Commit e258e5ae authored by Matthieu Dorier's avatar Matthieu Dorier

added files for JLSE

parent 200be2e5
JLSE
====
JLSE is not a supercomputer but a set of heterogeneous resources.
The `spack.yaml` file provided here was tested on the It machines
(see the full list of machines [here](https://www.jlse.anl.gov/hardware-under-development/)),
and may not work on other machine types.
Programming environment
-----------------------
As described [here](https://wiki.jlse.anl.gov/display/JLSEdocs/JLSE+Software),
JLSE provides many modules, including some installed using Spack. To use
them you will need to execute the following.
```
module use /soft/modulefiles
module load spack/linux-rhel7-x86_64
```
The provided `spack.yaml` file uses the gcc 9.3.0 compiler along with
the `intel-mpi` implementation of MPI. These packages can be loaded as follows.
```
module load gcc/9.3.0-gcc-9.3.0-qfmcwfb
module load intelmpi/2019-gcc
```
Networking
----------
JLSE machines can use TCP. The corresponding transport in Mercury
is `ofi+tcp`, using the `fabrics=tcp,rxm` variant in libfabric.
Job management
--------------
JLSE uses the Cobalt workload manager.
The provided `job.qsub` script is an example
of job file. Please modify the header (lines starting with `#COBALT`)
to set relevant parameters.
Once modified, the job script may be submitted as follows.
```
$ qsub ./job.qsub
```
#!/bin/bash
#COBALT -n 2
#COBALT -t 1:00:00
#COBALT --mode script
#COBALT -q it
set -eu
echo "Setting up environment modules"
module use /soft/modulefiles
module load spack/linux-rhel7-x86_64
module load gcc/develop-gcc-9.3.0-42htf6e
module load intelmpi/2019-gcc
echo "Setting up spack"
source $HOME/spack/share/spack/setup-env.sh # XXX change this
spack env activate myenv # XXX change this
echo "Starting benchmark"
time mpirun -np 2 -f ${COBALT_NODEFILE} ...
echo "Done!"
spack:
specs:
- mochi-margo
concretization: together
compilers:
- compiler:
environment: {unset: []}
extra_rpaths: []
flags: {}
modules:
- spack/linux-rhel7-x86_64
- gcc/9.3.0-gcc-9.3.0-qfmcwfb
operating_system: rhel7
paths:
cc: gcc
cxx: g++
f77: gfortran
fc: gfortran
spec: gcc@9.3.0
target: x86_64
repos:
- /path/to/sds-repo
packages:
all:
providers:
mpi: [intel-mpi]
compiler:
- gcc@9.3.0
target:
- x86_64
version: []
buildable: true
autoconf:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: autoconf@2.69
modules:
- spack/linux-rhel7-x86_64
- autoconf/2.69-gcc-9.3.0-l3nosud
automake:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: automake@1.16.2
modules:
- spack/linux-rhel7-x86_64
- automake/1.16.2-gcc-9.3.0-judimac
binutils:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: binutils@2.34.0
modules:
- spack/linux-rhel7-x86_64
- binutils/2.34-gcc-9.3.0-rnwhrdg
bison:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: bison@3.4.2
modules:
- spack/linux-rhel7-x86_64
- bison/3.4.2-gcc-9.3.0-tkz5uzj
boost:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: boost@1.72.0
modules:
- spack/linux-rhel7-x86_64
- boost/1.72.0-gcc-9.3.0-bi3ct5p
bzip2:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: bzip2@1.0.6
modules:
- spack/linux-rhel7-x86_64
- bzip2/1.0.8-gcc-9.3.0-vatuhza
coreutils:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: coreutils@8.22
prefix: /usr
cmake:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: cmake@3.17.0
modules:
- spack/linux-rhel7-x86_64
- cmake/3.17.0-gcc-9.3.0-5dgh2gv
findutils:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: findutils@4.6.0
prefix: /usr
flex:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: flex@2.6.4
modules:
- spack/linux-rhel7-x86_64
- flex/2.6.4-gcc-9.3.0-xhptaic
gettext:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: gettext@0.20.1
modules:
- spack/linux-rhel7-x86_64
- gettext/0.20.1-gcc-9.3.0-4uprshc
git:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: git@2.26.0
modules:
- spack/linux-rhel7-x86_64
- git/2.26.0-gcc-9.3.0-7fqgilo
intel-mpi:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: intel-mpi@2019
modules:
- spack/linux-rhel7-x86_64
- gcc/9.3.0-gcc-9.3.0-qfmcwfb
- intelmpi/2019-gcc
libfabric:
variants: fabrics=tcp,rxm
version: []
target: []
compiler: []
buildable: true
providers: {}
libtool:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: libtool@2.4.6
modules:
- spack/linux-rhel7-x86_64
- libtool/2.4.6-gcc-9.3.0-y2q4tht
libuuid:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: libuuid@1.0.3
modules:
- spack/linux-rhel7-x86_64
- libuuid/1.0.3-gcc-9.3.0-f6rv6ex
m4:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: m4@1.4.18
modules:
- spack/linux-rhel7-x86_64
- m4/1.4.18-gcc-9.3.0-dnkbu5y
mercury:
variants: ~boostsys
version: []
target: []
compiler: []
buildable: true
providers: {}
ncurses:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: ncurses@6.2
modules:
- spack/linux-rhel7-x86_64
- ncurses/6.2-gcc-9.3.0-xvsnay4
numactl:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: numactl@2.0.12
modules:
- spack/linux-rhel7-x86_64
- numactl/2.0.12-gcc-9.3.0-fu7ypyk
openssl:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: openssl@1.1.1g
modules:
- spack/linux-rhel7-x86_64
- openssl/1.1.1g-gcc-9.3.0-56igdjg
perl:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: perl@5.30.3
modules:
- spack/linux-rhel7-x86_64
- perl/5.30.3-gcc-9.3.0-dy4ocwc
pkg-config:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: pkg-config@1.7.3
modules:
- spack/linux-rhel7-x86_64
- pkgconf/1.7.3-gcc-9.3.0-jrr7kf3
tar:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: tar@1.32
modules:
- spack/linux-rhel7-x86_64
- tar/1.32-gcc-9.3.0-g3rvopa
xz:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: xz@5.2.5
modules:
- spack/linux-rhel7-x86_64
- xz/5.2.5-gcc-9.3.0-6rgt4w7
zlib:
buildable: false
version: []
target: []
compiler: []
providers: {}
externals:
- spec: zlib@1.2.11
modules:
- spack/linux-rhel7-x86_64
- zlib/1.2.11-gcc-9.3.0-uubmvor
view: true
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