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GPFS/SpectrumScale ($HOME, project)

Introduction

IBM Spectrum Scale, formerly known as the General Parallel File System (GPFS), is global high-performance clustered file system available on all ULHPC computational systems through a DDN GridScaler/GS7K system.

It allows sharing homedirs and project data between users, systems, and eventually (i.e. if needed) with the "outside world". In terms of raw storage capacities, it represents more than 4PB.

Global Home directory $HOME

Home directories provide a convenient means for a user to have access to files such as dotfiles, source files, input files, configuration files regardless of the platform.

Refer to your home directory using the environment variable $HOME whenever possible. The absolute path may change, but the value of $HOME will always be correct.

$HOME quotas and backup policies

See quotas for detailed information about inode, space quotas, and file system purge policies. Your HOME is backuped weekly, according to the policy detailed in the ULHPC backup policies.

Global Project directory $PROJECTHOME=/work/projects/

Project directories are intended for sharing data within a group of researchers, under /work/projects/<name>

Refer to your project base home directory using the environment variable $PROJECTHOME=/work/projects whenever possible.

Global Project quotas and backup policies

See quotas for detailed information about inode, space quotas, and file system purge policies. Your projects backup directories are backuped weekly, according to the policy detailed in the ULHPC backup policies.

Access rights to project directory: Quota for clusterusers group in project directories is 0 !!!

When a project <name> is created, a group of the same name (<name>) is also created and researchers allowed to collaborate on the project are made members of this group,which grant them access to the project directory.

Be aware that your default group as a user is clusterusers which has (on purpose) a quota in project directories set to 0. You thus need to ensure you always write data in your project directory using the <name> group (instead of yoru default one.). This can be achieved by ensuring the setgid bit is set on all folders in the project directories: chmod g+s [...]

When using rsync to transfer file toward the project directory /work/projects/<name> as destination, be aware that rsync will not use the correct permissions when copying files into your project directory. As indicated in the Data transfer section, you also need to:

  • give new files the destination-default permissions with --no-p (--no-perms), and
  • use the default group <name> of the destination dir with --no-g (--no-group)
  • (eventually) instruct rsync to preserve whatever executable permissions existed on the source file and aren't masked at the destination using --chmod=ug=rwX

Your full rsync command becomes (adapt accordingly):

  rsync -avz {--update | --delete} --no-p --no-g [--chmod=ug=rwX] <source> /work/projects/<name>/[...]

For the same reason detailed above, in case you are using a build command or more generally any command meant to write data in your project directory /work/projects/<name>, you want to use the sg as follows:

# /!\ ADAPT <name> accordingly
sg <name> -c "<command> [...]"

This is particularly important if you are building dedicated software with Easybuild for members of the project - you typically want to do it as follows:

# /!\ ADAPT <name> accordingly
sg <name> -c "eb [...] -r --rebuild -D"   # Dry-run - enforce using the '<name>' group
sg <name> -c "eb [...] -r --rebuild"      # Dry-run - enforce using the '<name>' group

Storage System Implementation

The way the ULHPC GPFS file system is implemented is depicted on the below figure.

It is composed of:

  • Two NAS protocol servers (see below
  • One DDN GridScaler 7K system acquired as part of RFP 160019 deployed in 2017 and later extended, composed of
    • 1x DDN GS7K enclosure (~11GB/s IO throughput)
    • 4x SS8460 disk expansion enclosures
    • 350x HGST disks (7.2K RPM HDD, 6TB, Self Encrypted Disks (SED) configured over 35 RAID6 (8+2) pools
    • 28x Sandisk SSD 400GB disks
  • Another DDN GridScaler 7K system acquired as part of RFP 190027 deployed in 2020 as part of Aion and later extended.
    • 1x DDN GS7990-EDR embedded storage
    • 4x SS9012 disk expansion enclosures
    • 360x NL-SAS HDDs (6TB, Self Encrypted Disks (SED)) configured over 36 RAID6 (8+2) pools
    • 10x 3.2TB SED SAS-SSD for metadata.

There is no single point of failure within the storage solution and the setup is fully redundant. The data paths from the storage to the NSD servers are redundant and providing one link from each of the servers to each controller in the storage unit. There are redundant power supplies, redundant fans, redundant storage controller with mirrored cache and battery backup to secure the cache data when power is lost completely. The data paths to the enclosures are redundant so that links can fail, and the system will still be fully operational.

Filesystem Performance

The performance of the GS7990 storage system via native GPFS and RDMA based data transport for the HPC filesystem is expected to be in the range of at least 20GB/s for large sequential read and writes, using a filesystem block size of 16MB and scatter or cluster allocation. Performance measurement by IOR, a synthetic benchmark for testing the performance of distributed filesystems is planned upon finalization of the installation.

The IOR benchmark

IOR is a parallel IO benchmark that can be used to test the performance of parallel storage systems using various interfaces and access patterns. It supports a variety of different APIs to simulate IO load and is nowadays considered as a reference Parallel filesystem I/O benchmark. It recently embedded another well-known benchmark suite called MDTest, a synthetic MPI parallel benchmark for testing the metadata performance of filesystems (such as Lustre or Spectrum Scale GPFS) where each thread is operating its own working set (to create directory/files, read files, delete files or directory tree).

In complement to IOR, the IO-500 benchmarking suite (see also the white paper "Establishing the IO-500 Benchmark") will be performed. IO-500 aims at capturing user-experienced performance with measured performance representative for:

  • applications with well optimised I/O patterns;
  • applications with random-like workloads;
  • workloads involving metadata small/objects.

NAS/NFS Servers

Two NAS protocol servers are available, each connected via 2 x IB EDR links to the IB fabric and exporting the filesystem via NFS and SMB over 2 x 10GE links into the Ethernet network.


Last update: May 3, 2022