From 361e02b87ec1d279fb17ed3725646d90252729cb Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Fri, 3 Feb 2023 09:37:45 +0100 Subject: [PATCH 1/2] Recent LSF update broke bjobs command behavior (position of -o option relative to field names). --- .../roddy/execution/jobs/cluster/lsf/LSFJobManager.groovy | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManager.groovy b/src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManager.groovy index cd0e5201..30b7162e 100644 --- a/src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManager.groovy +++ b/src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManager.groovy @@ -35,8 +35,8 @@ class LSFJobManager extends AbstractLSFJobManager { final static String TIMESTAMP_PATTERN = /${MONTH}\s+${DAY}\s+${TIME}(\s+${YEAR})?(\s+${LSF_SUFFIX})?/ - private static final String LSF_COMMAND_QUERY_STATES = "bjobs -a -o -hms -json \"jobid job_name stat finish_time\"" - private static final String LSF_COMMAND_QUERY_EXTENDED_STATES = "bjobs -a -o -hms -json \"jobid job_name stat user queue " + + private static final String LSF_COMMAND_QUERY_STATES = "bjobs -a -hms -json -o \"jobid job_name stat finish_time\"" + private static final String LSF_COMMAND_QUERY_EXTENDED_STATES = "bjobs -a -hms -json -o \"jobid job_name stat user queue " + "job_description proj_name job_group job_priority pids exit_code from_host exec_host submit_time start_time " + "finish_time cpu_used run_time user_group swap max_mem runtimelimit sub_cwd " + "pend_reason exec_cwd output_file input_file effective_resreq exec_home slots error_file command dependency \"" From fc505d2b2de3ae5017eaa21d2252d4db46ee7e7a Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Fri, 3 Feb 2023 09:45:24 +0100 Subject: [PATCH 2/2] Like every year, the timeparsing tests break :( -- this is again a quickfix --- .../execution/jobs/cluster/lsf/LSFJobManagerSpec.groovy | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/test/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManagerSpec.groovy b/src/test/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManagerSpec.groovy index 87c44da5..289b7238 100644 --- a/src/test/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManagerSpec.groovy +++ b/src/test/groovy/de/dkfz/roddy/execution/jobs/cluster/lsf/LSFJobManagerSpec.groovy @@ -284,9 +284,9 @@ class LSFJobManagerSpec extends Specification { where: month | day | hour | minute | second | year | suffix | expectedYear | referenceDate - "Jan" | "01" | "01" | "02" | "" | "" | "" | 2021 | ZonedDateTime.of(2021, 1, 29, 19, 56, 0, 0, ZoneId.systemDefault()) - "Feb" | "02" | "01" | "02" | "" | "" | "L" | 2021 | ZonedDateTime.of(2021, 1, 29, 19, 56, 0, 0, ZoneId.systemDefault()) - "Feb" | "02" | "01" | "02" | "" | "" | "L" | 2021 | ZonedDateTime.of(2021, 2, 3, 19, 56, 0, 0, ZoneId.systemDefault()) + "Jan" | "01" | "01" | "02" | "" | "" | "" | 2022 | ZonedDateTime.of(2022, 1, 29, 19, 56, 0, 0, ZoneId.systemDefault()) + "Feb" | "02" | "01" | "02" | "" | "" | "L" | 2022 | ZonedDateTime.of(2022, 1, 29, 19, 56, 0, 0, ZoneId.systemDefault()) + "Feb" | "02" | "01" | "02" | "" | "" | "L" | 2022 | ZonedDateTime.of(2022, 2, 3, 19, 56, 0, 0, ZoneId.systemDefault()) "Mar" | "03" | "01" | "02" | "" | "1000" | "" | 1000 | ZonedDateTime.of(2021, 1, 29, 19, 56, 0, 0, ZoneId.systemDefault()) "Apr" | "04" | "01" | "02" | "" | "1001" | "L" | 1001 | ZonedDateTime.of(2021, 1, 29, 19, 56, 0, 0, ZoneId.systemDefault()) "May" | "5" | "01" | "02" | "03" | "1002" | "" | 1002 | ZonedDateTime.of(2021, 1, 29, 19, 56, 0, 0, ZoneId.systemDefault())