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fix mem high watermark reporting #502

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merged 4 commits into from
Dec 15, 2023
Merged

fix mem high watermark reporting #502

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64cc416
update max mem inspection
tomkinsc Dec 6, 2023
bff191a
account for other (GCP) possibility of cgroup v2 memory stat location…
tomkinsc Dec 15, 2023
7c1e3b6
Merge branch 'master' into ct-fix-mem-highwatermark-inspection
tomkinsc Dec 15, 2023
5d8f355
Merge branch 'master' into ct-fix-mem-highwatermark-inspection
tomkinsc Dec 15, 2023
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2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_assembly.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -517,7 +517,7 @@ task align_reads {
reports.py fastqc ~{sample_name}.mapped.bam ~{sample_name}.mapped_fastqc.html --out_zip ~{sample_name}.mapped_fastqc.zip

cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>

output {
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2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_demux.wdl
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Expand Up @@ -389,7 +389,7 @@ task illumina_demux {
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg | cut -f 3 -d ' ' > LOAD_15M
set +o pipefail
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>

output {
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2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_interhost.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ task subsample_by_cases {
set +o pipefail
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES

>>>
runtime {
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34 changes: 17 additions & 17 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -172,7 +172,7 @@ task nextclade_many_samples {
# gather runtime metrics
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -566,7 +566,7 @@ task nextstrain_build_subsample {
cd ..
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -815,7 +815,7 @@ task filter_subsample_sequences {
grep "strains passed all filters" STDOUT | cut -f 1 -d ' ' > OUT_COUNT
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -913,7 +913,7 @@ task filter_sequences_to_list {

cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1004,7 +1004,7 @@ task mafft_one_chr {
# profiling and stats
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1112,7 +1112,7 @@ task mafft_one_chr_chunked {
# profiling and stats
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1161,7 +1161,7 @@ task augur_mafft_align {
--nthreads auto
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1241,7 +1241,7 @@ task augur_mask_sites {
fi
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1300,7 +1300,7 @@ task draft_augur_tree {
--nthreads auto
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1384,7 +1384,7 @@ task refine_augur_tree {
~{"--vcf-reference " + vcf_reference}
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1437,7 +1437,7 @@ task ancestral_traits {
~{true="--confidence" false="" confidence}
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1499,7 +1499,7 @@ task ancestral_tree {
~{true="--infer-ambiguous" false="" infer_ambiguous}
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1548,7 +1548,7 @@ task translate_augur_tree {
~{"--vcf-reference " + vcf_reference} \
~{"--genes " + genes} \
--output-node-data ~{out_basename}_aa_muts.json
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1619,7 +1619,7 @@ task tip_frequencies {

cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1664,7 +1664,7 @@ task assign_clades_to_nodes {
--reference "~{ref_fasta}" \
--clades "~{clades_tsv}" \
--output-node-data "~{out_basename}_clades.json"
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1713,7 +1713,7 @@ task augur_import_beast {
~{"--tip-date-delimeter " + tip_date_delimiter}
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down Expand Up @@ -1816,7 +1816,7 @@ task export_auspice_json {
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
set +o pipefail
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: docker
Expand Down
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_reports.wdl
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Expand Up @@ -580,7 +580,7 @@ task compare_two_genomes {
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
set +o pipefail
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>

output {
Expand Down
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_utils.wdl
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Expand Up @@ -101,7 +101,7 @@ task zcat {
# gather runtime metrics
cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
cat /proc/loadavg > CPU_LOAD
{ cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
>>>
runtime {
docker: "quay.io/broadinstitute/viral-core:2.1.33"
Expand Down
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