Getting the installation directory back from spack #300

amklinv · 2023-10-26T17:37:35Z

amklinv
Oct 26, 2023

I am interested in adding the SNAP benchmark, which contains its own input files in the installation directory. How can I get the installation directory to use in my ramble file? Here is a snippet of my package:

class Snap(SpackApplication):
    '''Define SNAP application'''
    name = 'snap'

    maintainers('amklinv')

    tags('benchmark-app', 'mini-app', 'benchmark')

    default_compiler('gcc9', spack_spec='[email protected]')

    software_spec('impi2018',
                  spack_spec='[email protected]')

    software_spec('snap',
                  spack_spec='[email protected] +mpi +openmp',
                  compiler='gcc9')

    required_package('snap')

    workload('standard', executables=['execute'])

    executable('execute', 'gsnap {in_file} {out_file}', use_mpi=True)

    workload_variable('in_file', default='[SNAP INSTALLATION DIRECTORY GOES HERE]/qasnap/benchmark/inp',
                      description='Input file for results',
                      workloads=['standard'])

Answered by douglasjacobsen

Oct 27, 2023

Ah, sorry. I don't think we currently expand urls. The input_file directive is intended to be something you have to fetch externally, not locally.

I don't even think you need the input_file directive. Try this instead:

import os
from ramble.appkit import *
from ramble.expander import Expander


class Snap(SpackApplication):
    '''Define SNAP application'''
    name = 'snap'

    maintainers('klinveam')

    tags('benchmark-app', 'mini-app', 'benchmark')

    default_compiler('gcc9', spack_spec='[email protected]')

    software_spec('impi2018',
                  spack_spec='[email protected]')

    software_spec('snap',
                  spack_spec='[email protected] +mpi +openmp',
                  c…

View full answer

douglasjacobsen · 2023-10-26T20:27:29Z

douglasjacobsen
Oct 26, 2023
Maintainer

Hey @amklinv!

Since you have required_package('snap') you should be able to use '{snap}' to refer to spack's installation prefix for snap.

i.e. your workload variable can be:

    workload_variable('in_file', default='{snap}/qasnap/benchmark/inp',
                      description='Input file for results',
                      workloads=['standard'])

See: https://googlecloudplatform.github.io/ramble/workspace_config.html#spack-specific-generated-variables

And https://github.com/GoogleCloudPlatform/ramble/blob/develop/var/ramble/repos/builtin/applications/wrfv3/application.py#L42 for an example.

FWIW I should probably mention that this is not strictly because you have required_package('snap'). That just allows ramble to error if someone tries to use this snap application definition without having snap installed in the environment.

0 replies

amklinv · 2023-10-26T22:31:48Z

amklinv
Oct 26, 2023
Author

Thank you so much for the response! Unfortunately, it does not seem to be expanding {snap} correctly.

import os
from ramble.appkit import *
from ramble.expander import Expander


class Snap(SpackApplication):
    '''Define SNAP application'''
    name = 'snap'

    maintainers('klinveam')

    tags('benchmark-app', 'mini-app', 'benchmark')

    default_compiler('gcc9', spack_spec='[email protected]')

    software_spec('impi2018',
                  spack_spec='[email protected]')

    software_spec('snap',
                  spack_spec='[email protected] +mpi +openmp',
                  compiler='gcc9')

    required_package('snap')

    workload('standard', executables=['execute'], input='benchmark')

    executable('execute', 'gsnap {in_file} {out_file}', use_mpi=True)

    workload_variable('in_file', default='{snap}/qasnap/benchmark/inp',
                      description='Input file for results',
                      workloads=['standard'])

    workload_variable('out_file', default='{experiment_run_dir}/output',
                      description='Output file for results',
                      workloads=['standard'])

    input_file('benchmark',
               url='file://{in_file}',
               description='HPC Benchmarking input for SNAP',
               expand=False)

results in

==> [2023-10-26-16:25:08.736739] BEGINNING OF EXPAND_VAR STACK ON file://{in_file}
==> [2023-10-26-16:25:08.737217]    Math input is: "{snap}/qasnap/benchmark/inp"
==> [2023-10-26-16:25:08.737268] MathEvaluationError: Unsupported math AST node <class '_ast.Set'>:
	{'elts': [<_ast.Name object at 0x14fadcdf8eb8>], 'lineno': 1, 'col_offset': 0}
==> [2023-10-26-16:25:08.737323]    Math input is: "{snap}/qasnap/benchmark/inp"
==> [2023-10-26-16:25:08.737346] MathEvaluationError: Unsupported math AST node <class '_ast.Set'>:
	{'elts': [<_ast.Name object at 0x14fadcdf8f28>], 'lineno': 1, 'col_offset': 0}
==> [2023-10-26-16:25:08.737379] END OF EXPAND_VAR STACK file://{snap}/qasnap/benchmark/inp
==> [2023-10-26-16:25:08.738515] BEGINNING OF EXPAND_VAR STACK ON {workload_input_dir}
==> [2023-10-26-16:25:08.738692] END OF EXPAND_VAR STACK /home/klinalic/ramble/var/ramble/workspaces/snap/inputs/snap/standard
==> [2023-10-26-16:25:08.738729] BEGINNING OF EXPAND_VAR STACK ON {input_name}
==> [2023-10-26-16:25:08.738814] END OF EXPAND_VAR STACK inp
==> [2023-10-26-16:25:08.761947] BEGINNING OF EXPAND_VAR STACK ON export OMP_NUM_THREADS="{n_threads}";
==> [2023-10-26-16:25:08.762050] END OF EXPAND_VAR STACK export OMP_NUM_THREADS="1";
==> [2023-10-26-16:25:08.762096] BEGINNING OF EXPAND_VAR STACK ON . /home/klinalic/spack/share/spack/setup-env.sh
==> [2023-10-26-16:25:08.762134] END OF EXPAND_VAR STACK . /home/klinalic/spack/share/spack/setup-env.sh
==> [2023-10-26-16:25:08.762171] BEGINNING OF EXPAND_VAR STACK ON {env_path}
==> [2023-10-26-16:25:08.762290] END OF EXPAND_VAR STACK /home/klinalic/ramble/var/ramble/workspaces/snap/software/snap.standard
==> [2023-10-26-16:25:08.762546] BEGINNING OF EXPAND_VAR STACK ON spack env activate /home/klinalic/ramble/var/ramble/workspaces/snap/software/snap.standard
==> [2023-10-26-16:25:08.762602] END OF EXPAND_VAR STACK spack env activate /home/klinalic/ramble/var/ramble/workspaces/snap/software/snap.standard
==> [2023-10-26-16:25:08.762644] BEGINNING OF EXPAND_VAR STACK ON {mpi_command}
==> [2023-10-26-16:25:08.762722] END OF EXPAND_VAR STACK mpirun -n 16
==> [2023-10-26-16:25:08.762745] BEGINNING OF EXPAND_VAR STACK ON {log_file}
==> [2023-10-26-16:25:08.762935] END OF EXPAND_VAR STACK /home/klinalic/ramble/var/ramble/workspaces/snap/experiments/snap/standard/snap_exp/snap_exp.out
==> [2023-10-26-16:25:08.762961] BEGINNING OF EXPAND_VAR STACK ON  mpirun -n 16 gsnap {in_file} {out_file} >> "/home/klinalic/ramble/var/ramble/workspaces/snap/experiments/snap/standard/snap_exp/snap_exp.out"
==> [2023-10-26-16:25:08.763066]    Math input is: "{snap}/qasnap/benchmark/inp"
==> [2023-10-26-16:25:08.763092] MathEvaluationError: Unsupported math AST node <class '_ast.Set'>:
	{'elts': [<_ast.Name object at 0x14fadcdfd320>], 'lineno': 1, 'col_offset': 0}
==> [2023-10-26-16:25:08.763135]    Math input is: "{snap}/qasnap/benchmark/inp"
==> [2023-10-26-16:25:08.763156] MathEvaluationError: Unsupported math AST node <class '_ast.Set'>:
	{'elts': [<_ast.Name object at 0x14fadcdfdac8>], 'lineno': 1, 'col_offset': 0}
==> [2023-10-26-16:25:08.763327] END OF EXPAND_VAR STACK mpirun -n 16 gsnap {snap}/qasnap/benchmark/inp /home/klinalic/ramble/var/ramble/workspaces/snap/experiments/snap/standard/snap_exp/output >> "/home/klinalic/ramble/var/ramble/workspaces/snap/experiments/snap/standard/snap_exp/snap_exp.out"
==> [2023-10-26-16:25:08.763369] BEGINNING OF EXPAND_VAR STACK ON {experiment_run_dir}
==> [2023-10-26-16:25:08.763509] END OF EXPAND_VAR STACK /home/klinalic/ramble/var/ramble/workspaces/snap/experiments/snap/standard/snap_exp
==> [2023-10-26-16:25:08.763542]   Executing phase get_inputs
==> [2023-10-26-16:25:08.763578] BEGINNING OF EXPAND_VAR STACK ON {input_name}
==> [2023-10-26-16:25:08.763630] END OF EXPAND_VAR STACK benchmark
==> [2023-10-26-16:25:08.763748] Creating stage lock snap.standard.inp
==> [2023-10-26-16:25:08.766728] Reading config file /home/klinalic/ramble/etc/ramble/defaults/mirrors.yaml
==> [2023-10-26-16:25:08.768528] Checking existence of file://%7Bsnap%7D/qasnap/benchmark/inp
==> [2023-10-26-16:25:08.768906] Using current working directory as base for abspath
==> [2023-10-26-16:25:08.771030] FailedDownloadError: Failed to fetch file from URL: file://%7Bsnap%7D/qasnap/benchmark/inp
    Urllib fetch failed to verify url                      file://%7Bsnap%7D/qasnap/benchmark/inp
 with error Download failed: <urlopen error [Errno 2] No such file or directory: '/home/klinalic/{snap}/qasnap/benchmark/inp'>
==> [2023-10-26-16:25:08.771080] Fetching from file://{snap}/qasnap/benchmark/inp failed.

What am I doing wrong?

0 replies

douglasjacobsen · 2023-10-27T01:01:26Z

douglasjacobsen
Oct 27, 2023
Maintainer

Ah, sorry. I don't think we currently expand urls. The input_file directive is intended to be something you have to fetch externally, not locally.

I don't even think you need the input_file directive. Try this instead:

import os
from ramble.appkit import *
from ramble.expander import Expander


class Snap(SpackApplication):
    '''Define SNAP application'''
    name = 'snap'

    maintainers('klinveam')

    tags('benchmark-app', 'mini-app', 'benchmark')

    default_compiler('gcc9', spack_spec='[email protected]')

    software_spec('impi2018',
                  spack_spec='[email protected]')

    software_spec('snap',
                  spack_spec='[email protected] +mpi +openmp',
                  compiler='gcc9')

    required_package('snap')

    workload('standard', executables=['execute'])

    executable('execute', 'gsnap {in_file} {out_file}', use_mpi=True)

    workload_variable('in_file', default='{snap}/qasnap/benchmark/inp',
                      description='Input file for results',
                      workloads=['standard'])

    workload_variable('out_file', default='{experiment_run_dir}/output',
                      description='Output file for results',
                      workloads=['standard'])

2 replies

douglasjacobsen Oct 27, 2023
Maintainer

One other thing I should mention. When using ramble workspace setup --dry-run no spack commands are executed. As a result, paths are not populated, so you'd still see '{snap}' in the resulting templates.

However, I just tested this on my system and I was able to have '{snap}' change into ...spack/opt/spack/linux-centos7-x86_64/gcc-8.5.0/snap-master-j26cahnqmvubabs4kgou3coggbyqog22/qasnap/benchmark/inp

douglasjacobsen Nov 1, 2023
Maintainer

@amklinv I'm going to mark this discussion answered, but please feel free to re-open if you run into more issues.

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Getting the installation directory back from spack #300

amklinv Oct 26, 2023

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