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Merged
bbimber merged 3 commits into from
Oct 19, 2020
Merged

Merge discvr-20.7 to develop #51

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347af77
prepare to migrate to new-lustre
bbimber Oct 15, 2020
f895c36
Remove unnecessary error logging
bbimber Oct 18, 2020
73036d2
Merge discvr-20.7 to develop
bbimber Oct 19, 2020
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4 changes: 2 additions & 2 deletions GenotypeAssays/resources/web/genotypeassays/panel/HaplotypePanel.js
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Original file line number Diff line number Diff line change
Expand Up @@ -591,14 +591,14 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
}
else {
rankedPctMatches[totalPctPresent] = rankedPctMatches[totalPctPresent] || [];
if (rankedPctMatches[totalPctPresent].indexOf(names) == -1) {
if (rankedPctMatches[totalPctPresent].indexOf(names) === -1) {
rankedPctMatches[totalPctPresent].push(names);
}

pctExplainedByMatch[names] = totalPctPresent;

rankedMatches[matchesUnion.length] = rankedMatches[matchesUnion.length] || [];
if (rankedMatches[matchesUnion.length].indexOf(names) == -1) {
if (rankedMatches[matchesUnion.length].indexOf(names) === -1) {
rankedMatches[matchesUnion.length].push(names);
}
}
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2 changes: 1 addition & 1 deletion primeseq/src/org/labkey/primeseq/pipeline/ExacloudResourceSettings.java
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Expand Up @@ -32,7 +32,7 @@ public List<ToolParameterDescriptor> getParams()
put("minValue", 512);
}}, 1028),
ToolParameterDescriptor.create("localSSD", "Request Nodes With SSD Scratch", "If selected, -C ssdscratch will be added to the submit script, which limits to node with faster SSD scratch space. This might be important for I/O intense jobs.", "checkbox", null, null),
ToolParameterDescriptor.create("useGScratch", "Use GScratch Working Space", "If selected, this job will use the GCratch pilot as working space, which may be faster in some cases than lustre.", "checkbox", null, null),
ToolParameterDescriptor.create("useLustre", "Use Old Lustre Working Space", "If selected, this job will use the older Lustre working space.", "checkbox", null, null),
ToolParameterDescriptor.create("useExclusive", "Use Exclusive Flag", "If selected, the job allocation can not share nodes with other running jobs. This should not be selected unless you are sure about this. It can help protect memory-intensive, long-running jobs.", "checkbox", null, null),
ToolParameterDescriptor.create("covidRelated", "COVID Related Job", "If selected, this job will be flagged as --comment=COVID to help ACC track these jobs.", "checkbox", null, null)
);
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28 changes: 5 additions & 23 deletions primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java
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Expand Up @@ -279,13 +279,8 @@ public void addExtraSubmitScriptLines(PipelineJob job, RemoteExecutionEngine eng
possiblyAddSSD(job, engine, lines);
possiblyAddExclusive(job, engine, lines);

possiblyAddGScratch(job, engine, lines);
possiblyAddCOVID(job, lines);
}
else
{
job.getLogger().error("This job type does not implement HasJobParams");
}
}

private void possiblyAddCOVID(PipelineJob job, List<String> lines)
Expand Down Expand Up @@ -314,10 +309,10 @@ public Map<String, Object> getEnvironmentVars(PipelineJob job, RemoteExecutionEn
{
Map<String, Object> ret = new HashMap<>();

if (job instanceof HasJobParams && getGScratchValue((HasJobParams)job))
if (job instanceof HasJobParams && getUseLustreValue((HasJobParams)job))
{
job.getLogger().info("Requiring using GScratch pilot as working space");
ret.put("USE_GSCRATCH", "1");
job.getLogger().info("Requiring using original lustre as working space");
ret.put("USE_LUSTRE", "1");
}

return ret;
Expand Down Expand Up @@ -419,10 +414,10 @@ private void possiblyAddSSD(PipelineJob job, RemoteExecutionEngine engine, List<
}
}

private boolean getGScratchValue(HasJobParams job)
private boolean getUseLustreValue(HasJobParams job)
{
Map<String, String> params = (job).getJobParams();
String val = StringUtils.trimToNull(params.get("resourceSettings.resourceSettings.useGScratch"));
String val = StringUtils.trimToNull(params.get("resourceSettings.resourceSettings.useLustre"));
if (val == null)
{
return false;
Expand All @@ -431,19 +426,6 @@ private boolean getGScratchValue(HasJobParams job)
return Boolean.parseBoolean(val);
}

private void possiblyAddGScratch(PipelineJob job, RemoteExecutionEngine engine, List<String> lines)
{
if (getGScratchValue((HasJobParams)job))
{
job.getLogger().info("Requiring infiniband node, because GScratch was selected as working space");
String line = "#SBATCH -C IB";
if (!lines.contains(line))
{
lines.add(line);
}
}
}

private void possiblyAddQOS(PipelineJob job, RemoteExecutionEngine engine, List<String> lines)
{
//first remove existing
Expand Down