From c5822f8fe2a98b31a828b37bcd14eed586d54e5a Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 23 Sep 2024 22:08:00 +0200 Subject: [PATCH] Remove empty resourceLimit entries --- conf/bigpurple.config | 5 ----- conf/csiro_petrichor.config | 5 ----- conf/ebi_codon.config | 5 ----- conf/ebi_codon_slurm.config | 5 ----- conf/embl_hd.config | 5 ----- conf/gis.config | 5 ----- conf/googlebatch.config | 5 ----- conf/googlels.config | 5 ----- conf/mccleary.config | 9 ++++----- conf/nci_gadi.config | 5 ----- conf/nygc.config | 5 ----- conf/pawsey_setonix.config | 3 +-- conf/qmul_apocrita.config | 5 ----- conf/roslin.config | 5 ----- conf/software_license.config | 5 ----- conf/tubingen_apg.config | 9 ++++----- conf/ucd_sonic.config | 5 ----- conf/ucl_cscluster.config | 5 ----- conf/ucl_myriad.config | 5 ----- conf/unc_lccc.config | 7 +++---- conf/york_viking.config | 5 ----- 21 files changed, 12 insertions(+), 101 deletions(-) diff --git a/conf/bigpurple.config b/conf/bigpurple.config index b7a42c332..094688e07 100644 --- a/conf/bigpurple.config +++ b/conf/bigpurple.config @@ -18,11 +18,6 @@ singularity { } process { -resourceLimits = [ - memory: , - cpus: , - time: -] beforeScript = """ module load singularity/3.1 module load squashfs-tools/4.3 diff --git a/conf/csiro_petrichor.config b/conf/csiro_petrichor.config index 9d6c6dc51..4673d104d 100644 --- a/conf/csiro_petrichor.config +++ b/conf/csiro_petrichor.config @@ -19,11 +19,6 @@ singularity { // Define process resource limits process { -resourceLimits = [ - memory: , - cpus: , - time: -] executor = 'slurm' clusterOptions = "--account=${System.getenv('SBATCH_ACCOUNT')}" module = 'singularity/3.8.7' diff --git a/conf/ebi_codon.config b/conf/ebi_codon.config index a2abf56b7..ee1ce7ede 100644 --- a/conf/ebi_codon.config +++ b/conf/ebi_codon.config @@ -20,11 +20,6 @@ singularity { } process { -resourceLimits = [ - memory: , - cpus: , - time: -] queue = { if (task.time > 7.day && task.memory > 300.GB) { "long_bigmem" diff --git a/conf/ebi_codon_slurm.config b/conf/ebi_codon_slurm.config index 073d2d2d1..336e65ab9 100644 --- a/conf/ebi_codon_slurm.config +++ b/conf/ebi_codon_slurm.config @@ -20,11 +20,6 @@ singularity { } process { -resourceLimits = [ - memory: , - cpus: , - time: -] // this is to avoid errors for missing files due to shared filesystem latency maxRetries = 3 errorStrategy = { task.exitStatus == 0 ? "retry" : "terminate" } diff --git a/conf/embl_hd.config b/conf/embl_hd.config index 24aa218f2..397b5a82f 100644 --- a/conf/embl_hd.config +++ b/conf/embl_hd.config @@ -14,11 +14,6 @@ apptainer { } process { -resourceLimits = [ - memory: , - cpus: , - time: -] def scratch_dir = System.getenv("SCRATCHDIR") maxRetries = 3 cache = 'lenient' diff --git a/conf/gis.config b/conf/gis.config index 426200880..77c0cde31 100644 --- a/conf/gis.config +++ b/conf/gis.config @@ -6,11 +6,6 @@ params { } process { -resourceLimits = [ - memory: , - cpus: , - time: -] executor = 'sge' clusterOptions = { "-l mem_free=" + task.memory.toString().replaceAll(/[\sB]/, '') } penv = 'OpenMP' diff --git a/conf/googlebatch.config b/conf/googlebatch.config index f0aae8752..f99cb3a1a 100644 --- a/conf/googlebatch.config +++ b/conf/googlebatch.config @@ -25,11 +25,6 @@ params { workDir = params.workdir_bucket process { -resourceLimits = [ - memory: , - cpus: , - time: -] executor = 'google-batch' } google { diff --git a/conf/googlels.config b/conf/googlels.config index c1c1c0841..9dff26ec9 100644 --- a/conf/googlels.config +++ b/conf/googlels.config @@ -24,11 +24,6 @@ params { workDir = params.workdir_bucket process { -resourceLimits = [ - memory: , - cpus: , - time: -] executor = 'google-lifesciences' } google { diff --git a/conf/mccleary.config b/conf/mccleary.config index 24162de13..a4a2d150e 100644 --- a/conf/mccleary.config +++ b/conf/mccleary.config @@ -24,12 +24,11 @@ executor { process { resourceLimits = [ memory: 983.GB, - cpus: 64, - time: + cpus: 64 ] - queue = { task.time > 24.h ? 'week' : 'day' } - scratch = 'true' - executor = 'slurm' + queue = { task.time > 24.h ? 'week' : 'day' } + scratch = 'true' + executor = 'slurm' } params { diff --git a/conf/nci_gadi.config b/conf/nci_gadi.config index 05cd4c962..e726bf0e2 100644 --- a/conf/nci_gadi.config +++ b/conf/nci_gadi.config @@ -24,11 +24,6 @@ executor { // Define process resource limits process { -resourceLimits = [ - memory: , - cpus: , - time: -] executor = 'pbspro' project = System.getenv("PROJECT") storage = 'scratch/params.project' diff --git a/conf/nygc.config b/conf/nygc.config index e3699fe41..05ceab01f 100644 --- a/conf/nygc.config +++ b/conf/nygc.config @@ -8,11 +8,6 @@ singularity { } process { -resourceLimits = [ - memory: , - cpus: , - time: -] executor = 'slurm' queue = { task.accelerator ? 'gpu' : (task.memory > 100.GB ? 'bigmem' : 'pe2') } } diff --git a/conf/pawsey_setonix.config b/conf/pawsey_setonix.config index 523a56651..5ae758db7 100644 --- a/conf/pawsey_setonix.config +++ b/conf/pawsey_setonix.config @@ -24,8 +24,7 @@ executor { process { resourceLimits = [ memory: 230.Gb, - cpus: 64, - time: + cpus: 64 ] executor = 'slurm' clusterOptions = "--account=${System.getenv('PAWSEY_PROJECT')}" diff --git a/conf/qmul_apocrita.config b/conf/qmul_apocrita.config index 5b55093c7..bc3b87649 100644 --- a/conf/qmul_apocrita.config +++ b/conf/qmul_apocrita.config @@ -12,11 +12,6 @@ executor { apptainer.runOptions = "-B ${HOME},${PWD}" process { -resourceLimits = [ - memory: , - cpus: , - time: -] //NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED penv = 'smp' diff --git a/conf/roslin.config b/conf/roslin.config index b4c764976..d61c4f8a3 100644 --- a/conf/roslin.config +++ b/conf/roslin.config @@ -10,11 +10,6 @@ executor { } process { -resourceLimits = [ - memory: , - cpus: , - time: -] stageInMode = 'symlink' scratch = 'false' penv = { task.cpus > 1 ? "sharedmem" : null } diff --git a/conf/software_license.config b/conf/software_license.config index f7e85a053..1c9767316 100755 --- a/conf/software_license.config +++ b/conf/software_license.config @@ -10,11 +10,6 @@ params { if (params.sentieon_extension) { process { -resourceLimits = [ - memory: , - cpus: , - time: -] withLabel: 'sentieon' { ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64 ?: '' ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64 ?: '' diff --git a/conf/tubingen_apg.config b/conf/tubingen_apg.config index 3c17fd3b1..b082fd7f3 100644 --- a/conf/tubingen_apg.config +++ b/conf/tubingen_apg.config @@ -13,12 +13,11 @@ cleanup = true process { resourceLimits = [ memory: 4.TB, - cpus: 256, - time: + cpus: 256 ] - executor = 'slurm' - queue = { task.time <= 2.h ? 'short' : task.time <= 48.h ? 'medium' : 'long' } - maxRetries = 2 + executor = 'slurm' + queue = { task.time <= 2.h ? 'short' : task.time <= 48.h ? 'medium' : 'long' } + maxRetries = 2 } executor { diff --git a/conf/ucd_sonic.config b/conf/ucd_sonic.config index 3e9e57c31..4336fd4eb 100644 --- a/conf/ucd_sonic.config +++ b/conf/ucd_sonic.config @@ -8,11 +8,6 @@ params { } process { -resourceLimits = [ - memory: , - cpus: 40, - time: 12.h -] executor = 'slurm' queue = 'shared' queueSize = 50 diff --git a/conf/ucl_cscluster.config b/conf/ucl_cscluster.config index 732f89c19..994d7300f 100644 --- a/conf/ucl_cscluster.config +++ b/conf/ucl_cscluster.config @@ -12,11 +12,6 @@ executor { singularity.runOptions = "-B ${HOME},${PWD}" process { -resourceLimits = [ - memory: , - cpus: , - time: -] //NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED penv = 'smp' diff --git a/conf/ucl_myriad.config b/conf/ucl_myriad.config index c9c28ad7b..809d5d820 100644 --- a/conf/ucl_myriad.config +++ b/conf/ucl_myriad.config @@ -12,11 +12,6 @@ executor { apptainer.runOptions = "-B ${HOME},${PWD}" process { -resourceLimits = [ - memory: , - cpus: , - time: -] //NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED penv = 'smp' diff --git a/conf/unc_lccc.config b/conf/unc_lccc.config index b455ed66c..c0fe7cece 100644 --- a/conf/unc_lccc.config +++ b/conf/unc_lccc.config @@ -7,11 +7,10 @@ params { process { resourceLimits = [ memory: 950.GB, - cpus: 90, - time: + cpus: 90 ] - executor = "slurm" - queue = "allnodes" + executor = "slurm" + queue = "allnodes" } singularity { diff --git a/conf/york_viking.config b/conf/york_viking.config index 868535d27..29709fbac 100644 --- a/conf/york_viking.config +++ b/conf/york_viking.config @@ -21,11 +21,6 @@ apptainer { } process { -resourceLimits = [ - memory: , - cpus: , - time: -] maxRetries = 3 clusterOptions = "--get-user-env --account=${System.getenv('USER_ACCOUNT')}" // Get user environment and assign account