job status and reason codes ↩

When using squeue, Slurm will report back the status of your launched jobs. If they are still waiting to enter execution, they will be followed by the reason. Slurm uses codes to display this information, so in this section we will be covering the meaning of the most relevant ones.

Job state codes

This list contains the usual state codes for jobs that have been submitted:

Job reason codes

This list contains the most common reason codes of the jobs that have been submitted and are still not in the running state:

Resource usage and job priorities ↩

Projects will have assinged a certain amount of compute hours or core hours that are available to use. One core hour is the computing time of one core during the time of one hour. That is a full node with 128 cores running a job for one hour will use up 128 core hours from the assigned budget. The accounting is solely based in the amount of compute hours used.

The priority of a job and therefore its scheduling in the queues is being determined by a multitude of factors. The most important and influential ones are the fairshare in between groups, waiting time in queues and job size. Our systems using Slurm, in general, favor large executions so that jobs using more cores have a higher priority. The time while waiting in queues for execution is being taken into account as well and jobs gain more and more priority the longer they are waiting. Finally our queue system implements a fairshare policy between groups. Users who did not run many jobs and consumed compute hours will get a higher priority for their jobs than groups that have a high usage. This is to allow everyone their fair share of compute time and the option to run jobs without one group or another being favoured. You can review your current fair share score using the command:

    sshare -la

Software Environment ↩

This cluster has OpenHPC available for software management.

All the software and numerical libraries installed by Support at the cluster can be found at /apps/.

The software installed using OpenHPC can be found at /opt/ohpc/pub/.

If you need something that is not there please contact us to get it installed (see Getting Help).

OpenHPC ↩

OpenHPC provides an integrated and tested collection of software components that can be used on the compute cluster.

To use the software installed with OpenHPC the module “openhpc” needs to be loaded

     module load openhpc

OpenHPC uses a module hierarchy strategy. Therefore, on the “module available” output is shown the modules that can be loaded with the modules already loaded. Once a compiler is loaded, the modules that depend on that compiler will appear on the “module available” output. After choosing an MPI implementation, the modules that depend on that compiler-MPI pairing will be available. If a compiler is swapped, then Lmod automatically unloads any modules that depend on the old compiler and reloads those modules that are dependent on the new compiler.

Compilation for the architecture ↩

To generate code that is optimized for the target architecture and supported features, you will have to use the corresponding compile flags. For compilations of MPI applications an MPI installation needs to be loaded in your session as well. For example OpenMPI via module load openmpi3/3.1.4

C Compilers ↩

The GCC provided by the system is version 4.8.5. For better support of new and old hardware features we have different versions that can be loaded via the provided modules. For example in the Huawei cluster you can find GCC 8.3.0 and GCC 11.2:

    module load gnu8/8.3.0
    module load gcc/11.2

Distributed Memory Parallelism

To compile MPI programs it is recommended to use the following handy wrappers: mpicc, mpicxx for C and C++ source code. You need to choose the Parallel environment first: module load openmpi3. These wrappers will include all the necessary libraries to build MPI applications without having to specify all the details by hand.

    % mpicc a.c -o a.exe
    % mpicxx a.C -o a.exe

Shared Memory Parallelism

OpenMP directives are fully supported by the GCC C and C++ compilers. To use it, the flag -fopenmp must be added to the compile line.

    % gcc -fopenmp -o exename filename.c
    % g++ -fopenmp -o exename filename.C

FORTRAN Compilers ↩

In the cluster you can find these compilers :

gfortran -> GNU Compilers for FORTRAN

    % man gfortran

By default, the compilers expect all FORTRAN source files to have the extension “.f”, and all FORTRAN source files that require preprocessing to have the extension “.F”. The same applies to FORTRAN 90 source files with extensions “.f90” and “.F90”.

Distributed Memory Parallelism

In order to use MPI, again you can use the wrappers mpif77 or mpif90 depending on the source code type. You can always man mpif77 to see a detailed list of options to configure the wrappers, ie: change the default compiler.

    % mpif77 a.f -o a.exe

Shared Memory Parallelism

OpenMP directives are fully supported by the GCC Fortran compiler when the option “-fopenmp” is set:

    % gfortran -fopenmp

Modules Environment ↩

The Environment Modules package (http://modules.sourceforge.net/) provides a dynamic modification of a user’s environment via modulefiles. Each modulefile contains the information needed to configure the shell for an application or a compilation. Modules can be loaded and unloaded dynamically, in a clean fashion. All popular shells are supported, including bash, ksh, zsh, sh, csh, tcsh, as well as some scripting languages such as perl.

Installed software packages are divided into five categories:

Modules tool usage

Modules can be invoked in two ways: by name alone or by name and version. Invoking them by name implies loading the default module version. This is usually the most recent version that has been tested to be stable (recommended) or the only version available. 

    % module load gnu8

Invoking by version loads the version specified of the application. As of this writing, the previous command and the following one load the same module.

    % module load openmpi3/3.1.4

The most important commands for modules are these:

You can run “module help” any time to check the command’s usage and options or check the module(1) manpage for further information.

Module custom stack size

The stack size is 10 MB by default. You can check your stack size at any time using the command:

    % ulimit -s

If by any chance this stack size doesn’t fit your needs, you can add to your job script a command to have a custom set value after the module load commands. This way, you can have an appropiate stack size while using the compute nodes:

    % ulimit -Ss <new_size_in_KB>

BSC Commands ↩

The Support team at BSC has provided some commands useful for user’s awareness and ease of use in our HPC machines. At this moment, the only available BSC command for this system is:

All available commands have a dedicated manpage (not all commands are available for all machines). You can check more information about these commands checking their respective manpage:

% man <bsc_command>

For example:
% man bsc_queues

Getting help ↩

BSC provides users with excellent consulting assistance. User support consultants are available during normal business hours, Monday to Friday, 09 a.m. to 18 p.m. (CEST time).

User questions and support are handled at: support@bsc.es

If you need assistance, please supply us with the nature of the problem, the date and time that the problem occurred, and the location of any other relevant information, such as output files. Please contact BSC if you have any questions or comments regarding policies or procedures.

Our address is:

Barcelona Supercomputing Center – Centro Nacional de Supercomputación
C/ Jordi Girona, 31, Edificio Capilla 08034 Barcelona

Frequently Asked Questions (FAQ) ↩

You can check the answers to most common questions at BSC’s Support Knowledge Center. There you will find online and updated versions of our documentation, including this guide, and a listing with deeper answers to the most common questions we receive as well as advanced specific questions unfit for a general-purpose user guide.

Appendices ↩

SSH ↩

SSH is a program that enables secure logins over an insecure network. It encrypts all the data passing both ways, so that if it is intercepted it cannot be read. It also replaces the old an insecure tools like telnet, rlogin, rcp, ftp,etc. SSH is a client-server software. Both machines must have ssh installed for it to work.

We have already installed a ssh server in our machines. You must have installed an ssh client in your local machine. SSH is available without charge for almost all versions of UNIX (including Linux and MacOS X). For UNIX and derivatives, we recommend using the OpenSSH client, downloadable from http://www.openssh.org, and for Windows users we recommend using Putty, a free SSH client that can be downloaded from http://www.putty.org. Otherwise, any client compatible with SSH version 2 can be used. If you want to try a simpler client with multi-tab capabilities, we also recommend using Solar-PuTTY (https://www.solarwinds.com/free-tools/solar-putty).

This section describes installing, configuring and using PuTTy on Windows machines, as it is the most known Windows SSH client. No matter your client, you will need to specify the following information:

For example with putty client:

Putty client
Putty client

This is the first window that you will see at putty startup. Once finished, press the Open button. If it is your first connection to the machine, your will get a Warning telling you that the host key from the server is unknown, and will ask you if you are agree to cache the new host key, press Yes.

Putty certificate security alert
Putty certificate security alert

IMPORTANT: If you see this warning another time and you haven’t modified or reinstalled the ssh client, please do not log in, and contact us as soon as possible (see Getting Help).

Finally, a new window will appear asking for your login and password:

Cluster login
Cluster login

Generating SSH keys with PuTTY

First of all, open PuTTY Key Generator. You should select Type RSA and 2048 or 4096 bits, then hit the “Generate” button.

Public key PuTTY window selection
Public key PuTTY window selection

After that, you will have to move the mouse pointer inside the blue rectangle, as in picture:

PuTTY box where you have to move your mouse
PuTTY box where you have to move your mouse

You will find and output similar to the following picture when completed

PuTTY dialog when completed
PuTTY dialog when completed

This is your public key, you can copy the text in the upper text box to the notepad and save the file. On the other hand, click on “Save private key” as in the previous picture, then export this file to your desired path.

You can close PuTTY Key Generator and open PuTTY by this time,

To use your recently saved private key go to Connection -> SSH -> Auth, click on Browse… and select the file.

PuTTY SSH private key selection
PuTTY SSH private key selection

Transferring files on Windows ↩

To transfer files to or from the cluster you need a secure FTP (SFTP) o secure copy (SCP) client. There are several different clients, but as previously mentioned, we recommend using the Putty clients for transferring files: psftp and pscp. You can find them at the same web page as PuTTY (http://www.putty.org), you just have to go to the download page for PuTTY and you will see them in the “alternative binary files” section of the page. They will most likely be included in the general PuTTY installer too.

Some other possible tools for users requiring graphical file transfers could be:

Using PSFTP

You will need a command window to execute psftp (press start button, click run and type cmd). The program first asks for the machine name (mn1.bsc.es), and then for the username and password. Once you are connected, it’s like a Unix command line.

With command help you will obtain a list of all possible commands. But the most useful are:

You will be able to copy files from your local machine to the cluster, and from the cluster to your local machine. The syntax is the same that cp command except that for remote files you need to specify the remote machine:

Copy a file from the cluster:
> pscp.exe username@mn1.bsc.es:remote_file local_file
Copy a file to the cluster:
> pscp.exe local_file username@mn1.bsc.es:remote_file

Using X11 ↩

In order to start remote X applications you need and X-Server running in your local machine. Here are two of the most common X-servers for Windows:

The only Open Source X-server listed here is Cygwin/X, you need to pay for the other.

Once the X-Server is running run putty with X11 forwarding enabled:

Putty X11 configuration
Putty X11 configuration

On the other hand, XQuartz is the most common application for this purpose in macOS. You can download it from its website:

https://www.xquartz.org

For older versions of macOS or XQuartz you may need to add these commands to your .zshrc file and open a new terminal:

export DISPLAY=:0
/opt/X11/bin/xhost +

This will allow you to use the local terminal as well as xterm to launch graphical applications remotely.

If you installed another version of XQuartz in the past, you may need to launch the following commands to get a clean installation:

    $ launchctl unload /Library/LaunchAgents/org.macosforge.xquartz.startx.plist
    $ sudo launchctl unload /Library/LaunchDaemons/org.macosforge.xquartz.privileged_startx.plist
    $ sudo rm -rf /opt/X11* /Library/Launch*/org.macosforge.xquartz.* /Applications/Utilities/XQuartz.app /etc/*paths.d/*XQuartz
    $ sudo pkgutil --forget org.macosforge.xquartz.pkg

I tried running a X11 graphical application and got a GLX error, what can I do?

If you are running on a macOS/Linux system and, when you try to use some kind of graphical interface through remote SSH X11 remote forwarding, you get an error similar to this:

X Error of failed request: BadValue (integer parameter out of range for operation)
    Major opcode of failed request: 154 (GLX)
    Minor opcode of failed request: 3 (X_GLXCreateContext)
    Value in failed request: 0x0
    Serial number of failed request: 61
    Current serial number in output stream: 62

Try to do this fix:

macOS:

    $ defaults find xquartz | grep domain

You should get something like ‘org.macosforge.xquartz.X11’ or ‘org.xquartz.x11’, use this text in the following command (we will use org.xquartz.x11 for this example):

    $ defaults write org.xquartz.x11 enable_iglx -bool true

Linux:

    Section "ServerFlags"
        Option "AllowIndirectGLX" "on"
        Option "IndirectGLX" "on"
    EndSection

This solves the error most of the time. The error is related to the fact that some OS versions have disabled indirect GLX by default, or disabled it at some point during an OS update.

Requesting and installing a .X509 user certificate ↩

If you are a BSC employee (and you also have a PRACE account), you may be interested in obtaining and configuring a x.509 Grid certificate. If that is the case, you should follow this guide. First, you should obtain a certificate following the details of this guide (you must be logged in the BSC intranet):

Once you have finished requesting the certificate, you must download it in a “.p12” format. This procedure may be different depending on which browser you are using. For example, if you are using Mozilla Firefox, you should be able to do it following these steps:

Once you have obtained the copy of your certificate, you must set up your environment in your HPC account. To acomplish that, follow these steps:

    module load prace globus
    cd ~/.globus
    openssl pkcs12 -nocerts -in usercert.p12 -out userkey.pem 
    chmod 0400 userkey.pem 
    openssl pkcs12 -clcerts -nokeys -in usercert.p12 -out usercert.pem 
    chmod 0444 usercert.pem

Once you have finished all the steps, your personal certificate should be fully installed.