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Revert singularity|apptainer run as default
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Signed-off-by: Paolo Di Tommaso <[email protected]>
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@pditommaso
pditommaso committed Sep 10, 2023
1 parent 80f7cd4 commit c1cc60d
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Showing 5 changed files with 56 additions and 56 deletions.
2 changes: 1 addition & 1 deletion modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
}

private String defaultRunCommand() {
final result = SysEnv.get("NXF_${getBinaryName().toUpperCase()}_RUN_COMMAND", 'run')
final result = SysEnv.get("NXF_${getBinaryName().toUpperCase()}_RUN_COMMAND", 'exec')
if( result !in ['run','exec'] )
throw new IllegalArgumentException("Invalid singularity launch command '$result' - it should be either 'run' or 'exec'")
return result
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50 changes: 25 additions & 25 deletions modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,9 @@ import spock.lang.Unroll
*/
class ApptainerBuilderTest extends Specification {

def 'should get the legacy exec command line' () {
def 'should get the run command line and auto mounts disabled' () {
given:
SysEnv.push(NXF_APPTAINER_RUN_COMMAND:'exec', NXF_APPTAINER_AUTO_MOUNTS:'false')
SysEnv.push(NXF_APPTAINER_RUN_COMMAND:'run', NXF_APPTAINER_AUTO_MOUNTS:'false')
and:
def path1 = Paths.get('/foo/data/file1')
def path2 = Paths.get('/bar/data/file2')
Expand All @@ -38,55 +38,55 @@ class ApptainerBuilderTest extends Specification {
expect:
new ApptainerBuilder('busybox')
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid busybox'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid busybox'

new ApptainerBuilder('busybox')
.params(engineOptions: '-q -v')
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v exec --no-home --pid busybox'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v run --no-home --pid busybox'

new ApptainerBuilder('busybox')
.params(runOptions: '--contain --writable')
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid --contain --writable busybox'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid --contain --writable busybox'

new ApptainerBuilder('ubuntu')
.addMount(path1)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid ubuntu'

new ApptainerBuilder('ubuntu')
.addMount(path1)
.addMount(path2)
.params(autoMounts: true)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'

new ApptainerBuilder('ubuntu')
.addMount(path1)
.addMount(path1)
.params(autoMounts: true)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'

new ApptainerBuilder('ubuntu')
.addMount(path1)
.addMount(path1)
.params(autoMounts: true)
.params(readOnlyInputs: true)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'

new ApptainerBuilder('ubuntu')
.addMount(path3)
.params(autoMounts: true)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'

new ApptainerBuilder('ubuntu')
.params(newPidNamespace: false)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home ubuntu'

cleanup:
SysEnv.pop()
Expand All @@ -102,56 +102,56 @@ class ApptainerBuilderTest extends Specification {
expect:
new ApptainerBuilder('busybox')
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" busybox'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" busybox'

new ApptainerBuilder('busybox')
.params(engineOptions: '-q -v')
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v run --no-home --pid -B "$PWD" busybox'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v exec --no-home --pid -B "$PWD" busybox'

new ApptainerBuilder('busybox')
.params(runOptions: '--contain --writable')
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" --contain --writable busybox'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" --contain --writable busybox'

new ApptainerBuilder('ubuntu')
.addMount(path1)
.params(autoMounts: false)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid ubuntu'

new ApptainerBuilder('ubuntu')
.addMount(path1)
.addMount(path2)
.params(autoMounts: true)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'

new ApptainerBuilder('ubuntu')
.addMount(path1)
.addMount(path1)
.params(autoMounts: true)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'

new ApptainerBuilder('ubuntu')
.addMount(path1)
.addMount(path1)
.params(autoMounts: true)
.params(readOnlyInputs: true)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'

new ApptainerBuilder('ubuntu')
.addMount(path3)
.params(autoMounts: true)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'

new ApptainerBuilder('ubuntu')
.params(newPidNamespace: false)
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home -B "$PWD" ubuntu'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home -B "$PWD" ubuntu'

}

Expand Down Expand Up @@ -201,12 +201,12 @@ class ApptainerBuilderTest extends Specification {
.addEnv('X=1')
.addEnv(ALPHA:'aaa', BETA: 'bbb')
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} APPTAINERENV_X="1" APPTAINERENV_ALPHA="aaa" APPTAINERENV_BETA="bbb" apptainer run --no-home --pid -B "$PWD" busybox'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} APPTAINERENV_X="1" APPTAINERENV_ALPHA="aaa" APPTAINERENV_BETA="bbb" apptainer exec --no-home --pid -B "$PWD" busybox'

new ApptainerBuilder('busybox')
.addEnv('CUDA_VISIBLE_DEVICES')
.build()
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+APPTAINERENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} apptainer run --no-home --pid -B "$PWD" busybox'
.runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+APPTAINERENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} apptainer exec --no-home --pid -B "$PWD" busybox'

}

Expand All @@ -216,17 +216,17 @@ class ApptainerBuilderTest extends Specification {
when:
def cmd = new ApptainerBuilder('ubuntu.img').build().getRunCommand()
then:
cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img'
cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img'

when:
cmd = new ApptainerBuilder('ubuntu.img').build().getRunCommand('bwa --this --that file.fastq')
then:
cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'

when:
cmd = new ApptainerBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
then:
cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
}

@Unroll
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