From c0ee3225ad976f9f25e73948fbfa2fb13a7d9d88 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 10 Feb 2022 11:02:52 +0100 Subject: [PATCH 1/6] Add times for 365d --- conf/pipeline/eager/eva.config | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 67c3b5a..e6f673e 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -19,36 +19,43 @@ process { withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 1.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'sc_small'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'sc_medium'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'mc_small'{ cpus = { check_max( 2, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'mc_medium' { cpus = { check_max( 4, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'mc_large'{ - cpus = { check_max( 8, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } + cpus = { check_max( 8, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'mc_huge'{ cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 256.GB * task.attempt, 'memory' ) } + time = '365.d' } // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use From 39c2d9b25b96e49bc58672a3ff3fedccc443edf2 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 10 Feb 2022 11:19:16 +0100 Subject: [PATCH 2/6] Oops --- conf/pipeline/eager/eva.config | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index e6f673e..12bb4da 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -19,43 +19,42 @@ process { withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 1.GB * task.attempt, 'memory' ) } - time = '365.d' + time = '365d' } withLabel:'sc_small'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } - time = '365.d' + time = '365d' } withLabel:'sc_medium'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = '365.d' + time = '365d' } withLabel:'mc_small'{ cpus = { check_max( 2, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } - time = '365.d' + time = '365d' } withLabel:'mc_medium' { cpus = { check_max( 4, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = '365.d' + time = '365d' } withLabel:'mc_large'{ - cpus = { check_max( 8, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = '365.d' + cpus = { check_max( 8, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = '365d' } withLabel:'mc_huge'{ cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 256.GB * task.attempt, 'memory' ) } - time = '365.d' } // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use From dd94895f168f2764f6580ca6a0f468af478ce2c3 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 10 Feb 2022 11:22:45 +0100 Subject: [PATCH 3/6] remove quotes --- conf/pipeline/eager/eva.config | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 12bb4da..64138af 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -19,37 +19,37 @@ process { withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 1.GB * task.attempt, 'memory' ) } - time = '365d' + time = 365d } withLabel:'sc_small'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } - time = '365d' + time = 365d } withLabel:'sc_medium'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = '365d' + time = 365d } withLabel:'mc_small'{ cpus = { check_max( 2, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } - time = '365d' + time = 365d } withLabel:'mc_medium' { cpus = { check_max( 4, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = '365d' + time = 365d } withLabel:'mc_large'{ cpus = { check_max( 8, 'cpus' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = '365d' + time = 365d } withLabel:'mc_huge'{ From dbd78f8075c9d4a3483cd3da23a4a38b1ac97af6 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 10 Feb 2022 11:26:18 +0100 Subject: [PATCH 4/6] Re add `.` --- conf/pipeline/eager/eva.config | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 64138af..669097d 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -19,37 +19,37 @@ process { withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 1.GB * task.attempt, 'memory' ) } - time = 365d + time = 365.d } withLabel:'sc_small'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } - time = 365d + time = 365.d } withLabel:'sc_medium'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = 365d + time = 365.d } withLabel:'mc_small'{ cpus = { check_max( 2, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } - time = 365d + time = 365.d } withLabel:'mc_medium' { cpus = { check_max( 4, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = 365d + time = 365.d } withLabel:'mc_large'{ cpus = { check_max( 8, 'cpus' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = 365d + time = 365.d } withLabel:'mc_huge'{ From d7d0f5ceccea4d28ceab5c5e4c1fa75642955073 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 10 Feb 2022 11:32:49 +0100 Subject: [PATCH 5/6] Change base time --- conf/eva.config | 2 +- conf/pipeline/eager/eva.config | 6 ------ 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/conf/eva.config b/conf/eva.config index 8b52dda..432b667 100644 --- a/conf/eva.config +++ b/conf/eva.config @@ -30,7 +30,7 @@ profiles { config_profile_description = 'MPI-EVA archgen profile, provided by nf-core/configs.' max_memory = 256.GB max_cpus = 32 - max_time = 720.h + max_time = 365.d //Illumina iGenomes reference file path } diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 669097d..67c3b5a 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -19,37 +19,31 @@ process { withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 1.GB * task.attempt, 'memory' ) } - time = 365.d } withLabel:'sc_small'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } - time = 365.d } withLabel:'sc_medium'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = 365.d } withLabel:'mc_small'{ cpus = { check_max( 2, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } - time = 365.d } withLabel:'mc_medium' { cpus = { check_max( 4, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = 365.d } withLabel:'mc_large'{ cpus = { check_max( 8, 'cpus' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = 365.d } withLabel:'mc_huge'{ From 88ddc9eee7a158200cd5e2423ad5d721c4eeaebe Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 10 Feb 2022 11:34:57 +0100 Subject: [PATCH 6/6] fffff --- conf/pipeline/eager/eva.config | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 67c3b5a..eccccbb 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -19,36 +19,43 @@ process { withLabel:'sc_tiny'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 1.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'sc_small'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'sc_medium'{ cpus = { check_max( 1, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'mc_small'{ cpus = { check_max( 2, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'mc_medium' { cpus = { check_max( 4, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'mc_large'{ cpus = { check_max( 8, 'cpus' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = '365.d' } withLabel:'mc_huge'{ cpus = { check_max( 32, 'cpus' ) } memory = { check_max( 256.GB * task.attempt, 'memory' ) } + time = '365.d' } // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use