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[ERP-2588] Fix array job instructions #60

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Merged
merged 1 commit into from
Sep 27, 2024
Merged

[ERP-2588] Fix array job instructions #60

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1 change: 1 addition & 0 deletions src/components/tool/guide/EresearchJob/EresearchInstructions.js
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Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,7 @@ export function EresearchInstructions({ config }) {
<LyraStatusInstructions
jobType={config.jobType}
jobName={batchJobName}
jobInstanceType={config.jobInstanceType}
/>
<TeardownInstructions
service={config.service}
Expand Down
15 changes: 7 additions & 8 deletions src/components/tool/guide/Instructions/StartInstructions.js
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Expand Up @@ -43,12 +43,6 @@ export function LyraStartInstructions({
const jobParameters = [
jobType === "Interactive" ? " -I -S /bin/bash" : "",
jobType !== "Interactive" && jobName !== "" ? ' -N "' + jobName + '"' : "",
jobType === "Batch" && jobInstanceType === "Array"
? " -J " + arrayConfig?.firstIndex + "-" + arrayConfig?.upperBound
: "",
jobType === "Batch" && jobInstanceType === "Array" && arrayConfig?.step > 1
? ":" + arrayConfig?.step
: "",
];

const wallTimeStr =
Expand All @@ -66,6 +60,11 @@ export function LyraStartInstructions({
`#PBS -N ${jobName}`,
`#PBS -l walltime=${wallTimeStr}`,
`#PBS -l ${resources.join(":")}`,
...(jobInstanceType === "Array"
? [
`#PBS -J ${arrayConfig?.firstIndex}-${arrayConfig?.upperBound}${arrayConfig?.step > 1 ? `:${arrayConfig?.step}` : ""}`,
]
: []),
"",
"cd $PBS_O_WORKDIR",
"",
Expand Down Expand Up @@ -101,7 +100,7 @@ export function LyraStartInstructions({
</InstructionText>
<CommandBox
command={[
`cat <<'EOF' > ${jobName}.pbs`,
`cat <<'EOF' > ${scriptPath || `${jobName}.pbs`}`,
...batchJobScript,
"EOF",
"",
Expand All @@ -111,7 +110,7 @@ export function LyraStartInstructions({
Run the following command to confirm the contents of the script:
</InstructionText>
<CommandBox
command={`cat ${jobName}.pbs`}
command={`cat ${scriptPath || `${jobName}.pbs`}`}
output={batchJobScript.join("\n")}
/>
</>
Expand Down
145 changes: 111 additions & 34 deletions src/components/tool/guide/Instructions/StatusInstructions.js
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ import InstructionInput from "./InstructionInput";
import InstructionHeading from "./components/InstructionHeading";
import InstructionText from "./components/InstructionText";

export function LyraStatusInstructions({ jobType, jobName }) {
export function LyraStatusInstructions({ jobType, jobName, jobInstanceType }) {
const [jobId, setJobId] = useState("");
const jobIdOrPlaceholder = jobId || "1234567";
const jobIdOrPlaceholder = jobId || "12345678";
return (
<>
<InstructionText>
Expand All @@ -28,17 +28,52 @@ export function LyraStatusInstructions({ jobType, jobName }) {
errorText="Job ID must only contain numbers"
/>
<InstructionHeading>Job status</InstructionHeading>
<InstructionText>
Check the status of your jobs by running the following command:
</InstructionText>
<CommandBox
command="qstat -xu $USER"
output={`pbs:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
----------- -------- ----- -------- ------ --- --- ------ ----- - -----
{jobInstanceType === "Standalone" && (
<>
<InstructionText>
Check the status of your jobs by running the following command:
</InstructionText>
<CommandBox
command="qstat -xu $USER"
output={`pbs:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
------------ -------- ----- -------- ------ --- --- ------ ----- - -----
${jobIdOrPlaceholder}.pbs username quick job-name -- 1 4 32gb 01:00 Q --`}
/>
/>
</>
)}
{jobInstanceType === "Array" && (
<>
<InstructionText>
Check the status of your array jobs by running the following
command:
</InstructionText>
<CommandBox
command="qstat -Jxu $USER"
output={`pbs:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
-------------- -------- ----- -------- ------ --- --- ------ ----- - -----
${jobIdOrPlaceholder}[].pbs username quick job-name -- 1 4 32gb 01:00 Q --`}
/>
<InstructionText>
Check the status of your array sub-jobs by running the following
command:
</InstructionText>
<CommandBox
command="qstat -Jtxu $USER"
output={`pbs:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
--------------- -------- ----- -------- ------ --- --- ------ ----- - -----
${jobIdOrPlaceholder}[0].pbs username quick job-name -- 1 4 32gb 01:00 Q --
${jobIdOrPlaceholder}[1].pbs username quick job-name -- 1 4 32gb 01:00 Q --
${jobIdOrPlaceholder}[2].pbs username quick job-name -- 1 4 32gb 01:00 Q --
`}
/>
</>
)}
<InstructionText>
The job status will be shown in the <Code>S</Code> column.
</InstructionText>
Expand Down Expand Up @@ -105,39 +140,81 @@ ${jobIdOrPlaceholder}.pbs username quick job-name -- 1 4 32gb 01:00 Q
<InstructionText>
Run the following command to see the output files:
</InstructionText>
<CommandBox
command={`ls -lh ${jobName}.*`}
output={[
`-rw------- 1 username default 100 Jan 01 00:00 ${jobName}.e${jobIdOrPlaceholder}`,
`-rw------- 1 username default 80 Jan 01 00:00 ${jobName}.o${jobIdOrPlaceholder}`,
].join("\n")}
/>
{jobInstanceType === "Standalone" && (
<CommandBox
command={`ls -lh ${jobName}.*`}
output={[
`-rw------- 1 username default 100 Jan 01 00:00 ${jobName}.e${jobIdOrPlaceholder}`,
`-rw------- 1 username default 80 Jan 01 00:00 ${jobName}.o${jobIdOrPlaceholder}`,
].join("\n")}
/>
)}
{jobInstanceType === "Array" && (
<CommandBox
command={`ls -lh ${jobName}.*`}
output={[
`-rw------- 1 username default 100 Jan 01 00:00 ${jobName}.e${jobIdOrPlaceholder}.0`,
`-rw------- 1 username default 100 Jan 01 00:00 ${jobName}.e${jobIdOrPlaceholder}.1`,
`-rw------- 1 username default 80 Jan 01 00:00 ${jobName}.o${jobIdOrPlaceholder}.0`,
`-rw------- 1 username default 80 Jan 01 00:00 ${jobName}.o${jobIdOrPlaceholder}.1`,
].join("\n")}
/>
)}
<InstructionText>
Run the following command to see the output of the job:
</InstructionText>
<CommandBox
command={`cat ${jobName}.o${jobIdOrPlaceholder}`}
output={[
"Hello, world!",
`PBS Job ${jobIdOrPlaceholder}.pbs`,
"CPU time : 00:00:00",
"Wall time : 00:00:01",
"Mem usage : 0b",
].join("\n")}
/>
{jobInstanceType === "Standalone" && (
<CommandBox
command={`cat ${jobName}.o${jobId || "*"}`}
output={[
`Running job 'job-name' (${jobIdOrPlaceholder}.pbs) in the following directory: /home/username`,
`PBS Job ${jobIdOrPlaceholder}.pbs`,
"CPU time : 00:00:00",
"Wall time : 00:00:01",
"Mem usage : 0b",
].join("\n")}
/>
)}
{jobInstanceType === "Array" && (
<CommandBox
command={`cat ${jobName}.o${jobId || "*"}.*`}
output={[
`Running job 'job-name' (${jobIdOrPlaceholder}[0].pbs) in the following directory: /home/username`,
`PBS Job ${jobIdOrPlaceholder}[1].pbs`,
"CPU time : 00:00:00",
"Wall time : 00:00:01",
"Mem usage : 0b",
`Running job 'job-name' (${jobIdOrPlaceholder}[1].pbs) in the following directory: /home/username`,
`PBS Job ${jobIdOrPlaceholder}[1].pbs`,
"CPU time : 00:00:00",
"Wall time : 00:00:01",
"Mem usage : 0b",
].join("\n")}
/>
)}
<InstructionText>
Run the following command to see the error output of the job:
</InstructionText>
<CommandBox
command={`cat ${jobName}.e${jobIdOrPlaceholder}`}
output={`Data written to stderr`}
/>
{jobInstanceType === "Standalone" && (
<CommandBox
command={`cat ${jobName}.e${jobId || "*"}`}
output={`Data written to stderr`}
/>
)}
{jobInstanceType === "Array" && (
<CommandBox
command={`cat ${jobName}.e${jobId || "*"}.*`}
output={["Data written to stderr", "Data written to stderr"].join(
"\n",
)}
/>
)}
<InstructionText>
Use the following command to get more detailed information about the
job, including resource usage.
</InstructionText>
<CommandBox
command={`qstat -fx ${jobIdOrPlaceholder}`}
command={`qstat -fx ${jobId || "{jobId}"}`}
output={`Job Id: ${jobIdOrPlaceholder}.pbs
...
resources_used.cpupercent = 99
Expand Down
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