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Figure 1. Delta System

Delta is supported by the National Science Foundation under Grant No. OAC-2005572.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Delta is now accepting proposals.

Status Updates and Notices

Delta is tentatively scheduled to enter production in Q3 2022.

key: light grey font is work in progress

Items in light grey font are in progress and coming soon.  Example software or feature not yet implemented.

Introduction

Delta is a dedicated, ACCESS-allocated resource allocated resource designed by HPE and NCSA, delivering a highly capable GPU-focused compute environment for GPU and CPU workloads.  Besides offering a mix of standard and reduced precision GPU resources, Delta also offers GPU-dense nodes with both NVIDIA and AMD GPUs.  Delta provides high performance node-local SSD scratch filesystems, as well as both standard Lustre and relaxed-POSIX parallel filesystems spanning the entire resource.

Delta's CPU nodes are each powered by two 64-core AMD EPYC 7763 ("Milan") processors, with 256 GB of DDR4 memory.  The Delta GPU resource has four node types: one with 4 NVIDIA A100 GPUs (40 GB HBM2 RAM each) connected via NVLINK and 1 64-core AMD EPYC 7763 ("Milan") processor, the second with 4 NVIDIA A40 GPUs (48 GB GDDR6 RAM) connected via PCIe 4.0 and 1 64-core AMD EPYC 7763 ("Milan") processor, the third with 8 NVIDIA A100 GPUs in a dual socket AMD EPYC 7763 (128-cores per node) node with 2 TB of DDR4 RAM and NVLINK,  and the fourth with 8 AMD MI100 GPUs (32GB HBM2 RAM each) in a dual socket AMD EPYC 7763 (128-cores per node) node with 2 TB of DDR4 RAM and PCIe 4.0. 

Delta has 124 standard CPU nodes, 100 4-way A100-based GPU nodes, 100 4-way A40-based GPU nodes, 5 8-way A100-based GPU nodes, and 1 8-way MI100-based GPU node.  Every Delta node has high-performance node-local SSD storage (740 GB for CPU nodes, 1.5 TB for GPU nodes), and is connected to the 7 PB Lustre parallel filesystem via the high-speed interconnect.  The Delta resource uses the SLURM workload manager for job scheduling.  

Delta supports the ACCESS core software stack, including remote login, remote computation, data movement, science workflow support, and science gateway support toolkits.

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Account Administration

  • For ACCESS projects please use the  ACCESS user portal for project and account management.
  • Non-ACCESS Account and Project administration, such as adding a someone to a project, is handled by NCSA Identity and NCSA group management tools. For more information, please see the NCSA Allocation and Account Management documentation page. 

Configuring Your Account

  • Bash is the default shell, submit a support request to change your default shell
  • Environment variables: ACCESS CUE, SLURM batch
  • Using Modules 

System Architecture

Delta is designed to help applications transition from CPU-only to GPU or hybrid CPU-GPU codes. Delta has some important architectural features to facilitate new discovery and insight:

  • A single processor architecture (AMD) across all node types: CPU and GPU
  • Support for NVIDIA A100 MIG GPU partitioning allowing for fractional use of the A100s if your workload isn't able to exploit an entire A100 efficiently
  • Ray tracing hardware support from the NVIDIA A40 GPUs
  • Nine large memory (2 TB) nodes 
  • A low latency and high bandwidth HPE/Cray Slingshot interconnect between compute nodes
  • Lustre for home, projects and scratch file systems
  • support for relaxed and non-posix IO
  • Shared-node jobs and the single core and single MIG GPU slice
  • Resources for persistent services in support of Gateways, Open OnDemand, and Data Transport nodes.
  • Unique AMD MI-100 resource  

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Model Compute Nodes

The Delta compute ecosystem is composed of five node types:

  1. Dual-socket CPU-only compute nodes
  2. Single socket 4-way NVIDIA A100 GPU compute nodes
  3. Single socket 4-way NVIDIA A40 GPU compute nodes
  4. Dual-socket 8-way NVIDIA A100 GPU compute nodes
  5. Single socket 8-way AMD MI100 GPU compute nodes

The CPU-only and 4-way GPU nodes have 256 GB of RAM per node while the 8-way GPU nodes have 2 TB of RAM. The CPU-only node has 0.74 TB of local storage while all GPU nodes have 1.5 TB of local storage.

Table. CPU Compute Node Specifications

SpecificationValue

Number of nodes

132

CPU AMD  EPYC 7763
"Milan" (PCIe Gen4)
Sockets per node2

Cores per socket

64

Cores per node128

Hardware threads per core

1

Hardware threads per node

128

Clock rate (GHz)

~ 2.45

RAM (GB)

256

Cache (KB) L1/L2/L3

 64/512/32768

Local storage (TB)

0.74 TB

The AMD CPUs are set for 4 NUMA domains per socket (NPS=4). 

Table. 4-way NVIDIA A40 GPU Compute Node Specifications 

SpecificationValue
Number of nodes100
GPUNVIDIA A40 

(Vendor page)

GPUs per node4
GPU Memory (GB)48 DDR6 with ECC
CPUAMD Milan
CPU sockets per node1

Cores per socket

64

Cores per node64

Hardware threads per core

1

Hardware threads per node

64

Clock rate (GHz)

~ 2.45

RAM (GB)

256

Cache (KB) L1/L2/L3

 64/512/32768

Local storage (TB)

1.5 TB

The AMD CPUs are set for 4 NUMA domains per socket (NPS=4). 
The A40 GPUs are connected via PCIe Gen4 and have the following affinitization to NUMA nodes on the CPU. Note that the relationship between GPU index and NUMA domain are inverse.

Table. 4-way NVIDIA A40 Mapping and GPU-CPU Affinitization 


GPU0GPU1GPU2GPU3HSNCPU AffinityNUMA Affinity
GPU0XSYSSYSSYSSYS48-633
GPU1SYSXSYSSYSSYS32-472
GPU2SYSSYSXSYSSYS16-311
GPU3SYSSYSSYSXPHB0-150
HSNSYSSYSSYSPHB

Table Legend

X    = Self
SYS  = Connection traversing PCIe as well as the SMP interconnect between NUMA nodes (e.g., QPI/UPI)
NODE = Connection traversing PCIe as well as the interconnect between PCIe Host Bridges within a NUMA node
PHB  = Connection traversing PCIe as well as a PCIe Host Bridge (typically the CPU)
NV#  = Connection traversing a bonded set of # NVLinks

Table. 4-way NVIDIA A100 GPU Compute Node Specifications 

SpecificationValue
Number of nodes100
GPUNVIDIA A100

(Vendor page)

GPUs per node4
GPU Memory (GB)40 
CPUAMD Milan
CPU sockets per node1

Cores per socket

64

Cores per node64

Hardware threads per core

1

Hardware threads per node

64

Clock rate (GHz)

~ 2.45

RAM (GB)

256

Cache (KB) L1/L2/L3

 64/512/32768

Local storage (TB)

1.5 TB

The AMD CPUs are set for 4 NUMA domains per socket (NPS=4). 

Table. 4-way NVIDIA A100 Mapping and GPU-CPU Affinitization


GPU0GPU1GPU2GPU3HSNCPU AffinityNUMA Affinity
GPU0XNV4NV4NV4SYS48-633
GPU1NV4XNV4NV4SYS32-472
GPU2NV4NV4XNV4SYS16-311
GPU3NV4NV4NV4XPHB0-150
HSNSYSSYSSYSPHB

Table Legend

X    = Self
SYS  = Connection traversing PCIe as well as the SMP interconnect between NUMA nodes (e.g., QPI/UPI)
NODE = Connection traversing PCIe as well as the interconnect between PCIe Host Bridges within a NUMA node
PHB  = Connection traversing PCIe as well as a PCIe Host Bridge (typically the CPU)
NV#  = Connection traversing a bonded set of # NVLinks

Table. 8-way NVIDIA A100 GPU Large Memory Compute Node Specifications 

SpecificationValue
Number of nodes6
GPUNVIDIA A100

(Vendor page)

GPUs per node8
GPU Memory (GB)40 
CPUAMD Milan
CPU sockets per node2

Cores per socket

64

Cores per node128

Hardware threads per core

1

Hardware threads per node

128

Clock rate (GHz)

~ 2.45

RAM (GB)

2,048

Cache (KB) L1/L2/L3

 64/512/32768

Local storage (TB)

1.5 TB

The AMD CPUs are set for 4 NUMA domains per socket (NPS=4). 

Table. 8-way NVIDIA A100 Mapping and GPU-CPU Affinitization 


GPU0GPU1GPU2GPU3GPU4GPU5GPU6GPU7HSNCPU AffinityNUMA Affinity
GPU0XNV12NV12NV12NV12NV12NV12NV12SYS48-633
GPU1NV12XNV12NV12NV12NV12NV12NV12SYS48-633
GPU2NV12NV12XNV12NV12NV12NV12NV12SYS16-311
GPU3NV12NV12NV12XNV12NV12NV12NV12SYS16-311
GPU0NV12NV12NV12NV12XNV12NV12NV12SYS112-1277
GPU1NV12NV12NV12NV12NV12XNV12NV12SYS112-1277
GPU2NV12NV12NV12NV12NV12NV12XNV12SYS80-955
GPU3NV12NV12NV12NV12NV12NV12NV12XSYS80-955
HSNSYSSYSSYSSYSSYSSYSSYSSYSX

Table Legend

X    = Self
SYS  = Connection traversing PCIe as well as the SMP interconnect between NUMA nodes (e.g., QPI/UPI)
NODE = Connection traversing PCIe as well as the interconnect between PCIe Host Bridges within a NUMA node
PHB  = Connection traversing PCIe as well as a PCIe Host Bridge (typically the CPU)
NV#  = Connection traversing a bonded set of # NVLinks

Table. 8-way AMD MI100 GPU Large Memory Compute Node Specifications 

SpecificationValue
Number of nodes1
GPUAMD MI100  

(Vendor page)

GPUs per node8
GPU Memory (GB)32
CPUAMD Milan
CPU sockets per node2

Cores per socket

64

Cores per node128

Hardware threads per core

1

Hardware threads per node

128

Clock rate (GHz)

~ 2.45

RAM (GB)

2,048

Cache (KB) L1/L2/L3

 64/512/32768

Local storage (TB)

1.5 TB

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Login Nodes

Login nodes provide interactive support for code compilation. 

Specialized Nodes

Delta will support data transfer nodes (serving the "NCSA Delta" Globus Online collection) and nodes in support of other services.

Network

Delta is connected to the NPCF core router & exit infrastructure via two 100Gbps connections, NCSA's 400Gbps+ of WAN connectivity carry traffic to/from users on an optimal peering. 

Delta resources are inter-connected with HPE/Cray's 100Gbps/200Gbps SlingShot interconnect.  

File Systems

Note:  Users of Delta have access to 3 file systems at the time of system launch, a fourth relaxed-POSIX file system will be made available at a later date. 

Delta
The Delta storage infrastructure provides users with their $HOME and $SCRATCH areas.  These file systems are mounted across all Delta nodes and are accessible on the Delta DTN Endpoints.  The aggregate performance of this subsystem is 70GB/s and it has 6PB of usable space.  These file systems run Lustre via DDN's ExaScaler 6 stack (Lustre 2.14 based).

Hardware:
DDN SFA7990XE (Quantity: 3), each unit contains

  • One additional SS9012 enclosure
  • 168 x 16TB SAS Drives
  • 7 x 1.92TB SAS SSDs

The $HOME file system has 4 OSTs and is set with a default stripe size of 1. 

The $SCRATCH file system has 8 OSTs and has Lustre Progressive File Layout (PFL) enabled which automatically restripes a file as the file grows. The thresholds for PFL striping for $SCRATCH are

File sizestripe count
0-32M1 OST
32M-512M4 OST
512M+8 OST

Best Practices

  • To reduce the load on the file system metadata services, the ls option for context dependent font coloring, --color, is disabled by default. 

Future Hardware:
An additional pool of NVME flash from DDN has been installed in early summer 2022.  This flash is initially deployed as a tier for "hot" data in scratch.  This subsystem will have an aggregate performance of 500GB/s and will have 3PB of raw capacity. As noted above this subsystem will transition to an independent relaxed POSIX namespace file system, communications on that timeline will be announced as updates are available.  

Taiga
Taiga is NCSA’s global file system which provides users with their $WORK area.  This file system is mounted across all Delta systems at /taiga (also /taiga/nsf/delta is bind mounted at /projects) and is accessible on both the Delta and Taiga DTN endpoints.  For NCSA & Illinois researchers, Taiga is also mounted on NCSA's HAL and Radiant systems.  This storage subsystem has an aggregate performance of 140GB/s and 1PB of its capacity allocated to users of the Delta system. /taiga is a Lustre file system running DDN Exascaler software.  

Hardware:
DDN SFA400NVXE (Quantity: 2), each unit contains

  • 4 x SS9012 enclosures
  • NVME for metadata and small files

DDN SFA18XE (Quantity: 1) *coming soon*, each unit contains

  • 10 x SS9012 enclosures
  • NVME for for metadata and small files

$WORK and $SCRATCH

A "module reset" in a job script will populate $WORK and $SCRATCH environment variables automatically, or you may set them as WORK=/projects/<account>/$USER , SCRATCH=/scratch/<account>/$USER .

File System

Quota

SnapshotsPurged

Key Features

HOME (/u)

25GB. 400,000 files per user.No/TBANoArea for software, scripts, job files, etc. NOT intended as a source/destination for I/O during jobs

WORK (/projects)

500 GB. Up to 1-25 TB  by allocation requestNo/TBANoArea for shared data for a project, common data sets, software, results, etc.

SCRATCH (/scratch)

1000 GB. Up to 1-100 TB by allocation request.NoYes; files older than 30-days (access time)Area for computation, largest allocations, where I/O from jobs should occur
/tmp0.74-1.50 TB shared or dedicated depending on node usage by job(s), no quotas in placeNoAfter each jobLocally attached disk for fast small file IO. 
quota usage

The quota command allows you to view your use of the file systems and use by your projects. Below is a sample output for a person "user" who is in two projects: aaaa, and bbbb. The home directory quota does not depend on which project group the file is written with. 

quota command
<user>@dt-login01 ~]$ quota
Quota usage for user <user>:
-------------------------------------------------------------------------------------------
| Directory Path | User | User | User  | User | User   | User |
|                | Block| Soft | Hard  | File | Soft   | Hard |
|                | Used | Quota| Limit | Used | Quota  | Limit|
--------------------------------------------------------------------------------------
| /u/<user>      | 20k  | 25G  | 27.5G | 5    | 300000 | 330000 |
--------------------------------------------------------------------------------------
Quota usage for groups user <user> is a member of:
-------------------------------------------------------------------------------------
| Directory Path | Group | Group | Group | Group | Group  | Group |
|                | Block | Soft  | Hard  | File  | Soft   | Hard  |
|                | Used  | Quota | Limit | Used  | Quota  | Limit |
-------------------------------------------------------------------------------------------
| /projects/aaaa | 8k    | 500G  | 550G  | 2     | 300000 | 330000 |
| /projects/bbbb | 24k   | 500G  | 550G  | 6     | 300000 | 330000 |
| /scratch/aaaa  | 8k    | 552G  | 607.2G| 2     | 500000 | 550000 |
| /scratch/bbbb  | 24k   | 9.766T| 10.74T| 6     | 500000 | 550000 |
------------------------------------------------------------------------------------------

File System Dependency Specification for Jobs

We request that jobs specify file system or systems being used in order for us to respond to resource availability issues. We assume that all jobs depend on the HOME file system. 

Table of Slurm Feature/constraint labels

File systemFeature/constraint labelNote
WORK (/projects)projects
SCRACH (/scratch)scratch
IME (/ime)imedepends on scratch
TAIGA (/taiga)taiga

The Slurm constraint specifier and slurm Feature attribute for jobs are used to add file system dependencies to a job.

Slurm Feature Specification

For already submitted and pending (PD) jobs, please use the Slurm Feature attribute as follows:

$ scontrol update job=JOBID Features="feature1&feature2"

For example, to add scratch and ime Features to an already submitted job:

$ scontrol update job=713210 Features="scratch&ime"

To verify the setting:

$ scontrol show job 713210 | grep Feature
   Features=scratch&ime DelayBoot=00:00:00

Slurm constraint Specification

To add Slurm job constraint attributes when submitting a job with sbatch (or with srun as a command line argument) use the following:

#SBATCH --constraint="constraint1&constraint2.."

For example, to add scratch and ime constraints to when submitting a job:

#SBATCH --constraint="scratch&ime"

To verify the setting:

$ scontrol show job 713267 | grep Feature
   Features=scratch&ime DelayBoot=00:00:00

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Accessing the System

Direct Access 

Direct access to the Delta login nodes is via ssh using your NCSA username, password and NCS Duo MFA.  Please see NCSA Allocation and Account Management page for links to NCSA Identity and NCSA Duo services. The login nodes provide access to the CPU and GPU resources on Delta.

login node hostnameexample usage with ssh
dt-login01.delta.ncsa.illinois.edu
ssh -Y username@dt-login01.delta.ncsa.illinois.edu  
( -Y allows X11 forwarding from linux hosts )
dt-login02.delta.ncsa.illinois.edu
ssh -l username dt-login02.delta.ncsa.illinois.edu
( -l username alt. syntax for user@host )

login.delta.ncsa.illinois.edu

(round robin DNS name for the set of login nodes)

ssh username@login.delta.ncsa.illinois.edu

Please see NCSA Allocation and Account Management for the steps to change your NCSA password for direct access and set up NCSA DUO.  Please contact help@ncsa.illinois.edu for assistance if you do not know your NCSA username.

Use of ssh-key pairs is disabled for general use. Please contact NCSA Help at help@ncsa.illinois.edu for key-pair use by Gateway allocations.

maintaining persistent sessions: tmux

tmux is available on the login nodes to maintain persistent sessions.  See the tmux man page for more information.  Use the targeted login hostnames (dt-login01 or dt-login02) to attach to the login node where you started tmux after making note of the hostname.  Avoid the round-robin hostname when using tmux.


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Citizenship

You share Delta with thousands of other users , and what you do on the system affects others. Exercise good citizenship to ensure that your activity does not adversely impact the system and the research community with whom you share it. Here are some rules of thumb:

  • Don’t run production jobs on the login nodes (very short time debug tests are fine)
  • Don’t stress filesystems with known-harmful access patterns (many thousands of small files in a single directory)
  • submit an informative help-desk ticket including loaded modules (module list) and stdout/stderr messages

Managing and Transferring Files

File Systems

Each user has a home directory, $HOME,  located at /u/$USER.

For example, a user (with username auser) who has an allocated project with a local project serial code abcd will see the following entries in their $HOME and entries in the project and scratch file systems. To determine the mapping of ACCESS project to local project please use the accounts  command.

Directory access changes can be made using the facl command. Contact help@ncsa.illinois.edu if you need assistance with enabling access to specific users and projects.

$ ls -ld /u/$USER
drwxrwx---+ 12 root root 12345 Feb 21 11:54 /u/$USER

$ ls -ld /projects/abcd
drwxrws---+  45 root   delta_abcd      4096 Feb 21 11:54 /projects/abcd

$ ls -l /projects/abcd
total 0
drwxrws---+ 2 auser delta_abcd 6 Feb 21 11:54 auser
drwxrws---+ 2 buser delta_abcd 6 Feb 21 11:54 buser
...

$ ls -ld /scratch/abcd
drwxrws---+  45 root   delta_abcd      4096 Feb 21 11:54 /scratch/abcd

$ ls -l /scratch/abcd
total 0
drwxrws---+ 2 auser delta_abcd 6 Feb 21 11:54 auser
drwxrws---+ 2 buser delta_abcd 6 Feb 21 11:54 buser
...

To avoid issues when file systems become unstable or non-responsive, we  recommend not putting symbolic links from $HOME to the project and scratch spaces. 


/tmp on compute nodes (job duration)

The high performance ssd storage (740GB cpu, 1.5TB gpu)  is available in /tmp (unique to each node and job–not a shared filesystem) and may contain less than the expected free space if the node(s) are running multiple jobs.  Codes that need to perform i/o to many small files should target /tmp on each node of the job and save results to other filesystems before the job ends.

Transferring your Files

To transfer files to and from the Delta system :

GUI apps need to support DUO 2-factor authentication

Many GUI applications that support ssh/scp/sftp will work with DUO.  A good first step is to use the interactive (not stored/saved) password option with those apps.  The interactive login should present you with the 1st password prompt (your kerberos password) followed by the 2nd password prompt for DUO (push to device or passcode from DUO app).


Sharing Files with Collaborators

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Building Software

The Delta programming environment supports the GNU, AMD (AOCC), Intel and NVIDIA HPC compilers. Support for the HPE/Cray Programming environment is forthcoming. 

Modules provide access to the compiler + MPI environment. 

The default environment includes the GCC 11.2.0 compiler + OpenMPI with support for cuda and gdrcopy. nvcc is in the cuda module and is loaded by default.

AMD recommended compiler flags for GNU, AOCC, and Intel compilers for Milan processors can be found in the AMD Compiler Options Quick Reference Guide for Epyc 7xx3 processors

Serial

To build (compile and link) a serial program in Fortran, C, and C++:

gccaoccnvhpc
gfortran myprog.f
gcc myprog.c
g++ myprog.cc
flang myprog.f
clang myprog.c
clang myprog.cc
nvfortran myprog.f
nvc myprog.c
nvc++ myprog.cc

MPI

To build (compile and link) a MPI program in Fortran, C, and C++:

MPI Implementationmodulefiles for MPI/CompilerBuild Commands


OpenMPI
(Home Page  /  Documentation)

aocc/3.2.0 openmpi

gcc/11.2.0 openmpi

nvhpc/22.2 openmpi
Fortran 77:mpif77 myprog.f
Fortran 90:mpif90 myprog.f90
C:mpicc myprog.c
C++:mpic++ myprog.cc

OpenMP

To build an OpenMP program, use the  -fopenmp  / -mp  option:

gccaoccnvhpc
gfortran -fopenmp myprog.f
gcc -fopenmp myprog.c
g++ -fopenmp myprog.cc
flang -fopenmp myprog.f
clang -fopenmp myprog.c
clang -fopenmp myprog.cc
nvfortran -mp myprog.f
nvc -mp myprog.c
nvc++ -mp myprog.cc

Hybrid MPI/OpenMP

To build an MPI/OpenMP hybrid program, use the  -fopenmp  /  -mp  option with the MPI compiling commands:

GCC
PGI/NVHPC
mpif77 -fopenmp myprog.f
mpif90 -fopenmp myprog.f90
mpicc -fopenmp myprog.c

mpic++ -fopenmp myprog.cc

mpif77 -mp myprog.f
mpif90 -mp myprog.f90
mpicc -mp myprog.c

mpic++ -mp myprog.cc
Cray xthi.c sample code

Document - XC Series User Application Placement Guide CLE6..0UP01 S-2496 | HPE Support

This code can be compiled using the methods show above.  The code appears in some of the batch script examples below to demonstrate core placement options.

xthi.c
#define _GNU_SOURCE

#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <sched.h>
#include <mpi.h>
#include <omp.h>

/* Borrowed from util-linux-2.13-pre7/schedutils/taskset.c */
static char *cpuset_to_cstr(cpu_set_t *mask, char *str)
{
  char *ptr = str;
  int i, j, entry_made = 0;
  for (i = 0; i < CPU_SETSIZE; i++) {
    if (CPU_ISSET(i, mask)) {
      int run = 0;
      entry_made = 1;
      for (j = i + 1; j < CPU_SETSIZE; j++) {
        if (CPU_ISSET(j, mask)) run++;
        else break;
      }
      if (!run)
        sprintf(ptr, "%d,", i);
      else if (run == 1) {
        sprintf(ptr, "%d,%d,", i, i + 1);
        i++;
      } else {
        sprintf(ptr, "%d-%d,", i, i + run);
        i += run;
      }
      while (*ptr != 0) ptr++;
    }
  }
  ptr -= entry_made;
  *ptr = 0;
  return(str);
}

int main(int argc, char *argv[])
{
  int rank, thread;
  cpu_set_t coremask;
  char clbuf[7 * CPU_SETSIZE], hnbuf[64];

  MPI_Init(&argc, &argv);
  MPI_Comm_rank(MPI_COMM_WORLD, &rank);
  memset(clbuf, 0, sizeof(clbuf));
  memset(hnbuf, 0, sizeof(hnbuf));
  (void)gethostname(hnbuf, sizeof(hnbuf));
  #pragma omp parallel private(thread, coremask, clbuf)
  {
    thread = omp_get_thread_num();
    (void)sched_getaffinity(0, sizeof(coremask), &coremask);
    cpuset_to_cstr(&coremask, clbuf);
    #pragma omp barrier
    printf("Hello from rank %d, thread %d, on %s. (core affinity = %s)\n",
            rank, thread, hnbuf, clbuf);
  }
  MPI_Finalize();
  return(0);
}

A version of xthi is also available from ORNL

% git clone https://github.com/olcf/XC30-Training/blob/master/affinity/Xthi.c

OpenACC

To build an OpenACC program, use the  -acc  option and the  -mp  option for multi-threaded:

NON-MULTITHREADED
MULTITHREADED
nvfortran -acc myprog.f
nvc -acc myprog.c
nvc++ -acc myprog.cc

nvfortran -acc -mp myprog.f
nvc -acc -mp myprog.c
nvc++ -acc -mp myprog.cc

CUDA

Cuda compilers (nvcc) are included in the cuda module which is loaded by default under modtree/gpu.  For the cuda fortran compiler and other Nvidia development tools, load the "nvhpc" module.

nv* commands when nvhpc is loaded
[arnoldg@dt-login03 namd]$ nv
nvaccelerror             nvidia-bug-report.sh     nvlink
nvaccelinfo              nvidia-cuda-mps-control  nv-nsight-cu
nvc                      nvidia-cuda-mps-server   nv-nsight-cu-cli
nvc++                    nvidia-debugdump         nvprepro
nvcc                     nvidia-modprobe          nvprof
nvcpuid                  nvidia-persistenced      nvprune
nvcudainit               nvidia-powerd            nvsize
nvdecode                 nvidia-settings          nvunzip
nvdisasm                 nvidia-sleep.sh          nvvp
nvextract                nvidia-smi               nvzip
nvfortran                nvidia-xconfig

See also: https://developer.nvidia.com/hpc-sdk

HIP / ROCM (AMD MI100)

To access the development environment for the gpuMI100x8 partition, start a job on the node with srun or sbatch.  Then set your PATH to prefix /opt/rocm/bin where the HIP and ROCM tools are installed.  A sample batch script to obtain an xterm is shown along with setting the path on the compute node:

interactive xterm batch script for slurm
#!/bin/bash -x

MYACCOUNT=$1
GPUS=--gpus-per-node=1
PARTITION=gpuMI100x8-interactive
srun --tasks-per-node=1 --nodes=1 --cpus-per-task=1 \
  --mem=16g \
  --partition=$PARTITION \
  --time=00:30:00 \
  --account=$MYACCOUNT \
  $GPUS --x11 \
  xterm


AMD HIP development environment on gpud01
[arnoldg@gpud01 bin]$ export PATH=/opt/rocm/bin:$PATH
[arnoldg@gpud01 bin]$ hipcc
No Arguments passed, exiting ...
[arnoldg@gpud01 bin]$ 


See also: https://developer.amd.com/resources/rocm-learning-center/fundamentals-of-hip-programming/ , https://rocmdocs.amd.com/en/latest/

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Software

Delta software is provisioned, when possible, using spack to produce modules for use via the lmod based module system. Select NVIDIA NGC containers are made available (see the container section below) and are periodically updated from the NVIDIA NGC site.  An automated list of available software can be found on the ACCESS website.

modules/lmod 

Delta provides two sets of modules and a variety of compilers in each set.  The default environment is modtree/gpu which loads a recent version of gnu compilers , the openmpi implementation of MPI, and cuda.  The environment with gpu support will build binaries that run on both the gpu nodes (with cuda) and cpu nodes (potentially with warning messages because those nodes lack cuda drivers).  For situations where the same version of software is to be deployed on both gpu and cpu nodes but with separate builds, the modtree/cpu environment provides the same default compiler and MPI but without cuda.  Use module spider package_name to search for software in lmod and see the steps to load it for your environment.

module (lmod) commandexample

module list

(display the currently loaded modules)

$ module list

Currently Loaded Modules:
  1) gcc/11.2.0   3) openmpi/4.1.2   5) modtree/gpu
  2) ucx/1.11.2   4) cuda/11.6.1

module load <package_name>

(loads a package or metamodule such as modtree/gpu or netcdf-c)

$ module load modtree/cpu

Due to MODULEPATH changes, the following have been reloaded:
  1) gcc/11.2.0     2) openmpi/4.1.2     3) ucx/1.11.2

The following have been reloaded with a version change:
  1) modtree/gpu => modtree/cpu

module spider <package_name>

(finds modules and displays the ways to load them)


module -r spider "regular expression"

$ module spider openblas

----------------------------------------------------------------------------
  openblas: openblas/0.3.20
----------------------------------------------------------------------------

    You will need to load all module(s) on any one of the lines below before the
 "openblas/0.3.20" module is available to load.

      aocc/3.2.0
      gcc/11.2.0
 
    Help:
      OpenBLAS: An optimized BLAS library 
$ module -r spider "^r$"

----------------------------------------------------------------------------
  r:
----------------------------------------------------------------------------
     Versions:
        r/4.1.3
...

see also: User Guide for Lmod

Please open a service request ticket by sending email to help@ncsa.illinois.edu for help with software not currently installed on the Delta system. For single user or single project use cases the preference is for the user to use the spack software package manager to install software locally against the system spack installation as documented <here>. Delta support staff are available to provide limited assistance. For general installation requests the Delta project office will review requests for broad use and installation effort.

Python

On Delta, you may install your own python software stacks as needed.  There are a couple choices when customizing your python setup.  You may use any of these methods with any of the python versions or instances described below (or you may install your own python versions):

  1. pip3 : pip3 install --user <python_package>
    1. useful when you need just 1 python environment per python version or instance
  2. venv (python virtual environment)
    1. can name environments (metadata) and have multiple environments per python version or instance
  3. conda environments
    1. similar to venv but with more flexibility , see this comparison (1/2 way down the page)

NGC containers for gpu nodes

The Nvidia NGC containers on Delta provide optimized python frameworks built for Delta's A100 and A40 gpus.  Delta staff recommend using an NGC container when possible with the gpu nodes (or use the anaconda3_gpu module described later).

The default gcc (latest version) programming environment for either modtree/cpu or modtree/gpu contains:

Anaconda

anaconda3_cpu

Use python from the anaconda3_cpu module if you need some of the modules provided by Anaconda in your python workflow.  See the "managing environments" section of the Conda getting started guide to learn how to customize Conda for your workflow and add extra python modules to your environment.  We recommend starting with anaconda3_cpu for modtree/cpu and the cpu nodes, do not use this module with gpus, use anaconda3_gpu instead.

anaconda and containers

If you use anaconda with NGC containers, take care to use the python from the container and not the python from anaconda or one of its environments.  The container's python should be 1st in $PATH.  You may --bind the anaconda directory or other paths into the container so that you can start your conda environments, but with the container's python (/usr/bin/python).

older versions of python and modules

https://repo.anaconda.com/archive/   contains previous Anaconda versions.  The bundles are not small, but using one from Anaconda would ensure that you get software that was built to work together at a point in time.  If you require an older version of a python lib/module, we suggest looking back in time at the Anaconda site.

$ module load modtree/cpu
$ module load gcc anaconda3_cpu
$ which conda
/sw/external/python/anaconda3_cpu/conda
$ module list Currently Loaded Modules:
  1) cue-login-env/1.0   6) libfabric/1.14.0     11) ucx/1.11.2
  2) default             7) lustre/2.14.0_ddn23  12) openmpi/4.1.2
  3) gcc/11.2.0          8) openssh/8.0p1        13) modtree/cpu
  4) knem/1.1.4          9) pmix/3.2.3           14) anaconda3_cpu/4.13.0
  5) libevent/2.1.8     10) rdma-core/32.0

List of modules in anaconda3_cpu

The current list of modules available in anaconda3_cpu is shown via "conda list", including tensorflow, pytorch, etc:

anaconda3_cpu modules: conda list
# packages in environment at /sw/external/python/anaconda3_cpu: # Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0            py39h06a4308_1  
_libgcc_mutex             0.1                        main  
_openmp_mutex             4.5                       1_gnu  
absl-py                   1.1.0                    pypi_0    pypi
aiobotocore               2.3.3                    pypi_0    pypi
aiohttp                   3.8.1            py39h7f8727e_1  
aioitertools              0.10.0                   pypi_0    pypi
aiosignal                 1.2.0              pyhd3eb1b0_0  
alabaster                 0.7.12             pyhd3eb1b0_0  
anaconda                  2022.05                  py39_0  
anaconda-client           1.9.0            py39h06a4308_0  
anaconda-navigator        2.1.4            py39h06a4308_0  
anaconda-project          0.10.2             pyhd3eb1b0_0  
anyio                     3.5.0            py39h06a4308_0  
appdirs                   1.4.4              pyhd3eb1b0_0  
argon2-cffi               21.3.0             pyhd3eb1b0_0  
argon2-cffi-bindings      21.2.0           py39h7f8727e_0  
arrow                     1.2.2              pyhd3eb1b0_0  
astroid                   2.6.6            py39h06a4308_0  
astropy                   5.0.4            py39hce1f21e_0  
asttokens                 2.0.5              pyhd3eb1b0_0  
astunparse                1.6.3                    pypi_0    pypi
async-timeout             4.0.1              pyhd3eb1b0_0  
atomicwrites              1.4.0                      py_0  
attrs                     21.4.0             pyhd3eb1b0_0  
automat                   20.2.0                     py_0  
autopep8                  1.6.0              pyhd3eb1b0_0  
awscli                    1.25.14                  pypi_0    pypi
babel                     2.9.1              pyhd3eb1b0_0  
backcall                  0.2.0              pyhd3eb1b0_0  
backports                 1.1                pyhd3eb1b0_0  
backports.functools_lru_cache 1.6.4              pyhd3eb1b0_0  
backports.tempfile        1.0                pyhd3eb1b0_1  
backports.weakref         1.0.post1                  py_1  
bcrypt                    3.2.0            py39he8ac12f_0  
beautifulsoup4            4.11.1           py39h06a4308_0  
binaryornot               0.4.4              pyhd3eb1b0_1  
bitarray                  2.4.1            py39h7f8727e_0  
bkcharts                  0.2              py39h06a4308_0  
black                     19.10b0                    py_0  
blas                      1.0                         mkl  
bleach                    4.1.0              pyhd3eb1b0_0  
blosc                     1.21.0               h8c45485_0  
bokeh                     2.4.2            py39h06a4308_0  
boto3                     1.21.32            pyhd3eb1b0_0  
botocore                  1.24.21                  pypi_0    pypi
bottleneck                1.3.4            py39hce1f21e_0  
brotli                    1.0.9                he6710b0_2  
brotlipy                  0.7.0           py39h27cfd23_1003  
brunsli                   0.1                  h2531618_0  
bzip2                     1.0.8                h7b6447c_0  
c-ares                    1.18.1               h7f8727e_0  
ca-certificates           2022.3.29            h06a4308_1  
cachetools                4.2.2              pyhd3eb1b0_0  
certifi                   2021.10.8        py39h06a4308_2  
cffi                      1.15.0           py39hd667e15_1  
cfitsio                   3.470                hf0d0db6_6  
chardet                   4.0.0           py39h06a4308_1003  
charls                    2.2.0                h2531618_0  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
click                     8.0.4            py39h06a4308_0  
cloudpickle               2.0.0              pyhd3eb1b0_0  
clyent                    1.2.2            py39h06a4308_1  
colorama                  0.4.4              pyhd3eb1b0_0  
colorcet                  2.0.6              pyhd3eb1b0_0  
conda                     4.13.0           py39h06a4308_0  
conda-build               3.21.8           py39h06a4308_2  
conda-content-trust       0.1.1              pyhd3eb1b0_0  
conda-env                 2.6.0                         1  
conda-pack                0.6.0              pyhd3eb1b0_0  
conda-package-handling    1.8.1            py39h7f8727e_0  
conda-repo-cli            1.0.4              pyhd3eb1b0_0  
conda-token               0.3.0              pyhd3eb1b0_0  
conda-verify              3.4.2                      py_1  
constantly                15.1.0             pyh2b92418_0  
cookiecutter              1.7.3              pyhd3eb1b0_0  
cpuonly                   2.0                           0    pytorch-nightly
cryptography              3.4.8            py39hd23ed53_0  
cssselect                 1.1.0              pyhd3eb1b0_0  
curl                      7.82.0               h7f8727e_0  
cycler                    0.11.0             pyhd3eb1b0_0  
cython                    0.29.28          py39h295c915_0  
cytoolz                   0.11.0           py39h27cfd23_0  
daal4py                   2021.5.0         py39h78b71dc_0  
dal                       2021.5.1           h06a4308_803  
dask                      2022.2.1           pyhd3eb1b0_0  
dask-core                 2022.2.1           pyhd3eb1b0_0  
dataclasses               0.8                pyh6d0b6a4_7  
datashader                0.13.0             pyhd3eb1b0_1  
datashape                 0.5.4            py39h06a4308_1  
dbus                      1.13.18              hb2f20db_0  
debugpy                   1.5.1            py39h295c915_0  
decorator                 5.1.1              pyhd3eb1b0_0  
defusedxml                0.7.1              pyhd3eb1b0_0  
diff-match-patch          20200713           pyhd3eb1b0_0  
dill                      0.3.5.1                  pypi_0    pypi
distributed               2022.2.1           pyhd3eb1b0_0  
docutils                  0.16                     pypi_0    pypi
entrypoints               0.4              py39h06a4308_0  
et_xmlfile                1.1.0            py39h06a4308_0  
etils                     0.7.1                    pypi_0    pypi
executing                 0.8.3              pyhd3eb1b0_0  
expat                     2.4.4                h295c915_0  
ffmpeg                    4.2.2                h20bf706_0  
filelock                  3.6.0              pyhd3eb1b0_0  
flake8                    3.9.2              pyhd3eb1b0_0  
flask                     1.1.2              pyhd3eb1b0_0  
flatbuffers               1.12                     pypi_0    pypi
fontconfig                2.13.1               h6c09931_0  
fonttools                 4.25.0             pyhd3eb1b0_0  
freetype                  2.11.0               h70c0345_0  
frozenlist                1.2.0            py39h7f8727e_0  
fsspec                    2022.5.0                 pypi_0    pypi
funcx                     1.0.2                    pypi_0    pypi
funcx-common              0.0.15                   pypi_0    pypi
future                    0.18.2           py39h06a4308_1  
gast                      0.4.0                    pypi_0    pypi
gensim                    4.1.2            py39h295c915_0  
giflib                    5.2.1                h7b6447c_0  
glib                      2.69.1               h4ff587b_1  
glob2                     0.7                pyhd3eb1b0_0  
globus-cli                3.8.0                    pypi_0    pypi
globus-sdk                3.11.0                   pypi_0    pypi
gmp                       6.2.1                h2531618_2  
gmpy2                     2.1.2            py39heeb90bb_0  
gnutls                    3.6.15               he1e5248_0  
google-api-core           1.25.1             pyhd3eb1b0_0  
google-auth               1.33.0             pyhd3eb1b0_0  
google-auth-oauthlib      0.4.6                    pypi_0    pypi
google-cloud-core         1.7.1              pyhd3eb1b0_0  
google-cloud-storage      1.31.0                     py_0  
google-crc32c             1.1.2            py39h27cfd23_0  
google-pasta              0.2.0                    pypi_0    pypi
google-resumable-media    1.3.1              pyhd3eb1b0_1  
googleapis-common-protos  1.53.0           py39h06a4308_0  
greenlet                  1.1.1            py39h295c915_0  
grpcio                    1.42.0           py39hce63b2e_0  
gst-plugins-base          1.14.0               h8213a91_2  
gstreamer                 1.14.0               h28cd5cc_2  
gviz-api                  1.10.0                   pypi_0    pypi
h5py                      3.6.0            py39ha0f2276_0  
hdf5                      1.10.6               hb1b8bf9_0  
heapdict                  1.0.1              pyhd3eb1b0_0  
holoviews                 1.14.8             pyhd3eb1b0_0  
hvplot                    0.7.3              pyhd3eb1b0_1  
hyperlink                 21.0.0             pyhd3eb1b0_0  
icu                       58.2                 he6710b0_3  
idna                      3.3                pyhd3eb1b0_0  
imagecodecs               2021.8.26        py39h4cda21f_0  
imageio                   2.9.0              pyhd3eb1b0_0  
imagesize                 1.3.0              pyhd3eb1b0_0  
importlib-metadata        4.11.3           py39h06a4308_0  
importlib-resources       5.9.0                    pypi_0    pypi
importlib_metadata        4.11.3               hd3eb1b0_0  
incremental               21.3.0             pyhd3eb1b0_0  
inflection                0.5.1            py39h06a4308_0  
iniconfig                 1.1.1              pyhd3eb1b0_0  
intake                    0.6.5              pyhd3eb1b0_0  
intel-openmp              2021.4.0          h06a4308_3561  
intervaltree              3.1.0              pyhd3eb1b0_0  
ipykernel                 6.9.1            py39h06a4308_0  
ipython                   8.2.0            py39h06a4308_0  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
ipywidgets                7.6.5              pyhd3eb1b0_1  
isort                     5.9.3              pyhd3eb1b0_0  
itemadapter               0.3.0              pyhd3eb1b0_0  
itemloaders               1.0.4              pyhd3eb1b0_1  
itsdangerous              2.0.1              pyhd3eb1b0_0  
jax                       0.3.16                   pypi_0    pypi
jaxlib                    0.3.15                   pypi_0    pypi
jdcal                     1.4.1              pyhd3eb1b0_0  
jedi                      0.18.1           py39h06a4308_1  
jeepney                   0.7.1              pyhd3eb1b0_0  
jinja2                    2.11.3             pyhd3eb1b0_0  
jinja2-time               0.2.0              pyhd3eb1b0_3  
jmespath                  0.10.0             pyhd3eb1b0_0  
joblib                    1.1.0              pyhd3eb1b0_0  
jpeg                      9e                   h7f8727e_0  
jq                        1.6               h27cfd23_1000  
json5                     0.9.6              pyhd3eb1b0_0  
jsonschema                4.4.0            py39h06a4308_0  
jupyter                   1.0.0            py39h06a4308_7  
jupyter_client            6.1.12             pyhd3eb1b0_0  
jupyter_console           6.4.0              pyhd3eb1b0_0  
jupyter_core              4.9.2            py39h06a4308_0  
jupyter_server            1.13.5             pyhd3eb1b0_0  
jupyterlab                3.3.2              pyhd3eb1b0_0  
jupyterlab_pygments       0.1.2                      py_0  
jupyterlab_server         2.10.3             pyhd3eb1b0_1  
jupyterlab_widgets        1.0.0              pyhd3eb1b0_1  
jxrlib                    1.1                  h7b6447c_2  
keras                     2.9.0                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
keyring                   23.4.0           py39h06a4308_0  
kiwisolver                1.3.2            py39h295c915_0  
krb5                      1.19.2               hac12032_0  
lame                      3.100                h7b6447c_0  
lazy-object-proxy         1.6.0            py39h27cfd23_0  
lcms2                     2.12                 h3be6417_0  
ld_impl_linux-64          2.35.1               h7274673_9  
lerc                      3.0                  h295c915_0  
libaec                    1.0.4                he6710b0_1  
libarchive                3.4.2                h62408e4_0  
libclang                  14.0.1                   pypi_0    pypi
libcrc32c                 1.1.1                he6710b0_2  
libcurl                   7.82.0               h0b77cf5_0  
libdeflate                1.8                  h7f8727e_5  
libedit                   3.1.20210910         h7f8727e_0  
libev                     4.33                 h7f8727e_1  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.3.0               h5101ec6_17  
libgfortran-ng            7.5.0               ha8ba4b0_17  
libgfortran4              7.5.0               ha8ba4b0_17  
libgomp                   9.3.0               h5101ec6_17  
libidn2                   2.3.2                h7f8727e_0  
liblief                   0.11.5               h295c915_1  
libllvm11                 11.1.0               h3826bc1_1  
libnghttp2                1.46.0               hce63b2e_0  
libopus                   1.3.1                h7b6447c_0  
libpng                    1.6.37               hbc83047_0  
libprotobuf               3.19.1               h4ff587b_0  
libsodium                 1.0.18               h7b6447c_0  
libspatialindex           1.9.3                h2531618_0  
libssh2                   1.10.0               h8f2d780_0  
libstdcxx-ng              9.3.0               hd4cf53a_17  
libtasn1                  4.16.0               h27cfd23_0  
libtiff                   4.2.0                h85742a9_0  
libunistring              0.9.10               h27cfd23_0  
libuuid                   1.0.3                h7f8727e_2  
libvpx                    1.7.0                h439df22_0  
libwebp                   1.2.2                h55f646e_0  
libwebp-base              1.2.2                h7f8727e_0  
libxcb                    1.14                 h7b6447c_0  
libxml2                   2.9.12               h03d6c58_0  
libxslt                   1.1.34               hc22bd24_0  
libzopfli                 1.0.3                he6710b0_0  
llvmlite                  0.38.0           py39h4ff587b_0  
locket                    0.2.1            py39h06a4308_2  
lxml                      4.8.0            py39h1f438cf_0  
lz4-c                     1.9.3                h295c915_1  
lzo                       2.10                 h7b6447c_2  
markdown                  3.3.4            py39h06a4308_0  
markupsafe                2.0.1            py39h27cfd23_0  
matplotlib                3.5.1            py39h06a4308_1  
matplotlib-base           3.5.1            py39ha18d171_1  
matplotlib-inline         0.1.2              pyhd3eb1b0_2  
mccabe                    0.6.1            py39h06a4308_1  
mistune                   0.8.4           py39h27cfd23_1000  
mkl                       2021.4.0           h06a4308_640  
mkl-service               2.4.0            py39h7f8727e_0  
mkl_fft                   1.3.1            py39hd3c417c_0  
mkl_random                1.2.2            py39h51133e4_0  
mock                      4.0.3              pyhd3eb1b0_0  
mpc                       1.1.0                h10f8cd9_1  
mpfr                      4.0.2                hb69a4c5_1  
mpi                       1.0                       mpich  
mpich                     3.3.2                hc856adb_0  
mpmath                    1.2.1            py39h06a4308_0  
msgpack-python            1.0.2            py39hff7bd54_1  
multidict                 5.2.0            py39h7f8727e_2  
multipledispatch          0.6.0            py39h06a4308_0  
munkres                   1.1.4                      py_0  
mypy_extensions           0.4.3            py39h06a4308_1  
navigator-updater         0.2.1                    py39_1  
nbclassic                 0.3.5              pyhd3eb1b0_0  
nbclient                  0.5.13           py39h06a4308_0  
nbconvert                 6.4.4            py39h06a4308_0  
nbformat                  5.3.0            py39h06a4308_0  
ncurses                   6.3                  h7f8727e_2  
nest-asyncio              1.5.5            py39h06a4308_0  
nettle                    3.7.3                hbbd107a_1  
networkx                  2.7.1              pyhd3eb1b0_0  
nltk                      3.7                pyhd3eb1b0_0  
nose                      1.3.7           pyhd3eb1b0_1008  
notebook                  6.4.8            py39h06a4308_0  
numba                     0.55.1           py39h51133e4_0  
numexpr                   2.8.1            py39h6abb31d_0  
numpy                     1.21.5           py39he7a7128_1  
numpy-base                1.21.5           py39hf524024_1  
numpydoc                  1.2                pyhd3eb1b0_0  
oauthlib                  3.2.0                    pypi_0    pypi
olefile                   0.46               pyhd3eb1b0_0  
oniguruma                 6.9.7.1              h27cfd23_0  
openh264                  2.1.1                h4ff587b_0  
openjpeg                  2.4.0                h3ad879b_0  
openpyxl                  3.0.9              pyhd3eb1b0_0  
openssl                   1.1.1n               h7f8727e_0  
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 21.3               pyhd3eb1b0_0  
pandas                    1.4.2            py39h295c915_0  
pandocfilters             1.5.0              pyhd3eb1b0_0  
panel                     0.13.0           py39h06a4308_0  
param                     1.12.0             pyhd3eb1b0_0  
parsel                    1.6.0            py39h06a4308_0  
parso                     0.8.3              pyhd3eb1b0_0  
partd                     1.2.0              pyhd3eb1b0_1  
patchelf                  0.13                 h295c915_0  
pathspec                  0.7.0                      py_0  
patsy                     0.5.2            py39h06a4308_1  
pcre                      8.45                 h295c915_0  
pep8                      1.7.1            py39h06a4308_0  
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    9.0.1            py39h22f2fdc_0  
pip                       21.2.4           py39h06a4308_0  
pkginfo                   1.8.2              pyhd3eb1b0_0  
plotly                    5.6.0              pyhd3eb1b0_0  
pluggy                    1.0.0            py39h06a4308_1  
poyo                      0.5.0              pyhd3eb1b0_0  
prometheus_client         0.13.1             pyhd3eb1b0_0  
prompt-toolkit            3.0.20             pyhd3eb1b0_0  
prompt_toolkit            3.0.20               hd3eb1b0_0  
protego                   0.1.16                     py_0  
protobuf                  3.19.1           py39h295c915_0  
psutil                    5.8.0            py39h27cfd23_1  
ptyprocess                0.7.0              pyhd3eb1b0_2  
pure_eval                 0.2.2              pyhd3eb1b0_0  
py                        1.11.0             pyhd3eb1b0_0  
py-lief                   0.11.5           py39h295c915_1  
pyasn1                    0.4.8              pyhd3eb1b0_0  
pyasn1-modules            0.2.8                      py_0  
pycodestyle               2.7.0              pyhd3eb1b0_0  
pycosat                   0.6.3            py39h27cfd23_0  
pycparser                 2.21               pyhd3eb1b0_0  
pyct                      0.4.6            py39h06a4308_0  
pycurl                    7.44.1           py39h8f2d780_1  
pydantic                  1.10.2                   pypi_0    pypi
pydispatcher              2.0.5            py39h06a4308_2  
pydocstyle                6.1.1              pyhd3eb1b0_0  
pyerfa                    2.0.0            py39h27cfd23_0  
pyflakes                  2.3.1              pyhd3eb1b0_0  
pygments                  2.11.2             pyhd3eb1b0_0  
pyhamcrest                2.0.2              pyhd3eb1b0_2  
pyjwt                     2.1.0            py39h06a4308_0  
pylint                    2.9.6            py39h06a4308_1  
pyls-spyder               0.4.0              pyhd3eb1b0_0  
pyodbc                    4.0.32           py39h295c915_1  
pyopenssl                 21.0.0             pyhd3eb1b0_1  
pyparsing                 3.0.4              pyhd3eb1b0_0  
pyqt                      5.9.2            py39h2531618_6  
pyrsistent                0.18.0           py39heee7806_0  
pysocks                   1.7.1            py39h06a4308_0  
pytables                  3.6.1            py39h77479fe_1  
pytest                    7.1.1            py39h06a4308_0  
python                    3.9.12               h12debd9_0  
python-dateutil           2.8.2              pyhd3eb1b0_0  
python-fastjsonschema     2.15.1             pyhd3eb1b0_0  
python-libarchive-c       2.9                pyhd3eb1b0_1  
python-lsp-black          1.0.0              pyhd3eb1b0_0  
python-lsp-jsonrpc        1.0.0              pyhd3eb1b0_0  
python-lsp-server         1.2.4              pyhd3eb1b0_0  
python-slugify            5.0.2              pyhd3eb1b0_0  
python-snappy             0.6.0            py39h2531618_3  
pytorch                   1.13.0.dev20220620     py3.9_cpu_0    pytorch-nightly
pytorch-mutex             1.0                         cpu    pytorch-nightly
pytz                      2021.3             pyhd3eb1b0_0  
pyviz_comms               2.0.2              pyhd3eb1b0_0  
pywavelets                1.3.0            py39h7f8727e_0  
pyxdg                     0.27               pyhd3eb1b0_0  
pyyaml                    5.4.1                    pypi_0    pypi
pyzmq                     22.3.0           py39h295c915_2  
qdarkstyle                3.0.2              pyhd3eb1b0_0  
qstylizer                 0.1.10             pyhd3eb1b0_0  
qt                        5.9.7                h5867ecd_1  
qtawesome                 1.0.3              pyhd3eb1b0_0  
qtconsole                 5.3.0              pyhd3eb1b0_0  
qtpy                      2.0.1              pyhd3eb1b0_0  
queuelib                  1.5.0            py39h06a4308_0  
readline                  8.1.2                h7f8727e_1  
regex                     2022.3.15        py39h7f8727e_0  
requests                  2.27.1             pyhd3eb1b0_0  
requests-file             1.5.1              pyhd3eb1b0_0  
requests-oauthlib         1.3.1                    pypi_0    pypi
ripgrep                   12.1.1                        0  
rope                      0.22.0             pyhd3eb1b0_0  
rsa                       4.7.2              pyhd3eb1b0_1  
rtree                     0.9.7            py39h06a4308_1  
ruamel_yaml               0.15.100         py39h27cfd23_0  
s3fs                      2022.5.0                 pypi_0    pypi
s3transfer                0.6.0                    pypi_0    pypi
scikit-image              0.19.2           py39h51133e4_0  
scikit-learn              1.0.2            py39h51133e4_1  
scikit-learn-intelex      2021.5.0         py39h06a4308_0  
scipy                     1.7.3            py39hc147768_0  
scrapy                    2.6.1            py39h06a4308_0  
seaborn                   0.11.2             pyhd3eb1b0_0  
secretstorage             3.3.1            py39h06a4308_0  
send2trash                1.8.0              pyhd3eb1b0_1  
service_identity          18.1.0             pyhd3eb1b0_1  
setuptools                61.2.0           py39h06a4308_0  
sip                       4.19.13          py39h295c915_0  
six                       1.16.0             pyhd3eb1b0_1  
smart_open                5.1.0              pyhd3eb1b0_0  
snappy                    1.1.9                h295c915_0  
sniffio                   1.2.0            py39h06a4308_1  
snowballstemmer           2.2.0              pyhd3eb1b0_0  
sortedcollections         2.1.0              pyhd3eb1b0_0  
sortedcontainers          2.4.0              pyhd3eb1b0_0  
soupsieve                 2.3.1              pyhd3eb1b0_0  
sphinx                    4.4.0              pyhd3eb1b0_0  
sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0  
sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0  
sphinxcontrib-htmlhelp    2.0.0              pyhd3eb1b0_0  
sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0  
sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0  
sphinxcontrib-serializinghtml 1.1.5              pyhd3eb1b0_0  
spyder                    5.1.5            py39h06a4308_1  
spyder-kernels            2.1.3            py39h06a4308_0  
sqlalchemy                1.4.32           py39h7f8727e_0  
sqlite                    3.38.2               hc218d9a_0  
stack_data                0.2.0              pyhd3eb1b0_0  
statsmodels               0.13.2           py39h7f8727e_0  
sympy                     1.10.1           py39h06a4308_0  
tabulate                  0.8.9            py39h06a4308_0  
tbb                       2021.5.0             hd09550d_0  
tbb4py                    2021.5.0         py39hd09550d_0  
tblib                     1.7.0              pyhd3eb1b0_0  
tenacity                  8.0.1            py39h06a4308_0  
tensorboard               2.9.1                    pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-profile 2.8.0                    pypi_0    pypi
tensorboard-plugin-wit    1.8.1                    pypi_0    pypi
tensorflow                2.9.1                    pypi_0    pypi
tensorflow-estimator      2.9.0                    pypi_0    pypi
tensorflow-io-gcs-filesystem 0.26.0                   pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
terminado                 0.13.1           py39h06a4308_0  
testpath                  0.5.0              pyhd3eb1b0_0  
text-unidecode            1.3                pyhd3eb1b0_0  
textdistance              4.2.1              pyhd3eb1b0_0  
threadpoolctl             2.2.0              pyh0d69192_0  
three-merge               0.1.1              pyhd3eb1b0_0  
tifffile                  2021.7.2           pyhd3eb1b0_2  
tinycss                   0.4             pyhd3eb1b0_1002  
tk                        8.6.11               h1ccaba5_0  
tldextract                3.2.0              pyhd3eb1b0_0  
toml                      0.10.2             pyhd3eb1b0_0  
tomli                     1.2.2              pyhd3eb1b0_0  
toolz                     0.11.2             pyhd3eb1b0_0  
torchaudio                0.13.0.dev20220621        py39_cpu    pytorch-nightly
torchvision               0.14.0.dev20220621        py39_cpu    pytorch-nightly
tornado                   6.1              py39h27cfd23_0  
tqdm                      4.64.0           py39h06a4308_0  
traitlets                 5.1.1              pyhd3eb1b0_0  
twisted                   22.2.0           py39h7f8727e_0  
typed-ast                 1.4.3            py39h7f8727e_1  
typing-extensions         4.1.1                hd3eb1b0_0  
typing_extensions         4.1.1              pyh06a4308_0  
tzdata                    2022a                hda174b7_0  
ujson                     5.1.0            py39h295c915_0  
unidecode                 1.2.0              pyhd3eb1b0_0  
unixodbc                  2.3.9                h7b6447c_0  
urllib3                   1.26.9           py39h06a4308_0  
w3lib                     1.21.0             pyhd3eb1b0_0  
watchdog                  2.1.6            py39h06a4308_0  
wcwidth                   0.2.5              pyhd3eb1b0_0  
webencodings              0.5.1            py39h06a4308_1  
websocket-client          0.58.0           py39h06a4308_4  
websockets                10.3                     pypi_0    pypi
werkzeug                  2.0.3              pyhd3eb1b0_0  
wget                      1.21.3               h0b77cf5_0  
wheel                     0.37.1             pyhd3eb1b0_0  
widgetsnbextension        3.5.2            py39h06a4308_0  
wrapt                     1.12.1           py39he8ac12f_1  
wurlitzer                 3.0.2            py39h06a4308_0  
x264                      1!157.20191217       h7b6447c_0  
xarray                    0.20.1             pyhd3eb1b0_1  
xlrd                      2.0.1              pyhd3eb1b0_0  
xlsxwriter                3.0.3              pyhd3eb1b0_0  
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h7b6447c_0  
yapf                      0.31.0             pyhd3eb1b0_0  
yarl                      1.6.3            py39h27cfd23_0  
zeromq                    4.3.4                h2531618_0  
zfp                       0.5.5                h295c915_6  
zict                      2.0.0              pyhd3eb1b0_0  
zipp                      3.7.0              pyhd3eb1b0_0  
zlib                      1.2.12               h7f8727e_2  
zope                      1.0              py39h06a4308_1  
zope.interface            5.4.0            py39h7f8727e_0  
zstd                      1.4.9                haebb681_0    

anaconda3_gpu (for cuda) , anaconda3_mi100 (for rocm)

Similar to the setup for anaconda_cpu, we have gpu versions of anaconda3 (module load anaconda3_gpu) and have installed pytorch and tensorflow cuda aware python modules into these versions.  You may use these module when working with the gpu nodes.  See conda list after loading the module to review what is already installed.  As with anaconda3_cpu, let Delta staff know if there are generally useful modules you would like us to try to install for the broader community. A sample tensorflow test script:

anaconda3_gpu tensorflow example
#!/bin/bash
#SBATCH --mem=64g
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=2     # <- match to OMP_NUM_THREADS
#SBATCH --partition=gpuA100x4-interactive 
#SBATCH --time=00:10:00
#SBATCH --account=YOUR_ACCOUNT-delta-gpu
#SBATCH --job-name=tf_anaconda
### GPU options ###
#SBATCH --gpus-per-node=1
#SBATCH --gpus-per-task=1
#SBATCH --gpu-bind=verbose,per_task:1
###SBATCH --gpu-bind=none     # <- or closest
 
module purge # drop modules and explicitly load the ones needed
             # (good job metadata and reproducibility)

module load anaconda3_gpu
module list  # job documentation and metadata

echo "job is starting on `hostname`"

which python3
conda list tensorflow
srun python3 \
  tf_gpu.py
exit

Jupyter notebooks

The Detla Open OnDemand portal provides an easier way to start a Jupyter notebook. Please see OpenOnDemand to access the portal.

The jupyter notebook executables are in your $PATH after loading the anaconda3 module.   Don't run jupyter on the shared login nodes.  Instead, follow these steps to attach a jupyter notebook running on a compute node to your local web browser:

1) Start a jupyter job via srun and note the hostname (you pick the port number for --port).

srun jupyter ( anaconda3_cpu on a cpu node )
$ srun --account=bbka-delta-cpu --partition=cpu-interactive \
  --time=00:30:00 --mem=32g \
  jupyter-notebook --no-browser \
  --port=8991 --ip=0.0.0.0
...
    Or copy and paste one of these URLs:
        http://cn093.delta.internal.ncsa.edu:8891/?token=e5b500e5aef67b1471ed1842b2676e0c0ae4b5652656feea
     or http://127.0.0.1:8991/?token=e5b500e5aef67b1471ed1842b2676e0c0ae4b5652656feea

Use the 2nd URL in step 3.  Note the internal hostname in the cluster for step 2.


When using a container with a gpu node, run the container's jupyter-notebook:

NGC container for gpus, jupyter-notebook, bind a directory
# container notebook example showing how to access a directory outside
# of $HOME ( /projects/bbka in the example )
$ srun --account=bbka-delta-gpu --partition=gpuA100x4-interactive \
  --time=00:30:00 --mem=64g --gpus-per-node=1 \
  singularity run --nv --bind /projects/bbka \
  /sw/external/NGC/pytorch:22.02-py3 jupyter-notebook \
  --notebook-dir /projects/bbka \
  --no-browser --port=8991 --ip=0.0.0.0
...
http://hostname:8888/?token=73d96b99f2cfc4c3932a3433d1b8003c052081c5411795d5

In step 3 to start the notebook in your browser, replace http://hostname:8888/ with http://127.0.0.1:8991/   ( the port number you selected with --port= )

You may not see the job hostname when running with a container, find it with squeue:

squeue -u $USER
$ squeue -u $USER
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
            156071 gpuA100x4 singular  arnoldg  R       1:00      1 gpua045

Then specifu the host your job is using in the next step (gpua045 for example ).

2) From your local desktop or laptop create an ssh tunnel to the compute node via a login node of delta.
ssh tunnel for jupyter
$ ssh -l my_delta_username \
  -L 127.0.0.1:8991:cn093.delta.internal.ncsa.edu:8991 \
  dt-login.delta.ncsa.illinois.edu

Authenticate with your login and 2-factor as usual.

3) Paste the 2nd URL (containing 127.0.0.1:port_number and the token string) from step 1 into your browser and you will be connected to the jupyter instance running on your compute node of Delta.

Python (a recent or latest version)

If you do not need all of the extra modules provided by Anaconda, use the basic python installation under the gcc module.  You can add modules via "pip3 install --user <modulename>",  setup virtual environments, and customize as needed for your workflow but starting from a smaller installed base of python than Anaconda.

$ module load gcc python
$ which python
/sw/spack/delta-2022-03/apps/python/3.10.4-gcc-11.2.0-3cjjp6w/bin/python
$ module list

Currently Loaded Modules:
  1) modtree/gpu   3) gcc/11.2.0    5) ucx/1.11.2      7) python/3.10.4
  2) default       4) cuda/11.6.1   6) openmpi/4.1.2

This is the list of modules available in the python from "pip3 list":

python modules: pip3 list
Package            Version
------------------ ---------
certifi            2021.10.8
cffi               1.15.0
charset-normalizer 2.0.12
click              8.1.2
cryptography       36.0.2
globus-cli         3.4.0
globus-sdk         3.5.0
idna               3.3
jmespath           0.10.0
pip                22.0.4
pycparser          2.21
PyJWT              2.3.0
requests           2.27.1
setuptools         58.1.0
urllib3            1.26.9

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Launching Applications

  • Launching One Serial Application
  • Launching One Multi-Threaded Application
  • Launching One MPI Application
  • Launching One Hybrid (MPI+Threads) Application
  • More Than One Serial Application in the Same Job
  • MPI Applications One at a Time
  • More than One MPI Application Running Concurrently
  • More than One OpenMP Application Running Concurrently

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Running Jobs

Job Accounting

The charge unit for Delta is the Service Unit (SU). This corresponds to the equivalent use of one compute core utilizing less than or equal to 2G of memory for one hour, or 1 GPU or fractional GPU using less than the corresponding amount of memory or cores for 1 hour (see table below). Keep in mind that your charges are based on the resources that are reserved for your job and don't necessarily reflect how the resources are used. Charges are based on either the number of cores or the fraction of the memory requested, whichever is larger. The minimum charge for any job is 1 SU.

Node Type

Service Unit Equivalence
CoresGPU FractionHost Memory
CPU NodeN/A2 GB

GPU Node

Quad A100161 A10062.5 GB
Quad A40161 A4062.5 GB
8-way A100161 A100250 GB
8-way MI100161 MI100250 GB

Please note that a weighting factor will discount the charge for the reduced-precision A40 nodes, as well as the novel AMD MI100 based node - this will be documented through the ACCESS SU converter.

Local Account Charging 

Use the accounts command to list the accounts available for charging. CPU and GPU resources will have individual charge names.  For example in the following, abcd-delta-cpu and abcd-delta-gpu   are available for user gbauer to use for the CPU and GPU resources. 

$ accounts
Project Summary for User 'kingda':

Project         Description                    Balance (Hours)    Deposited (Hours)
--------------  ---------------------------  -----------------  -------------------
bbka-delta-gpu  ncsa/delta staff allocation            5000000              5000000
bbka-delta-cpu  ncsa/delta staff allocation          100000000            100000000 

Job Accounting Considerations

  • A node-exclusive job that runs on a compute node for one hour will be charged 128 SUs (128 cores x 1 hour)
  • A node-exclusive job that runs on a 4-way GPU node for one hour will be charge 4 SUs (4 GPU x 1 hour)
  • A node-exclusive job that runs on a 8-way GPU node for one hour will be charge 8 SUs (8 GPU x 1 hour)

Accessing the Compute Nodes

Delta implements the Slurm batch environment to manage access to the compute nodes.  Use the Slurm commands to run batch jobs or for interactive access to compute nodes.  See: https://slurm.schedmd.com/quickstart.html for an introduction to Slurm. There are two ways to access compute nodes on Delta.

Batch jobs can be used to access compute nodes. Slurm provides a convenient direct way to submit batch jobs.  See https://slurm.schedmd.com/heterogeneous_jobs.html#submitting for details.

Sample Slurm batch job scripts are provided in the Job Scripts section below.

Direct ssh access to a compute node in a running batch job from a dt-loginNN node is enabled, once the job has started.

$ squeue --job jobid
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
             12345       cpu     bash   gbauer  R       0:17      1 cn001

Then in a terminal session:

$ ssh cn001
cn001.delta.internal.ncsa.edu (172.28.22.64)
  OS: RedHat 8.4   HW: HPE   CPU: 128x    RAM: 252 GB
  Site: mgmt  Role: compute
$ 

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Scheduler

For information, consult:

https://slurm.schedmd.com/quickstart.html

slurm quick reference guide

Partitions (Queues)

Table. Delta Production Partitions/Queues

Partition/Queue

Node Type

Max Nodes per Job

Max Duration

Max Running in Queue/user*

Charge Factor

cpu

CPU

TBD

48 hrTBD

1.0

cpu-interactiveCPUTBD30 minTBD2.0

gpuA100x4

gpuA100x4*

(asterisk indicates this is the default queue, but submit jobs to gpuA100x4)

quad A100TBD48 hrTBD

1.0

gpuA100x4-interactivequad-A100TBD1 hrTBD2.0
gpuA100x8octa-A100TBD48 hr

TBD

1.5

gpuA100x8-interactiveocta-A100TBD1 hrTBD3.0
gpuA40x4quad-A40TBD48 hrTBD0.6
gpuA40x4-interactivequad-A40TBD1 hrTBD1.2
gpuMI100x8octa-MI100TBD48 hrTBD

1.0

gpuMI100x8-interactiveocta-MI100TBD1 hrTBD2.0

sview view of slurm partitions

Node Policies

Node-sharing is the default for jobs. Node-exclusive mode can be obtained by specifying all the consumable resources for that node type or adding the following Slurm options:

--exclusive --mem=0

GPU NVIDIA MIG (GPU slicing) for the A100 will be supported at a future date.

Pre-emptive jobs will be supported at a future date.

Interactive Sessions

Interactive sessions can be implemented in several ways depending on what is needed.

To start up a bash shell terminal on a cpu or gpu node

  • single core with 1GB of memory, with one task on a cpu node
srun --account=account_name --partition=cpu-interactive \
  --nodes=1 --tasks=1 --tasks-per-node=1 \
  --cpus-per-task=1 --mem=16g \
  --pty bash
  • single core with 20GB of memory, with one task on a A40 gpu node
srun --account=account_name --partition=gpuA40x4-interactive \
  --nodes=1 --gpus-per-node=1 --tasks=1 \
  --tasks-per-node=1 --cpus-per-task=1 --mem=20g \
  --pty bash

interactive jobs: a case for mpirun

Since interactive jobs are already a child process of srun, one cannot srun applications from within them.  Use mpirun to launch mpi jobs from within an interactive job.  Within standard batch jobs submitted via sbatch, use srun to launch MPI codes.

Interactive X11 Support

To run an X11 based application on a compute node in an interactive session, the use of the --x11 switch with srun is needed. For example, to run a single core job that uses 1g of memory with X11 (in this case an xterm) do the following:

srun -A abcd-delta-cpu  --partition=cpu-interactive \
  --nodes=1 --tasks=1 --tasks-per-node=1 \ 
  --cpus-per-task=1 --mem=16g \
  --x11  xterm

File System Dependency Specification for Jobs

Please see the FileSystemDependencySpecificationforJobs section on setting job file system dependencies for jobs. 

Jobs that do not specify a dependency on the WORK(/projects)  and SCRATCH (/scratch) will be assumed to depend only on the HOME (/u) file system. 

Sample Job Scripts

  • Serial jobs

    serial example script
    $ cat job.slurm
    #!/bin/bash
    #SBATCH --mem=16g
    #SBATCH --nodes=1
    #SBATCH --ntasks-per-node=1
    #SBATCH --cpus-per-task=1    # <- match to OMP_NUM_THREADS
    #SBATCH --partition=cpu      # <- or one of: gpuA100x4 gpuA40x4 gpuA100x8 gpuMI100x8
    #SBATCH --account=account_name
    #SBATCH --job-name=myjobtest
    #SBATCH --time=00:10:00      # hh:mm:ss for the job
    #SBATCH --constraint="scratch"
    ### GPU options ###
    ##SBATCH --gpus-per-node=2
    ##SBATCH --gpu-bind=none     # <- or closest
    ##SBATCH --mail-user=you@yourinstitution.edu 
    ##SBATCH --mail-type="BEGIN,END" See sbatch or srun man pages for more email options  
    
    
    module reset # drop modules and explicitly load the ones needed
                 # (good job metadata and reproducibility)
                 # $WORK and $SCRATCH are now set
    module load python  # ... or any appropriate modules
    module list  # job documentation and metadata
    echo "job is starting on `hostname`"
    srun python3 myprog.py
  • MPI  

    mpi example script
    #!/bin/bash
    #SBATCH --mem=16g
    #SBATCH --nodes=2
    #SBATCH --ntasks-per-node=32
    #SBATCH --cpus-per-task=1    # <- match to OMP_NUM_THREADS
    #SBATCH --partition=cpu      # <- or one of: gpuA100x4 gpuA40x4 gpuA100x8 gpuMI100x8
    #SBATCH --account=account_name
    #SBATCH --job-name=mympi
    #SBATCH --time=00:10:00      # hh:mm:ss for the job
    #SBATCH --constraint="scratch"
    ### GPU options ###
    ##SBATCH --gpus-per-node=2
    ##SBATCH --gpu-bind=none     # <- or closest ##SBATCH --mail-user=you@yourinstitution.edu 
    ##SBATCH --mail-type="BEGIN,END" See sbatch or srun man pages for more email options 
    
    module reset # drop modules and explicitly load the ones needed
                 # (good job metadata and reproducibility)
                 # $WORK and $SCRATCH are now set
    module load gcc/11.2.0 openmpi  # ... or any appropriate modules
    module list  # job documentation and metadata
    echo "job is starting on `hostname`"
    srun osu_reduce
  • OpenMP   

    openmp example script
    #!/bin/bash
    #SBATCH --mem=16g
    #SBATCH --nodes=1
    #SBATCH --ntasks-per-node=1
    #SBATCH --cpus-per-task=32   # <- match to OMP_NUM_THREADS
    #SBATCH --partition=cpu      # <- or one of: gpuA100x4 gpuA40x4 gpuA100x8 gpuMI100x8
    #SBATCH --account=account_name
    #SBATCH --job-name=myopenmp
    #SBATCH --time=00:10:00      # hh:mm:ss for the job
    #SBATCH --constraint="scratch"
    ### GPU options ###
    ##SBATCH --gpus-per-node=2
    ##SBATCH --gpu-bind=none     # <- or closest
    ##SBATCH --mail-user=you@yourinstitution.edu 
    ##SBATCH --mail-type="BEGIN,END" See sbatch or srun man pages for more email options 
    
    module reset # drop modules and explicitly load the ones needed
                 # (good job metadata and reproducibility)
                 # $WORK and $SCRATCH are now set
    module load gcc/11.2.0  # ... or any appropriate modules
    module list  # job documentation and metadata
    echo "job is starting on `hostname`"
    export OMP_NUM_THREADS=32
    srun stream_gcc
  • Hybrid (MPI + OpenMP or MPI+X)

    mpi+x example script
    #!/bin/bash
    #SBATCH --mem=16g
    #SBATCH --nodes=2
    #SBATCH --ntasks-per-node=4
    #SBATCH --cpus-per-task=4    # <- match to OMP_NUM_THREADS
    #SBATCH --partition=cpu      # <- or one of: gpuA100x4 gpuA40x4 gpuA100x8 gpuMI100x8
    #SBATCH --account=account_name
    #SBATCH --job-name=mympi+x
    #SBATCH --time=00:10:00      # hh:mm:ss for the job
    #SBATCH --constraint="scratch"
    ### GPU options ###
    ##SBATCH --gpus-per-node=2
    ##SBATCH --gpu-bind=none     # <- or closest
    ##SBATCH --mail-user=you@yourinstitution.edu 
    ##SBATCH --mail-type="BEGIN,END" See sbatch or srun man pages for more email options 
    
    module reset # drop modules and explicitly load the ones needed
                 # (good job metadata and reproducibility)
                 # $WORK and $SCRATCH are now set
    module load gcc/11.2.0 openmpi # ... or any appropriate modules
    module list  # job documentation and metadata
    echo "job is starting on `hostname`"
    export OMP_NUM_THREADS=4
    srun xthi
  • 4 gpus together on a compute node

    4 gpus on a compute node
    #!/bin/bash
    #SBATCH --job-name="a.out_symmetric"
    #SBATCH --output="a.out.%j.%N.out"
    #SBATCH --partition=gpuA100x4
    #SBATCH --mem=220G
    #SBATCH --nodes=1
    #SBATCH --ntasks-per-node=4
    #SBATCH --cpus-per-task=16   # spread out to use 1 core per numa
    #SBATCH --constraint="scratch"
    #SBATCH --gpus-per-node=4
    #SBATCH --gpu-bind=closest   # select a cpu close to gpu on pci bus topology
    #SBATCH --account=bbjw-delta-gpu
    #SBATCH --exclusive  # dedicated node for this job
    #SBATCH --no-requeue
    #SBATCH -t 04:00:00
    
    export OMP_NUM_THREADS=1  # if code is not multithreaded, otherwise set to 8 or 16
    srun -N 1 -n 4 ./a.out > myjob.out 
  • Parametric / Array / HTC jobs

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Job Management 

Batch jobs are submitted through a job script  (as in the examples above) using the sbatch command. Job scripts generally start with a series of SLURM directives that describe requirements of the job such as number of nodes, wall time required, etc… to the batch system/scheduler (SLURM directives can also be specified as options on the sbatch command line; command line options take precedence over those in the script). The rest of the batch script consists of user commands.

The syntax for sbatch is:

sbatch [list of sbatch options] script_name

Refer to the sbatch man page for detailed information on the options.

squeue/scontrol/sinfo

Commands that display batch job and partition information .

SLURM EXAMPLE COMMANDDESCRIPTION
squeue -aList the status of all jobs on the system.
squeue -u $USERList the status of all your jobs in the batch system.
squeue -j JobIDList nodes allocated to a running job in addition to basic information..
scontrol show job JobIDList detailed information on a particular job.
sinfo -aList summary information on all the partition.

See the manual (man) pages for other available options.

Job Status

NODELIST(REASON)

MaxGRESPerAccount - a user has exceeded the number of cores or gpus allotted per user or project for a given partition.


Useful Batch Job Environment Variables

DESCRIPTION

SLURM ENVIRONMENT VARIABLE

DETAIL DESCRIPTION

JobID$SLURM_JOB_IDJob identifier assigned to the job
Job Submission Directory$SLURM_SUBMIT_DIRBy default, jobs start in the directory that the job was submitted from. So the "cd $SLURM_SUBMIT_DIR" command is not needed.
Machine(node) list$SLURM_NODELISTvariable name that contains the list of nodes assigned to the batch job
Array JobID$SLURM_ARRAY_JOB_ID
$SLURM_ARRAY_TASK_ID
each member of a job array is assigned a unique identifier

See the sbatch man page for additional environment variables available.

srun

The srun command initiates an interactive job on the compute nodes.

For example, the following command:

srun -A account_name --time=00:30:00 --nodes=1 --ntasks-per-node=64 \

--mem=16g --pty /bin/bash

will run an interactive job in the default queue with a wall clock limit of 30 minutes, using one node and 16 cores per node. You can also use other sbatch options such as those documented above.

After you enter the command, you will have to wait for SLURM to start the job. As with any job, your interactive job will wait in the queue until the specified number of nodes is available. If you specify a small number of nodes for smaller amounts of time, the wait should be shorter because your job will backfill among larger jobs. You will see something like this:

srun: job 123456 queued and waiting for resources

Once the job starts, you will see:

srun: job 123456 has been allocated resources

and will be presented with an interactive shell prompt on the launch node. At this point, you can use the appropriate command to start your program.

When you are done with your work, you can use the exit command to end the job.

scancel

The scancel command deletes a queued job or terminates a running job.

  • scancel JobID deletes/terminates a job.

Refunds

Refunds are considered, when appropriate, for jobs that failed due to circumstances beyond user control.

Projects wishing to request a refund should email  help@ncsa.illinois.edu. Please include the batch job ids and the standard error and output files produced by the job(s). 

Visualization

Delta A40 nodes support NVIDIA raytracing hardware.

  • describe visualization capabilities & software.
  • how to establish VNC/DVC/remote desktop

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Containers

Apptainer (formerly Singularity)

Container support on Delta is provided by Apptainer/Singularity. 

Docker images can be converted to Singularity sif format via the singularity pull  command. Commands can be run from within a container using singularity run  command (or apptainer run).

If you encounter quota issues with Apptainer/Singularity caching in ~/.singularity , the environment variable SINGULARITY_CACHEDIR can be used to use a different location such as a scratch space. 

Your $HOME is automatically available from containers run via Apptainer/Singularity.  You can "pip3 install --user" against a container's python, setup virtualenv's or similar while useing a containerized application.  Just run the container's /bin/bash to get a Singularity> prompt.  Here's an srun example of that with tensorflow:

srun the bash from a container to interact with programs inside it
$ srun \
 --mem=32g \
 --nodes=1 \
 --ntasks-per-node=1 \
 --cpus-per-task=1 \
 --partition=gpuA100x4-interactive \
 --account=bbka-delta-gpu \
 --gpus-per-node=1 \
 --gpus-per-task=1 \
 --gpu-bind=verbose,per_task:1 \
 --pty \
 apptainer run --nv \
 /sw/external/NGC/tensorflow:22.06-tf2-py3 /bin/bash 
# job starts ...
Singularity> hostname
gpua068.delta.internal.ncsa.edu
Singularity> which python  # the python in the container
/usr/bin/python
Singularity> python --version
Python 3.8.10
Singularity> 


NVIDIA NGC Containers

Delta provides NVIDIA NGC Docker containers that we have pre-built with Singularity.  Look for the latest binary containers in /sw/external/NGC/ The containers are used as shown in the sample scripts below:

PyTorch example script
#!/bin/bash
#SBATCH --mem=64g
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64     # <- match to OMP_NUM_THREADS, 64 requests whole node
#SBATCH --partition=gpuA100x4 # <- one of: gpuA100x4 gpuA40x4 gpuA100x8 gpuMI100x8
#SBATCH --account=bbka-delta-gpu
#SBATCH --job-name=pytorchNGC
### GPU options ###
#SBATCH --gpus-per-node=1
#SBATCH --gpus-per-task=1
#SBATCH --gpu-bind=verbose,per_task:1 
 
module reset # drop modules and explicitly load the ones needed
             # (good job metadata and reproducibility)
             # $WORK and $SCRATCH are now set
module list  # job documentation and metadata

echo "job is starting on `hostname`"

# run the container binary with arguments: python3 <program.py>
apptainer run --nv \
 /sw/external/NGC/pytorch:22.02-py3 python3 tensor_gpu.py
Tensorflow example script
#!/bin/bash
#SBATCH --mem=64g
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=64     # <- match to OMP_NUM_THREADS
#SBATCH --partition=gpuA100x4 # <- one of: gpuA100x4 gpuA40x4 gpuA100x8 gpuMI100x8
#SBATCH --account=bbka-delta-gpu
#SBATCH --job-name=tfNGC
### GPU options ###
#SBATCH --gpus-per-node=1
#SBATCH --gpus-per-task=1
#SBATCH --gpu-bind=verbose,per_task:1
 
module reset # drop modules and explicitly load the ones needed
             # (good job metadata and reproducibility)
             # $WORK and $SCRATCH are now set
module list  # job documentation and metadata

echo "job is starting on `hostname`"

# run the container binary with arguments: python3 <program.py>
singularity run --nv \
 /sw/external/NGC/tensorflow:22.06-tf2-py3 python3 \
 tf_matmul.py

Container list (as of March, 2022)

catalog.txt
caffe:20.03-py3 caffe2:18.08-py3
catalog.txt
cntk:18.08-py3
cp2k_v9.1.0.sif
cuquantum-appliance_22.03-cirq.sif
digits:21.09-tensorflow-py3
gromacs_2022.1.sif
hpc-benchmarks:21.4-hpl
lammps:patch_4May2022
matlab:r2021b
mxnet:21.09-py3
mxnet_22.08-py3.sif
namd_2.13-multinode.sif
namd_3.0-alpha11.sif
paraview_egl-py3-5.9.0.sif
pytorch:22.02-py3
pytorch_22.07-py3.sif
pytorch_22.08-py3.sif
tensorflow_19.09-py3.sif
tensorflow:22.02-tf1-py3
tensorflow:22.02-tf2-py3
tensorflow_22.05-tf1-py3.sif
tensorflow_22.05-tf2-py3.sif
tensorflow:22.06-tf1-py3
tensorflow:22.06-tf2-py3
tensorflow_22.07-tf2-py3.sif
tensorflow_22.08-tf1-py3.sif
tensorflow_22.08-tf2-py3.sif
tensorrt:22.02-py3
tensorrt_22.08-py3.sif
theano:18.08
torch:18.08-py2

see also:  https://catalog.ngc.nvidia.com/orgs/nvidia/containers

AMD Infinity Hub containers for MI100

The AMD node in partition gpuMI100x8 (-interactive) will run containers from the AMD Infinity Hub.  The Delta team has pre loaded the following containers in /sw/external/MI100 and will retrieve others upon request.

AMD MI100 containers in /sw/external/MI100
cp2k_8.2.sif
gromacs_2021.1.sif
lammps_2021.5.14_121.sif
milc_c30ed15e1-20210420.sif
namd_2.15a2-20211101.sif
namd3_3.0a9.sif
openmm_7.7.0_49.sif
pytorch_rocm5.0_ubuntu18.04_py3.7_pytorch_1.10.0.sif
tensorflow_rocm5.0-tf2.7-dev.sif

A sample batch script for pytorch resembles:

MI100 sample pytorch script
#!/bin/bash
#SBATCH --mem=64g
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --partition=gpuMI100x8 
#SBATCH --account=bbka-delta-gpu
#SBATCH --job-name=tfAMD
#SBATCH --reservation=amd
#SBATCH --time=00:15:00
### GPU options ###
#SBATCH --gpus-per-node=1
##SBATCH --gpus-per-task=1
##SBATCH --gpu-bind=none     # <- or closest
 
module purge # drop modules and explicitly load the ones needed
             # (good job metadata and reproducibility)

module list  # job documentation and metadata

echo "job is starting on `hostname`"

# https://apptainer.org/docs/user/1.0/gpu.html#amd-gpus-rocm
# https://pytorch.org/docs/stable/notes/hip.html
time \
apptainer run --rocm \
 ~arnoldg/delta/AMD/pytorch_rocm5.0_ubuntu18.04_py3.7_pytorch_1.10.0.sif \
 python3 tensor_gpu.py

exit


Other Containers

Extreme-scale Scientific Software Stack (E4S)

The E4S container with GPU (cuda and rocm) support is provided for users of specific ECP packages made available by the E4S project (https://e4s-project.github.io/). The singularity image is available as :

/sw/external/E4S/e4s-gpu-x86_64.sif
      
To use E4S with NVIDIA GPUs
$ srun --account=account_name --partition=gpuA100-interactive \
  --nodes=1 --gpus-per-node=1 --tasks=1 --tasks-per-node=1 \ 
  --cpus-per-task=1 --mem=20g \
  --pty bash
$ singularity exec --cleanenv /sw/external/E4S/e4s-gpu-x86_64.sif \
  /bin/bash --rcfile /etc/bash.bashrc


The spack package inside of the image will interact with a local spack installation. If  ~/.spack directory exists, it might need to be renamed. 

More information can be found at https://e4s-project.github.io/download.html

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Delta Science Gateway and Open OnDemand

Open OnDemand


The Delta Open OnDemand portal is now available for use. Current supported Interactive apps: Jupyter notebooks.

To connect to the Open OnDemand portal, director a browser to https://openondemand.delta.ncsa.illinois.edu/ and use your NCSA username, password with NCSA Duo with the CILogin page.

Delta Science Gateway

Protected Data (N/A)


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Help

For assistance with the use of Delta

  • ACCESS users can create a ticket via the Help Desk.

  • All other users (Illinois allocations, Diversity Allocations, etc) please send email to help@ncsa.illinois.edu.

Acknowledge

To acknowledge the NCSA Delta system in particular, please include the following

This research is part of the Delta research computing project, which is supported by the National Science Foundation (award OCI 2005572), and the State of Illinois. Delta is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications.

  • How to Acknowledge ACCESS

  • Acknowledgement for ACCESS Users

References

Supporting documentation resources:

https://www.rcac.purdue.edu/knowledge/anvil

https://nero-docs.stanford.edu/jupyter-slurm.html


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