6e5ee11ca95cd971984038cf65bae00d9c898707 galt Wed Jun 4 15:40:02 2014 -0700 Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history. diff --git src/parasol/para/para.c src/parasol/para/para.c index 765f468..2f13a30 100644 --- src/parasol/para/para.c +++ src/parasol/para/para.c @@ -1,2271 +1,2271 @@ /* para - para - manage a batch of jobs in parallel on a compute cluster.. */ #include "paraCommon.h" -#include "errabort.h" +#include "errAbort.h" #include "linefile.h" #include "options.h" #include "hash.h" #include "localmem.h" #include "dystring.h" #include "obscure.h" #include "portable.h" #include "net.h" #include "paraLib.h" #include "paraMessage.h" #include "jobDb.h" #include "jobResult.h" #include "verbose.h" #include "sqlNum.h" /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"retries" , OPTION_INT}, {"maxQueue" , OPTION_INT}, {"minPush" , OPTION_INT}, {"maxPush" , OPTION_INT}, {"warnTime" , OPTION_INT}, {"killTime" , OPTION_INT}, {"delayTime", OPTION_INT}, {"eta" , OPTION_BOOLEAN}, /* default, no longer used */ {"pri" , OPTION_STRING}, {"priority" , OPTION_STRING}, {"maxJob" , OPTION_STRING}, {"cpu" , OPTION_FLOAT}, {"ram" , OPTION_STRING}, {"batch" , OPTION_STRING}, {"jobCwd" , OPTION_STRING}, {NULL, 0} }; char *version = PARA_VERSION; /* Version number. */ static int numHappyDots; /* number of happy dots written */ void usage() /* Explain usage and exit. */ { errAbort( "para - version %s\n" "Manage a batch of jobs in parallel on a compute cluster.\n" "Normal usage is to do a 'para create' followed by 'para push' until\n" "job is done. Use 'para check' to check status.\n" "usage:\n\n" " para [options] command [command-specific arguments]\n\n" "The commands are:\n" "\n" "para create jobList\n" " This makes the job-tracking database from a text file with the\n" " command line for each job on a separate line.\n" " options:\n" " -cpu=N Number of CPUs used by the jobs, default 1.\n" " -ram=N Number of bytes of RAM used by the jobs.\n" " Default is RAM on node divided by number of cpus on node.\n" " Shorthand expressions allow t,g,m,k for tera, giga, mega, kilo.\n" " e.g. 4g = 4 Gigabytes.\n" " -batch=batchDir - specify the directory path that is used to store the\n" " batch control files. The batchDir can be an absolute path or a path\n" " relative to the current directory. The resulting path is use as the\n" " batch name. The directory is created if it doesn't exist. When\n" " creating a new batch, batchDir should not have been previously used as\n" " a batch name. The batchDir must be writable by the paraHub process.\n" " This does not affect the working directory assigned to jobs. It defaults\n" " to the directory where para is run. If used, this option must be specified\n" " on all para commands for the batch. For example to run two batches in the\n" " same directory:\n" " para -batch=b1 make jobs1\n" " para -batch=b2 make jobs2\n" "para push \n" " This pushes forward the batch of jobs by submitting jobs to parasol\n" " It will limit parasol queue size to something not too big and\n" " retry failed jobs.\n" " options:\n" " -retries=N Number of retries per job - default 4.\n" " -maxQueue=N Number of jobs to allow on parasol queue. \n" " Default 2000000.\n" " -minPush=N Minimum number of jobs to queue. \n" " Default 1. Overrides maxQueue.\n" " -maxPush=N Maximum number of jobs to queue - default 100000.\n" " -warnTime=N Number of minutes job runs before hang warning. \n" " Default 4320 (3 days).\n" " -killTime=N Number of minutes hung job runs before push kills it.\n" " By default kill off for backwards compatibility.\n" /* originally to be 2 weeks */ " -delayTime=N Number of seconds to delay before submitting next job \n" " to minimize i/o load at startup - default 0.\n" " -priority=x Set batch priority to high, medium, or low.\n" " Default medium (use high only with approval).\n" " If needed, use with make, push, create, shove, or try.\n" " Or, set batch priority to a specific numeric value - default %d.\n" " 1 is emergency high priority, \n" " %d is normal medium, \n" " %d is low for bottomfeeders.\n" " Setting priority higher than normal (1-%d) will be logged.\n" " Please keep low priority jobs short, they won't be pre-empted.\n" " -maxJob=x Limit the number of jobs the batch can run.\n" " Specify number of jobs, for example 10 or 'unlimited'.\n" " Default unlimited displays as -1.\n" " -jobCwd=dir - specify the directory path to use as the current working\n" " directory for each job. The dir can be an absolute path or a path\n" " relative to the current directory. It defaults to the directory where\n" " para is run.\n" "para try \n" " This is like para push, but only submits up to 10 jobs.\n" "para shove\n" " Push jobs in this database until all are done or one fails after N retries.\n" "para make jobList\n" " Create database and run all jobs in it if possible. If one job\n" " fails repeatedly this will fail. Suitable for inclusion in makefiles.\n" " Same as a 'create' followed by a 'shove'.\n" "para check\n" " This checks on the progress of the jobs.\n" "para stop\n" " This stops all the jobs in the batch.\n" "para chill\n" " Tells system to not launch more jobs in this batch, but\n" " does not stop jobs that are already running.\n" "para finished\n" " List jobs that have finished.\n" "para hung\n" " List hung jobs in the batch (running > killTime).\n" "para slow\n" " List slow jobs in the batch (running > warnTime).\n" "para crashed\n" " List jobs that crashed or failed output checks the last time they were run.\n" "para failed\n" " List jobs that crashed after repeated restarts.\n" "para status\n" " List individual job status, including times.\n" "para problems\n" " List jobs that had problems (even if successfully rerun).\n" " Includes host info.\n" "para running\n" " Print info on currently running jobs.\n" "para hippos time\n" " Print info on currently running jobs taking > 'time' (minutes) to run.\n" "para time\n" " List timing information.\n" "para recover jobList newJobList\n" " Generate a job list by selecting jobs from an existing list where\n" " the `check out' tests fail.\n" "para priority 999\n" " Set batch priority. Values explained under 'push' options above.\n" "para maxJob 999\n" " Set batch maxJob. Values explained under 'push' options above.\n" "para ram 999\n" " Set batch ram usage. Values explained under 'push' options above.\n" "para cpu 999\n" " Set batch cpu usage. Values explained under 'push' options above.\n" "para resetCounts\n" " Set batch done and crash counters to 0.\n" "para flushResults\n" " Flush results file. Warns if batch has jobs queued or running.\n" "para freeBatch\n" " Free all batch info on hub. Works only if batch has nothing queued or running.\n" "para showSickNodes\n" " Show sick nodes which have failed when running this batch.\n" "para clearSickNodes\n" " Clear sick nodes statistics and consecutive crash counts of batch.\n" "\n" "Common options\n" " -verbose=1 - set verbosity level.\n", version, NORMAL_PRIORITY, NORMAL_PRIORITY, NORMAL_PRIORITY * NORMAL_PRIORITY, NORMAL_PRIORITY-1 ); } /* Variables that can be set from command line. */ int retries = 4; int maxQueue = 2000000; int minPush = 1; int maxPush = 100000; int warnTime = 3*24*60; int killTime = 0; /* 0 = off, was originally going to be 2 weeks or 14*24*60; */ int sleepTime = 5*60; int delayTime = 0; int priority = NORMAL_PRIORITY; int maxJob = -1; float cpuUsage = 0; long long ramUsage = 0; char *batchDir = NULL; char *jobCwd = NULL; char resultsName[PATH_LEN]; char errDir[PATH_LEN]; /* Some variable we might want to move to a config file someday. */ char *resultsFileName = "para.results"; /* Name of results file. */ char *statusCommand = "parasol pstat2"; char *killCommand = "parasol remove job"; boolean sickBatch = FALSE; char *bookMarkFileName = "para.bookmark"; /* name of bookmark file */ char bookMarkName[PATH_LEN]; /* path to bookmark file */ off_t bookMark = 0; /* faster to resume from bookmark only reading new para.results */ off_t resultsSize = 0; /* where to stop reading results for the current cycle */ void beginHappy() /* Call before a loop where happy dots maybe written */ { numHappyDots = 0; } void endHappy() /* Call after a loop where happy dots may have been written. There maybe more * than one call to endHappy() for a beginHappy(). It's a good idea to call * this before outputing low-level error messages to keep messages readable * if dots are being written. */ { if (numHappyDots > 0) { verbose(1, "\n"); fflush(stderr); fflush(stdout); numHappyDots = 0; } } void vpprintf(FILE *f, char *format, va_list args) /* para printf; ensures happy dots are flushed */ { endHappy(); vfprintf(f, format, args); } void pprintf(FILE *f, char *format, ...) /* para printf; ensures happy dots are flushed */ { va_list args; va_start(args, format); vpprintf(f, format, args); va_end(args); } void paraVaWarn(char *format, va_list args) /* warn handler, flushes happyDots if needed. */ { endHappy(); if (format != NULL) { fflush(stdout); vfprintf(stderr, format, args); fprintf(stderr, "\n"); fflush(stderr); /* forces to log files */ } } enum jaState /* A job is in one of these states. */ { jaUnsubmitted, jaQueued, jaRunning, jaHung, jaCrashed, jaFinished, }; char *jaStateShortDesc[] = /* short description of job state; indexed by enum jaState */ { "unsub", "queue", "run", "hung", "crash", "done" }; enum jaState figureState(struct job *job) /* Figure out state of job. */ { struct submission *sub; if ((sub = job->submissionList) == NULL) return jaUnsubmitted; if (sub->inQueue) return jaQueued; if (sub->running) return jaRunning; if (sub->hung) return jaHung; if (sub->ranOk) return jaFinished; else return jaCrashed; } char *useWhats[] = {"cpu", "ram"}; void parseUsage(struct job* job, struct lineFile *lf) /* Parse out and keep CPU and RAM usage from the job command. */ { /* allow command-line options to be overridden by spec */ if (cpuUsage != 0) job->cpusUsed = cpuUsage; if (ramUsage != 0) job->ramUsed = ramUsage; char *pattern = "{use"; char *s, *e, *z; char *line = job->command; struct dyString *dy = dyStringNew(1024); s = line; for (;;) { e = stringIn(pattern, s); if (e == NULL) { dyStringAppend(dy, s); break; } else { char *parts[4]; int partCount; dyStringAppendN(dy, s, e-s); z = strchr(e, '}'); if (z == NULL) errAbort("{use without } line %d of %s", lf->lineIx, lf->fileName); *z = 0; partCount = chopLine(e, parts); if (partCount != 3) errAbort("Badly formatted 'use' clause in line %d of %s", lf->lineIx, lf->fileName); if (stringIx(parts[1], useWhats) < 0) errAbort("Unrecognized word '%s' in 'use' clause line %d of %s", parts[1], lf->lineIx, lf->fileName); if (sameString(parts[1], "cpu")) { job->cpusUsed = sqlFloat(parts[2]); } if (sameString(parts[1], "ram")) { job->ramUsed = paraParseRam(parts[2]); if (job->ramUsed == -1) errAbort("Invalid RAM expression '%s' in 'use' clause line %d of %s", parts[2], lf->lineIx, lf->fileName); } s = z+1; } } freeMem(job->command); job->command = cloneString(dy->string); dyStringFree(&dy); } /* Places that can be checked. */ char *checkWhens[] = {"in", "out"}; /* Types of checks. */ char *checkTypes[] = {"exists", "exists+", "line", "line+"}; struct job *jobFromLine(struct lineFile *lf, char *line) /* Parse out the beginnings of a job from input line. * Parse out and keep checks. */ { struct check *check; char *pattern = "{check"; char *s, *e, *z; struct dyString *dy = dyStringNew(1024); struct job *job; AllocVar(job); job->spec = cloneString(line); s = line; for (;;) { e = stringIn(pattern, s); if (e == NULL) { dyStringAppend(dy, s); break; } else { char *parts[5]; int partCount; dyStringAppendN(dy, s, e-s); z = strchr(e, '}'); if (z == NULL) errAbort("{check without } line %d of %s", lf->lineIx, lf->fileName); *z = 0; partCount = chopLine(e, parts); if (partCount != 4) errAbort("Badly formatted check line %d of %s", lf->lineIx, lf->fileName); AllocVar(check); slAddHead(&job->checkList, check); job->checkCount += 1; if (stringIx(parts[1], checkWhens) < 0) errAbort("Unrecognized word '%s' in check line %d of %s", parts[1], lf->lineIx, lf->fileName); check->when = cloneString(parts[1]); if (stringIx(parts[2], checkTypes) < 0) errAbort("Unrecognized word '%s' in check line %d of %s", parts[2], lf->lineIx, lf->fileName); check->what = cloneString(parts[2]); check->file = cloneString(parts[3]); dyStringAppend(dy, check->file); s = z+1; } } job->command = cloneString(dy->string); slReverse(&job->checkList); dyStringFree(&dy); parseUsage(job, lf); return job; } struct fileStatus /* Some info on a file. */ { bool exists; /* TRUE if file exists. */ bool hasData; /* TRUE if nonempty. */ bool completeLastLine; /* TRUE if last line ends with <lf> */ bool checkedLastLine; /* TRUE if done completeLastLine check */ bool reported; /* TRUE if reported error. */ }; struct fileStatus *basicFileCheck(char *file, struct hash *hash) /* Do quick file checks caching result */ { struct fileStatus *fi = hashFindVal(hash, file); struct stat statBuf; if (fi != NULL) return fi; lmAllocVar(hash->lm, fi); if (stat(file, &statBuf) == 0) { fi->exists = TRUE; fi->hasData = (statBuf.st_size > 0); } return fi; } struct fileStatus *completeLastLineCheck(char *file, struct hash *hash) /* Do slower checks for complete last line, caching result */ { struct fileStatus *fi = hashFindVal(hash, file); FILE *f; if ((fi != NULL) && (fi->checkedLastLine)) return fi; if (fi == NULL) lmAllocVar(hash->lm, fi); if ((f = fopen(file, "rb")) != NULL) { fi->exists = TRUE; if (fseek(f, -1, SEEK_END) == 0) { int c = fgetc(f); if (c >= 0) { fi->hasData = TRUE; if (c == '\n') fi->completeLastLine = TRUE; } } fclose(f); } fi->checkedLastLine = TRUE; return fi; } int doOneCheck(struct check *check, struct hash *hash, FILE *f) /* Do one check. Return error count from check. f maybe NULL to discard * errors. */ { struct fileStatus *fi; char *file = check->file; char *what = check->what; /* only do slower completeLastLine check if needed */ if (startsWith("line", what)) fi = completeLastLineCheck(file, hash); else fi = basicFileCheck(file, hash); if (!fi->reported) { if (!fi->exists) { if (f != NULL) pprintf(f, "%s does not exist\n", file); fi->reported = TRUE; return 1; } if (sameWord(what, "exists+")) { if (!fi->hasData) { if (f != NULL) pprintf(f, "%s is empty\n", file); fi->reported = TRUE; return 1; } } else if (sameWord(what, "line")) { if (fi->hasData && !fi->completeLastLine) { if (f != NULL) pprintf(f, "%s has an incomplete last line\n", file); fi->reported = TRUE; return 1; } } else if (sameWord(what, "line+")) { if (!fi->hasData) { if (f != NULL) pprintf(f, "%s is empty\n", file); fi->reported = TRUE; return 1; } else if (!fi->completeLastLine) { if (f != NULL) pprintf(f, "%s has an incomplete last line\n", file); fi->reported = TRUE; return 1; } } else if (sameString(what, "exists")) { /* Check already made. */ } else { warn("Unknown check '%s'", what); } } return fi->reported ? 1 : 0; } void occassionalDot() /* Write out a dot every 20 times this is called. */ { static int dotMod = 20; static int dot = 20; if ((--dot <= 0) && verboseDotsEnabled()) { verboseDot(); dot = dotMod; numHappyDots++; } } void occassionalSleep() /* Sleep every 1000 times this is called. */ { static int dotMod = 600; static int dot = 600; if (--dot <= 0) { fflush(stdout); fflush(stderr); sleep(1); dot = dotMod; } } int checkOneJob(struct job *job, char *when, struct hash *hash, FILE *f) /* Perform checks on one job if checks not already in hash. * Returns number of errors. */ { int errCount = 0; struct check *check; for (check = job->checkList; check != NULL; check = check->next) { if (sameWord(when, check->when)) { errCount += doOneCheck(check, hash, f); occassionalDot(); } } return errCount; } void doChecks(struct jobDb *db, char *when) /* Do checks on files where check->when matches when. */ { int errCount = 0; struct job *job; struct hash *hash = newHash(19); verbose(1, "Checking %sput files\n", when); beginHappy(); for (job = db->jobList; job != NULL; job = job->next) errCount += checkOneJob(job, when, hash, stderr); endHappy(); if (errCount > 0) errAbort("%d total errors in file check", errCount); freeHashAndVals(&hash); } void writeBatch(struct jobDb *db, char *fileName) /* Write out batch file. */ { FILE *f = mustOpen(fileName, "w"); struct job *job; for (job = db->jobList; job != NULL; job = job->next) { jobCommaOut(job, f); fprintf(f, "\n"); } if (ferror(f)) errAbort("error writing %s", fileName); carefulClose(&f); } void readBookMark() /* Read the value of the bookMark, an offset into the results file. * This should be called before reading the results file. */ { /* a bookmark should not exist if results file does not exist */ if ((!fileExists(resultsName)) && fileExists(bookMarkName)) unlink(bookMarkName); /* read bookmark position */ struct lineFile *lf = lineFileMayOpen(bookMarkName, TRUE); char *line; if (!lf) return; if (lineFileNext(lf, &line, NULL)) { bookMark = sqlLongLong(line); } lineFileClose(&lf); } void writeBookMark() /* Save the value of the bookMark, an offset into the results file. * This should be called after the batch has been safely updated. */ { FILE *f = mustOpen(bookMarkName, "w"); fprintf(f, "%llu\n", (unsigned long long) bookMark); carefulClose(&f); } void atomicWriteBatch(struct jobDb *db, char *fileName) /* Wrapper to avoid corruption file by two para process being run in the same * directory. */ { char hostName[128]; char tmpName[PATH_LEN]; long time = clock1000(); /* generate a unique name for tmp file */ if (gethostname(hostName, sizeof(hostName)) < 0) errnoAbort("can't get host name"); safef(tmpName, sizeof(tmpName), "%s.%d.%s.tmp", fileName, getpid(), hostName); writeBatch(db, tmpName); /* now rename (which is attomic) */ if (rename(tmpName, fileName) < 0) errnoAbort("can't rename %s to %s", tmpName, fileName); writeBookMark(); verbose(2, "atomicWriteBatch time: %.2f seconds\n", (clock1000() - time) / 1000.0); } struct jobDb *readBatch(char *batch) /* Read a batch file. */ { struct jobDb *db; struct job *job; struct lineFile *lf = lineFileOpen(batch, TRUE); char *line; long time = clock1000(); AllocVar(db); while (lineFileNext(lf, &line, NULL)) { line = skipLeadingSpaces(line); if (line[0] == '#' || line[0] == 0) continue; job = jobCommaIn(&line, NULL); slAddHead(&db->jobList, job); ++db->jobCount; } lineFileClose(&lf); slReverse(&db->jobList); verbose(1, "%d jobs in batch\n", db->jobCount); verbose(2, "readBatch time: %.2f seconds\n", (clock1000() - time) / 1000.0); return db; } char *hubSingleLineQuery(char *query) /* Send message to hub and get single line response. * This should be freeMem'd when done. */ { return pmHubSingleLineQuery(query, "localhost"); } struct slName *hubMultilineQuery(char *query) /* Send a command with a multiline response to hub, * and return response as a list of strings. */ { return pmHubMultilineQuery(query, "localhost"); } boolean batchRunning(char *batchName) /* Return TRUE if a batch is running. */ { #define NUMLISTBATCHCOLUMNS 12 struct slName *lineList = hubMultilineQuery("listBatches"), *lineEl; boolean ret = FALSE; for (lineEl = lineList; lineEl != NULL; lineEl = lineEl->next) { int wordCount; char *line = lineEl->name; char *row[NUMLISTBATCHCOLUMNS]; if (line[0] != '#') { char *b; wordCount = chopLine(line, row); b = row[NUMLISTBATCHCOLUMNS-1]; if (wordCount < NUMLISTBATCHCOLUMNS || b[0] != '/') errAbort("paraHub and para out of sync on listBatches"); if (sameString(b, batchName)) ret = TRUE; } } slFreeList(&lineList); return ret; } boolean thisBatchRunning() /* Return true if this batch is running */ { return batchRunning(batchDir); } struct jobDb *parseJobList(char *jobList) /* parse a job list */ { struct lineFile *lf = lineFileOpen(jobList, TRUE); char *line; struct jobDb *db; struct job *job; AllocVar(db); while (lineFileNext(lf, &line, NULL)) { line = trimSpaces(line); if (line == NULL || line[0] == '#' || line[0] == 0) continue; ++db->jobCount; job = jobFromLine(lf, line); slAddHead(&db->jobList, job); } lineFileClose(&lf); slReverse(&db->jobList); return db; } void sendSetPriorityMessage(int priority) /* Tell hub to change priority on batch */ { struct dyString *dy = newDyString(1024); char *result; if ((priority < 1) || (priority > MAX_PRIORITY)) errAbort("Priority %d out of range, should be 1 to %d",priority,MAX_PRIORITY); dyStringPrintf(dy, "setPriority %s %s %d", getUser(), resultsName, priority); result = hubSingleLineQuery(dy->string); dyStringFree(&dy); if (result == NULL || sameString(result, "0")) errAbort("Couldn't set priority for %s\n", batchDir); freez(&result); verbose(1, "Told hub to set priority %d\n",priority); } void paraPriority(char *val) /* Tell hub to change priority on batch */ { if (sameWord(val,"high")) priority = 1; else if (sameWord(val,"medium")) priority = NORMAL_PRIORITY; else if (sameWord(val,"low")) priority = NORMAL_PRIORITY * NORMAL_PRIORITY; else priority = atoi(val); sendSetPriorityMessage(priority); } void checkPrioritySetting() /* see if we can and need to set the priority */ { if (optionVal("pri",NULL)!=NULL) paraPriority(optionVal("pri","medium")); if (optionVal("priority",NULL)!=NULL) paraPriority(optionVal("priority","medium")); } void sendSetMaxJobMessage(int maxJob) /* Tell hub to change maxJob on batch */ { struct dyString *dy = newDyString(1024); char *result; if (maxJob <-1) errAbort("maxJob %d out of range, should be >=-1", maxJob); dyStringPrintf(dy, "setMaxJob %s %s %d", getUser(), resultsName, maxJob); result = hubSingleLineQuery(dy->string); dyStringFree(&dy); if (result == NULL || sameString(result, "-2")) errAbort("Couldn't set maxJob %d for %s", maxJob, batchDir); freez(&result); verbose(1, "Told hub to set maxJob %d\n",maxJob); } void paraMaxJob(char *val) /* Tell hub to change maxJob on batch */ { if (sameWord(val,"unlimited")) maxJob = -1; else maxJob = atoi(val); sendSetMaxJobMessage(maxJob); } void checkMaxJobSetting() /* see if we can and need to set maxJob */ { if (optionVal("maxJob",NULL)!=NULL) paraMaxJob(optionVal("maxJob","unlimited")); /* backwards compatibility */ if (optionVal("maxNode",NULL)!=NULL) paraMaxJob(optionVal("maxNode","unlimited")); } void paraCreate(char *batch, char *jobList) /* Create a batch database from a job list. */ { char backup[PATH_LEN]; struct jobDb *db; if (thisBatchRunning()) errAbort("This batch is currently running. Please para stop first."); makeDir(batchDir); makeDir(errDir); db = parseJobList(jobList); doChecks(db, "in"); safef(backup, sizeof(backup), "%s.bak", batch); atomicWriteBatch(db, backup); atomicWriteBatch(db, batch); verbose(1, "%d jobs written to %s\n", db->jobCount, batch); checkPrioritySetting(); checkMaxJobSetting(); } void paraRecover(char *batch, char *jobList, char *newJobList) /* Create a new job list from an existing list based on check outs that * failed. */ { struct jobDb *db; struct job *job; struct hash *hash = newHash(19); FILE *newFh = mustOpen(newJobList, "w"); db = parseJobList(jobList); beginHappy(); for (job = db->jobList; job != NULL; job = job->next) { if (checkOneJob(job, "out", hash, NULL)) fprintf(newFh, "%s\n", job->spec); } endHappy(); if (ferror(newFh)) errAbort("write failed: %s", newJobList); carefulClose(&newFh); jobDbFree(&db); freeHash(&hash); } boolean submitJob(struct job *job) /* Attempt to submit job. */ { struct dyString *cmd = dyStringNew(1024); struct submission *sub; char *jobId = NULL; dyStringPrintf(cmd, "addJob2 %s %s /dev/null /dev/null %s %f %lld %s", getUser(), jobCwd, resultsName, job->cpusUsed, job->ramUsed, job->command); pmCheckCommandSize(cmd->string, cmd->stringSize); jobId = hubSingleLineQuery(cmd->string); if (sameString(jobId,"0")) { warn("addJob failed - if batch is bad, correct problem and run para clearSickNodes."); freez(&jobId); } if (jobId != NULL) { AllocVar(sub); slAddHead(&job->submissionList, sub); job->submissionCount += 1; sub->submitTime = time(NULL); sub->host = cloneString("n/a"); sub->id = jobId; sub->inQueue = TRUE; sub->errFile = cloneString("n/a"); } dyStringFree(&cmd); return jobId != NULL; } boolean killJob(char *jobId) /* Tell hub to kill a job. Return TRUE on * success. */ { char buf[256]; char *result = NULL; boolean ok; snprintf(buf, sizeof(buf), "removeJob %s", jobId); result = hubSingleLineQuery(buf); ok = (result != NULL && sameString(result, "ok")); freez(&result); return ok; } void statusOutputChanged() /* Complain about status output format change and die. */ { errAbort("\n%s output format changed, please update markQueuedJobs in para.c", statusCommand); } int markQueuedJobs(struct jobDb *db) /* Mark jobs that are queued up. Return total number of jobs in queue. */ { struct hash *hash = newHash(max(12,digitsBaseTwo(db->jobCount)-3)); struct job *job; struct submission *sub; int queueSize = 0; long killSeconds = killTime*60; long warnSeconds = warnTime*60; long duration; time_t now = time(NULL); long queryTime = clock1000(); /* Get job list from paraHub. */ struct dyString *dy = newDyString(1024); dyStringPrintf(dy, "pstat2 %s %s", getUser(), resultsName); struct slName *lineList = hubMultilineQuery(dy->string), *lineEl; dyStringFree(&dy); now = time(NULL); /* need to refresh this after we get the info */ verbose(2, "pstat2 time: %.2f seconds\n", (clock1000() - queryTime) / 1000.0); long hashTime = clock1000(); verbose(2, "submission hash size: %d\n", hash->size); /* Make hash of submissions based on id and clear flags. */ for (job = db->jobList; job != NULL; job = job->next) { for (sub = job->submissionList; sub != NULL; sub = sub->next) { hashAdd(hash, sub->id, sub); sub->running = FALSE; sub->inQueue = FALSE; } } verbose(2, "submission hash time: %.2f seconds\n", (clock1000() - hashTime) / 1000.0); long pstatListTime = clock1000(); /* Read status output. */ for (lineEl = lineList; lineEl != NULL; lineEl = lineEl->next) { int wordCount; char *line = lineEl->name; char *row[6]; if (startsWith("Total Jobs:", line)) { wordCount = chopLine(line, row); queueSize = sqlSigned(row[2]); verbose(1, "%d jobs (including everybody's) in Parasol queue or running.\n", queueSize); continue; } if (startsWith("Sick Batch:", line)) { sickBatch = TRUE; warn("%s", line); continue; } if (startsWith("Results Size:", line)) { wordCount = chopLine(line, row); resultsSize = sqlLongLong(row[2]); continue; } wordCount = chopLine(line, row); if (wordCount < 6 && wordCount != 2) { warn("Expecting at least 6 words in pstat2 output," " found %d. paraHub and para out of sync.", wordCount); statusOutputChanged(); } else { char *state = row[0], *jobId = row[1], *ticks = NULL, *host = NULL; time_t t = 0; if (wordCount > 2) { ticks = row[4], host = row[5]; t = atol(ticks); } if ((sub = hashFindVal(hash, jobId)) != NULL) { if (sameString(state, "r")) { sub->running = TRUE; sub->startTime = t; if (sub->host) freeMem(sub->host); sub->host = cloneString(host); duration = now - sub->startTime; if (duration < 0) warn("Strange start time in jobId %s: %u (now=%u)", jobId, sub->startTime, (unsigned int) now); else { if (duration > killSeconds && killSeconds > 0) { sub->hung = TRUE; sub->slow = FALSE; sub->endTime = now; killJob(sub->id); verbose(1, "killed hung jobId: %s\n", sub->id); } else if (duration > warnSeconds) sub->slow = TRUE; } } else { sub->inQueue = TRUE; } } } } verbose(2, "pstat list time: %.2f seconds\n", (clock1000() - pstatListTime) / 1000.0); slFreeList(&lineList); freeHash(&hash); verbose(2, "markQueuedJobs time (includes pstat2, hash, list): %.2f seconds\n", (clock1000() - queryTime) / 1000.0); return queueSize; } struct hash *hashResults(char *fileName) /* Return hash of job results keyed on id as string. */ { long time = clock1000(); struct hash *hash = newHash(0); if (fileExists(fileName)) { struct jobResult *el, *list = jobResultLoadAll(fileName, &bookMark, resultsSize); for (el = list; el != NULL; el = el->next) hashAdd(hash, el->jobId, el); } verbose(2, "hashResults time: %.2f seconds\n", (clock1000() - time) / 1000.0); return hash; } void freeResults(struct hash **pHash) /* Free up results hash and elements in it. */ { struct hash *hash = *pHash; struct hashEl *list, *el; struct jobResult *jr; if ((hash = *pHash) != NULL) { list = hashElListHash(hash); for (el = list; el != NULL; el = el->next) { jr = el->val; jobResultFree(&jr); } hashElFreeList(&list); hashFree(pHash); } } boolean isStatusOk(int status) /* Convert wait() return status to return value. */ { return WIFEXITED(status) && (WEXITSTATUS(status) == 0); } double jrCpuTime(struct jobResult *jr) /* Get CPU time in seconds for job. */ { return 0.01 * (jr->usrTicks + jr->sysTicks); } double subRealTime(struct submission *sub) /* Get real time in seconds for job. */ { /* note sub->*Time are unsigned, so we need to convert to double * before subtracting or time moving backwards is not detected */ return ((double)sub->endTime) - ((double)sub->startTime); } void showSickNodes(boolean showSummary) /* Tell hub to show sick nodes on batch. */ { int count = 0; struct dyString *dy = newDyString(1024); dyStringPrintf(dy, "showSickNodes %s %s", getUser(), resultsName); struct slName *lineList = hubMultilineQuery(dy->string), *lineEl; for (lineEl = lineList; lineEl != NULL; lineEl = lineEl->next) { ++count; char *line = lineEl->name; /* In show summary mode, only print the last line, * which contains the totals. Only print this one * if there's more than one line (the total is greater than zero). */ if (!showSummary || !(lineEl->next || count == 1)) printf("%s\n", line); } slFreeList(&lineList); dyStringFree(&dy); } void markRunJobStatus(struct jobDb *db) /* Mark jobs based on results output file. * Returns hash of results. */ { struct job *job; struct submission *sub; struct hash *checkHash = newHash(0); struct hash *resultsHash = hashResults(resultsName); long time = clock1000(); verbose(1, "Checking finished jobs\n"); beginHappy(); for (job=db->jobList; job != NULL; job = job->next) { if ((sub = job->submissionList) != NULL) { /* Look for hitherto unclassified jobs that are either running or * possibly finished. */ if (!sub->queueError && !sub->inQueue && !sub->crashed && !sub->hung && !sub->running && !sub->ranOk) { struct jobResult *jr = hashFindVal(resultsHash, sub->id); if (jr == NULL) { if (!sickBatch) sub->trackingError = 3; } else { sub->startTime = jr->startTime; sub->endTime = jr->endTime; sub->cpuTime = jrCpuTime(jr); sub->status = jr->status; sub->gotStatus = TRUE; if (sub->host) freeMem(sub->host); sub->host = cloneString(jr->host); sub->inQueue = FALSE; sub->running = FALSE; sub->hung = FALSE; sub->slow = FALSE; if (sub->errFile) freeMem(sub->errFile); sub->errFile = cloneString(jr->errFile); if (isStatusOk(sub->status) && checkOneJob(job, "out", checkHash, stderr) == 0) sub->ranOk = TRUE; else sub->crashed = TRUE; } } } } endHappy(); freeHash(&checkHash); freeResults(&resultsHash); verbose(2, "markRunJobStatus time (includes hashResults): %.2f seconds\n", (clock1000() - time) / 1000.0); } boolean needsRerun(struct submission *sub) /* Return TRUE if submission needs to be rerun. */ { if (sub == NULL) return TRUE; return sub->submitError || sub->queueError || sub->crashed || sub->trackingError || sub->hung; } struct jobDb *paraCycle(char *batch) /* Cycle forward through batch. Return database. */ { struct jobDb *db = readBatch(batch); struct job *job; int queueSize; int pushCount = 0, retryCount = 0; int tryCount; boolean finished = FALSE; long time = clock1000(); queueSize = markQueuedJobs(db); markRunJobStatus(db); beginHappy(); if (!sickBatch) for (tryCount=1; tryCount<=retries && !finished; ++tryCount) { for (job = db->jobList; job != NULL; job = job->next) { if (job->submissionCount < tryCount && (job->submissionList == NULL || needsRerun(job->submissionList))) { if (!submitJob(job)) { finished = TRUE; break; } occassionalDot(); // occassionalSleep(); if (delayTime > 0) { atomicWriteBatch(db, batch); sleep(delayTime); } ++pushCount; if (tryCount > 1) ++retryCount; if (pushCount >= maxPush) { finished = TRUE; break; } if (pushCount + queueSize >= maxQueue && pushCount >= minPush) { finished = TRUE; break; } } } } endHappy(); atomicWriteBatch(db, batch); verbose(1, "updated job database on disk\n"); if (pushCount > 0) verbose(1, "Pushed Jobs: %d\n", pushCount); if (retryCount > 0) verbose(1, "Retried jobs: %d\n", retryCount); verbose(2, "paraCycle time: %.2f seconds\n", (clock1000() - time) / 1000.0); return db; } void paraPush(char *batch) /* Push forward batch one time. */ { struct jobDb *db = paraCycle(batch); jobDbFree(&db); } void clearSickNodes() /* Tell hub to clear sick nodes on batch */ { struct dyString *dy = newDyString(1024); char *result; dyStringPrintf(dy, "clearSickNodes %s %s", getUser(), resultsName); result = hubSingleLineQuery(dy->string); dyStringFree(&dy); if (!sameString(result, "0")) errAbort("Couldn't clear sick nodes for %s", batchDir); freez(&result); verbose(1, "Told hub to clear sick nodes\n"); } void paraShove(char *batch) /* Push batch of jobs and keep pushing until it's finished, polling * parasol every 5 minutes. */ { struct jobDb *db; struct job *job; struct submission *sub; int maxSleep = 5*60; int curSleep = 15; time_t start = time(NULL), now; int sickBatchTries = 0; #define MAXSICKBATCHTRIES 3 #define SICKBATCHSLEEP 10*60 for (;;) { boolean anyUnfinished = FALSE; db = paraCycle(batch); for (job = db->jobList; job != NULL; job = job->next) { if ((sub = job->submissionList) == NULL) anyUnfinished = TRUE; else { enum jaState state = figureState(job); if (job->submissionCount >= retries) { if (state != jaUnsubmitted && state != jaQueued && state != jaRunning) errAbort("Batch failed after %d tries on %s", retries, job->command); } if (state != jaFinished) anyUnfinished = TRUE; } } jobDbFree(&db); if (!anyUnfinished) break; showSickNodes(TRUE); fflush(stdout); fflush(stderr); if (sickBatch) { ++sickBatchTries; if (sickBatchTries >= MAXSICKBATCHTRIES) break; warn("Sick batch! will sleep %d minutes, clear sick nodes and retry", SICKBATCHSLEEP/60); sleep(SICKBATCHSLEEP); sickBatch = FALSE; clearSickNodes(); } else { sickBatchTries = 0; sleep(curSleep); if (curSleep < maxSleep) curSleep += 15; } now = time(NULL); verbose(1, "================\n"); verbose(1, "Checking job status %d minutes after launch\n", round((now-start)/60.0)); } if (sickBatch) errAbort("Sick batch! Correct problem and then run para clearSickNodes."); else verbose(1, "Successful batch!\n"); } void paraMake(char *batch, char *spec) /* Do a create and then a shove. */ { paraCreate(batch, spec); paraShove(batch); } void reportOnJobs(struct jobDb *db) /* Report on status of jobs. */ { int submitError = 0, inQueue = 0, queueError = 0, trackingError = 0, running = 0, crashed = 0, slow = 0, hung = 0, ranOk = 0, unsubmitted = 0, total = 0, failed = 0; struct job *job; struct submission *sub; for (job = db->jobList; job != NULL; job = job->next) { if ((sub = job->submissionList) != NULL) /* Get most recent submission if any. */ { if (sub->submitError) ++submitError; if (sub->queueError) ++queueError; if (sub->trackingError) ++trackingError; if (sub->inQueue) ++inQueue; if (sub->crashed) ++crashed; if (sub->slow) ++slow; if (sub->hung) ++hung; if (sub->running) ++running; if (sub->ranOk) ++ranOk; if (job->submissionCount >= retries && needsRerun(sub)) ++failed; } else ++unsubmitted; ++total; } if (unsubmitted > 0) printf("unsubmitted jobs: %d\n", unsubmitted); if (submitError > 0) printf("submission errors: %d\n", submitError); if (queueError > 0) printf("queue errors: %d\n", queueError); if (trackingError > 0) { if (!fileExists(resultsName)) printf("%s: file not found. paraHub can't write to this dir?\n", resultsName); else printf("tracking errors: %d\n", trackingError); } if (inQueue > 0) printf("queued and waiting: %d\n", inQueue); if (crashed > 0) printf("crashed: %d\n", crashed); if (slow > 0) printf("slow (> %d minutes): %d\n", warnTime, slow); if (hung > 0) printf("hung (> %d minutes): %d\n", killTime, hung); if (running > 0) printf("running: %d\n", running); if (ranOk > 0) printf("ranOk: %d\n", ranOk); if (failed > 0) printf("failed %d times: %d\n", retries, failed); printf("total jobs in batch: %d\n", total); } void paraListFailed(char *batch) /* List all jobs that failed. */ { struct jobDb *db = readBatch(batch); struct job *job; struct submission *sub; markQueuedJobs(db); markRunJobStatus(db); for (job = db->jobList; job != NULL; job = job->next) { sub = job->submissionList; if (sub != NULL) { if (job->submissionCount >= retries && needsRerun(sub)) printf("%s\n", job->spec); } } } void paraListState(char *batch, enum jaState targetState) /* List all jobs that match target state. */ { struct jobDb *db = readBatch(batch); struct job *job; markQueuedJobs(db); markRunJobStatus(db); for (job = db->jobList; job != NULL; job = job->next) { enum jaState state = figureState(job); if (state == targetState) printf("%s\n", job->spec); } } struct submission* getLastSubmission(struct job *job) /* get the last submission for a job, or NULL if not submitted */ { struct submission* sub = job->submissionList; while ((sub != NULL) && (sub->next != NULL)) sub = sub->next; return sub; } /* header for job status output */ static char *jobStatusHdr = "#state\ttries\treal\tcpu\thost\tjobid\tcmd\n"; void paraJobStatus(struct job *job, time_t now) /* Print status of a job. */ { enum jaState state = figureState(job); char *stateStr = jaStateShortDesc[state]; double realTime = 0.0; double cpuTime = 0.0; struct submission *sub = getLastSubmission(job); char *jobId = ""; char *host = ""; if (sub != NULL) { if (sub->trackingError) stateStr = "track"; if (state == jaRunning) realTime = (now - sub->startTime); else { realTime = subRealTime(sub); cpuTime = sub->cpuTime; jobId = sub->id; } host = sub->host; } subChar(job->command, '\t', ' '); /* tabs not allowed in column */ printf("%s\t%d\t%0.2f\t%0.2f\t%s\t%s\t%s\n", stateStr, job->submissionCount, realTime, cpuTime, host, jobId, job->command); } void paraStatus(char *batch) /* Print status of all jobs. */ { struct jobDb *db = readBatch(batch); struct job *job; time_t now = time(NULL); markQueuedJobs(db); markRunJobStatus(db); printf("%s", jobStatusHdr); for (job = db->jobList; job != NULL; job = job->next) paraJobStatus(job, now); } void printErrFile(struct submission *sub) /* Print error file if it exists. */ { char localName[PATH_LEN]; safef(localName, sizeof(localName), "%s/%s", errDir, sub->id); if (!fileExists(localName)) { pmFetchFile(sub->host, sub->errFile, localName); } if (fileExists(localName)) { char *buf; size_t size; printf("stderr:\n"); readInGulp(localName, &buf, &size); mustWrite(stdout, buf, size); freez(&buf); } } void problemReport(struct job *job, struct submission *sub, char *type) /* Print report on one problem. */ { struct check *check; struct hash *hash = newHash(0); printf("job: %s\n", job->command); printf("id: %s\n", sub->id); printf("failure type: %s\n", type); if (sameString(type, "crash")) { time_t startTime = sub->startTime; printf("host: %s\n", sub->host); printf("start time: %s", ctime(&startTime)); /* ctime adds \n */ printf("return: "); if (WIFEXITED(sub->status)) printf("%d\n", WEXITSTATUS(sub->status)); else if (WIFSIGNALED(sub->status)) printf("signal %d\n", WTERMSIG(sub->status)); else if (WIFSTOPPED(sub->status)) printf("stopped %d\n", WSTOPSIG(sub->status)); else printf("unknown wait status %d\n", sub->status); for (check = job->checkList; check != NULL; check = check->next) doOneCheck(check, hash, stdout); printErrFile(sub); } printf("\n"); hashFree(&hash); } void paraProblems(char *batch) /* List jobs that had problems (even if successfully rerun). Includes host info */ { struct jobDb *db = readBatch(batch); struct job *job; struct submission *sub; int problemCount = 0; markQueuedJobs(db); markRunJobStatus(db); for (job = db->jobList; job != NULL; job = job->next) { for (sub = job->submissionList; sub != NULL; sub = sub->next) { if (sub->hung) { problemReport(job, sub, "hung"); ++problemCount; } else if (sub->slow) { problemReport(job, sub, "slow"); ++problemCount; } else if (sub->trackingError) { problemReport(job, sub, "tracking error"); ++problemCount; } else if (needsRerun(sub)) { problemReport(job, sub, "crash"); ++problemCount; } } } printf("%d problems total\n", problemCount); } void runningReport(struct job *job, struct submission *sub) /* Print report on one running job. */ { time_t startTime = sub->startTime; int duration = time(NULL) - startTime; printf("command: %s\n", job->command); printf("jobId: %s\n", sub->id); printf("host: %s\n", sub->host); printf("start time: %s", ctime(&startTime)); /* ctime adds \n */ printf("run time so far: %d sec, %4.2f min, %4.2f hours, %4.2f days\n", duration, duration/60.0, duration/3600.0, duration/(3600.0*24.0)); if (sub->slow) printf("This is a slow job, running time > %d minutes.\n", warnTime); printf("\n"); } void paraRunning(char *batch, char *minTimeS) /* List jobs that are running. Includes host and time info */ { struct jobDb *db = readBatch(batch); struct job *job; struct submission *sub; int runCount = 0; int minTime = 0; if (minTimeS) minTime = atoi(minTimeS); markQueuedJobs(db); markRunJobStatus(db); for (job = db->jobList; job != NULL; job = job->next) { if ((sub = job->submissionList) != NULL && sub->running) { time_t startTime = sub->startTime; int duration = time(NULL) - startTime; if (duration > (minTime * 60)) { runningReport(job, sub); ++runCount; } } } printf("total %s running: %d\n", !minTimeS ? "jobs" : "hippos", runCount); } void sendChillMessage() /* Tell hub to chill out on job */ { struct dyString *dy = newDyString(1024); char *result; dyStringPrintf(dy, "chill %s %s", getUser(), resultsName); result = hubSingleLineQuery(dy->string); dyStringFree(&dy); if (result == NULL || !sameString(result, "ok")) errAbort("Couldn't chill %s\n", batchDir); freez(&result); verbose(1, "Told hub to chill out\n"); } void paraResetCounts() /* Send msg to hub to reset done and crashed counts on batch */ { struct dyString *dy = newDyString(1024); char *result; dyStringPrintf(dy, "resetCounts %s %s", getUser(), resultsName); result = hubSingleLineQuery(dy->string); dyStringFree(&dy); if (result == NULL || sameString(result, "-2")) errAbort("Couldn't reset done and crashed counts on batch %s\n", batchDir); freez(&result); verbose(1, "Told hub to reset done and crashed counts on batch %s\n", batchDir); } void freeBatch() /* Send msg to hub to reset done and crashed counts on batch */ { struct dyString *dy = newDyString(1024); char *result; dyStringPrintf(dy, "freeBatch %s %s", getUser(), resultsName); result = hubSingleLineQuery(dy->string); dyStringFree(&dy); verbose(1, "Told hub to free all batch-related resources\n"); if (result == NULL) errAbort("result == NULL"); if (sameOk(result, "-3")) errAbort("User not found."); if (sameOk(result, "-2")) errAbort("Batch not found."); if (sameOk(result, "-1")) warn("Unable to free batch. Jobs are queued or running."); if (sameOk(result, "0")) verbose(1, "Batch freed.\n"); freez(&result); } void flushResults() /* Send msg to hub to flush results file */ { struct dyString *dy = newDyString(1024); char *result; dyStringPrintf(dy, "flushResults %s %s", getUser(), resultsName); result = hubSingleLineQuery(dy->string); dyStringFree(&dy); verbose(1, "Told hub to flush the results file\n"); if (result == NULL) errAbort("result == NULL"); if (sameOk(result, "-3")) errAbort("User not found."); if (sameOk(result, "-2")) errAbort("Batch not found."); if (sameOk(result, "-1")) warn("Flushed results. Some jobs are still queued or running."); if (sameOk(result, "0")) verbose(1, "Flushed results.\n"); freez(&result); } void paraCheck(char *batch) /* Check on progress of a batch. */ { struct jobDb *db = readBatch(batch); markQueuedJobs(db); markRunJobStatus(db); reportOnJobs(db); atomicWriteBatch(db, batch); showSickNodes(TRUE); if (sickBatch) errAbort("Sick batch! Correct problem and then run para clearSickNodes."); } int cleanTrackingErrors(struct jobDb *db) /* Remove submissions with tracking errors. * Returns count of these submissions */ { int count = 0; struct job *job; struct submission *sub; for (job = db->jobList; job != NULL; job = job->next) { sub = job->submissionList; if (sub != NULL) { if (sub->trackingError) { job->submissionCount -= 1; job->submissionList = sub->next; ++count; } } } verbose(1, "Chilled %d jobs\n", count); return count; } void removeChilledSubmissions(char *batch) /* Remove submissions from job database if we * asked them to chill out. */ { struct jobDb *db = readBatch(batch); int chillCount; markQueuedJobs(db); markRunJobStatus(db); chillCount = cleanTrackingErrors(db); atomicWriteBatch(db, batch); } void paraChill(char *batch) /* Tells system to not launch more jobs in this batch, but * does not stop jobs that are already running.\n */ { sendChillMessage(); removeChilledSubmissions(batch); } void paraStopAll(char *batch) /* Stop batch of jobs. */ { struct jobDb *db = readBatch(batch); struct job *job; struct submission *sub; int killCount = 0, missCount = 0; markQueuedJobs(db); markRunJobStatus(db); cleanTrackingErrors(db); for (job = db->jobList; job != NULL; job = job->next) { sub = job->submissionList; if (sub != NULL) { if (sub->inQueue || sub->running) { if (killJob(sub->id)) { job->submissionCount -= 1; job->submissionList = sub->next; killCount += 1; } else { missCount += 1; } } } } verbose(1, "%d running jobs stopped\n", killCount); if (missCount > 0) printf("%d jobs not stopped - try another para stop in a little while\n", missCount); atomicWriteBatch(db, batch); } void paraStop(char *batch) /* Stop batch of jobs. */ { sendChillMessage(); /* Remove waiting jobs first, it's faster. */ paraStopAll(batch); } void printTimes(char *title, double seconds, boolean showYears) /* Print out times in seconds, hours, days, maybe years. */ { printf("%-27s %9llds %10.2fm %8.2fh %7.2fd", title, roundll(seconds), seconds/60, seconds/3600, seconds/(3600*24)); if (showYears) printf(" %6.3f y", seconds/(3600*24*365)); printf("\n"); } long calcFirstToLast(struct jobDb *db) /* Calculate time between first submission and last job finish. */ { boolean first = TRUE; struct job *job; struct submission *sub; long now = time(NULL); long subTime, firstSub = BIGNUM, endTime, lastEnd = 0; boolean gotEnd = FALSE; for (job = db->jobList; job != NULL; job = job->next) { if ((sub = job->submissionList) != NULL) { subTime = sub->submitTime; if (subTime != 0 && subTime < now) /* Protect against wacked out clocks. */ { if (first) { firstSub = subTime; first = FALSE; } else { if (subTime < firstSub) firstSub = subTime; } } if (sub->endTime != 0) { endTime = sub->endTime; if (endTime < now) /* Protect against wacked out clocks. */ { if (endTime > lastEnd) { lastEnd = endTime; gotEnd = TRUE; } } } } } if (gotEnd) return lastEnd - firstSub; else return now - firstSub; } void paraRam(char *batch, char *val) /* set batch ram = val */ { long long newRam = paraParseRam(val); if (newRam == -1) usage(); struct jobDb *db = readBatch(batch); struct job *job; for (job = db->jobList; job != NULL; job = job->next) { job->ramUsed = newRam; } atomicWriteBatch(db, batch); } void paraCpu(char *batch, char *val) /* set batch cpu = val */ { float newCpus = sqlFloat(val); if (newCpus < 0) usage(); struct jobDb *db = readBatch(batch); struct job *job; for (job = db->jobList; job != NULL; job = job->next) { job->cpusUsed = newCpus; } atomicWriteBatch(db, batch); } void paraTimes(char *batch) /* Report times of run. */ { struct jobDb *db = readBatch(batch); double totalCpu = 0, totalWall = 0; double oneWall, longestWall = 0; struct job *job; char *longestWallId = NULL; struct submission *sub; int jobCount = 0; int runningCount = 0; int timedCount = 0; int crashCount = 0; int queueCount = 0; double runTime = 0, longestRun = 0; int otherCount = 0; long now = time(NULL); double ioTime; markQueuedJobs(db); markRunJobStatus(db); for (job = db->jobList; job != NULL; job = job->next) { ++jobCount; if ((sub = job->submissionList) != NULL) { if (sub->running) { int oneTime = now - sub->startTime; if (oneTime < 0) warn("Strange start time in %s: %u", batch, sub->startTime); else runTime += oneTime; if (oneTime > longestRun) longestRun = oneTime; ++runningCount; } else if (sub->inQueue) { ++queueCount; } else if (sub->crashed || sub->hung) { ++crashCount; } else if (sub->ranOk) { ++timedCount; totalCpu += sub->cpuTime; oneWall = subRealTime(sub); if (oneWall < 0) /* Protect against clock reset. */ { warn("End before start job %s host %s", sub->id, sub->host); warn("Start %u, End %u", sub->startTime, sub->endTime); oneWall = totalCpu; } totalWall += oneWall; if (oneWall > longestWall) { longestWall = oneWall; longestWallId = sub->id; } } else { ++otherCount; } } } printf("Completed: %d of %d jobs\n", timedCount, jobCount); if (runningCount > 0) printf("Jobs currently running: %d\n", runningCount); if (crashCount > 0) printf("Crashed: %d jobs\n", crashCount); if (otherCount > 0) { if (!fileExists(resultsName)) printf("%s: file not found. paraHub can't write to this dir?\n", resultsName); else printf("Other count: %d jobs\n", otherCount); } if (queueCount > 0) printf("In queue waiting: %d jobs\n", queueCount); printTimes("CPU time in finished jobs:", totalCpu, TRUE); ioTime = totalWall - totalCpu; if (ioTime < 0) ioTime = 0; printTimes("IO & Wait Time:", ioTime, TRUE); if (runningCount > 0) { printTimes("Time in running jobs:", runTime, TRUE); } if (timedCount > 0) { printTimes("Average job time:", totalWall/timedCount, FALSE); if (runningCount > 0) printTimes("Longest running job:", longestRun, FALSE); printTimes("Longest finished job:", longestWall, FALSE); printTimes("Submission to last job:", calcFirstToLast(db), FALSE); if (runningCount < 1) printTimes("Estimated complete:", 0.0, FALSE); else { int jobsInBatch = db->jobCount; int jobsToRun = jobsInBatch - timedCount; double timeMultiple = (double)jobsToRun / (double)runningCount; verbose(2, "inBatch: %d, toRun: %d, multiple: %.3f\n", jobsInBatch, jobsToRun, timeMultiple); printTimes("Estimated complete:", timeMultiple*totalWall/timedCount, FALSE); } } atomicWriteBatch(db, batch); } static char *determineCwdOptDir(char *optName) /* determine batch or job directory from cwd and option */ { char path[PATH_LEN]; char *opt = optionVal(optName, NULL); if (opt == NULL) safecpy(path, sizeof(path), getCurrentDir()); else if (opt[0] != '/') { safecpy(path, sizeof(path), getCurrentDir()); safecat(path, sizeof(path), "/"); safecat(path, sizeof(path), opt); } else safecpy(path, sizeof(path), opt); // remove trailing "/" or "/." from name. While the whole path should be normalized, // this at least removes a common difference when using file name completion. if (endsWith(path, "/.")) path[strlen(path)-2] = '\0'; if (endsWith(path, "/")) path[strlen(path)-1] = '\0'; return cloneString(path); } int main(int argc, char *argv[]) /* Process command line. */ { char *command; char batch[PATH_LEN]; long startTime = clock1000(); optionInit(&argc, argv, optionSpecs); if (argc < 2) usage(); retries = optionInt("retries", retries); maxQueue = optionInt("maxQueue", maxQueue); minPush = optionInt("minPush", minPush); maxPush = optionInt("maxPush", maxPush); warnTime = optionInt("warnTime", warnTime); killTime = optionInt("killTime", killTime); delayTime = optionInt("delayTime", delayTime); if (optionExists("eta")) fprintf(stderr, "note: the -eta option is no longer required\n"); cpuUsage = optionFloat("cpu", cpuUsage); if (cpuUsage < 0) usage(); ramUsage = paraParseRam(optionVal("ram","0")); if (ramUsage == -1) usage(); batchDir = determineCwdOptDir("batch"); jobCwd = determineCwdOptDir("jobCwd"); safef(resultsName, sizeof(resultsName), "%s/%s", batchDir, resultsFileName); safef(errDir, sizeof(errDir), "%s/err", batchDir); safef(bookMarkName, sizeof(bookMarkName), "%s/%s", batchDir, bookMarkFileName); command = argv[1]; safef(batch, sizeof(batch), "%s/batch", batchDir); if (!sameWord(command,"create") && !sameWord(command,"make")) { checkPrioritySetting(); checkMaxJobSetting(); } pushWarnHandler(paraVaWarn); readBookMark(); /* read the para.bookmark file to initialize bookmark */ if (sameWord(command, "create") || sameWord(command, "creat")) { if (argc != 3) usage(); paraCreate(batch, argv[2]); } else if (sameWord(command, "recover")) { if (argc != 4) usage(); paraRecover(batch, argv[2], argv[3]); } else if (sameWord(command, "check")) { paraCheck(batch); } else if (sameWord(command, "push")) { paraPush(batch); } else if (sameWord(command, "shove")) { paraShove(batch); } else if (sameWord(command, "make")) { if (argc != 3) usage(); paraMake(batch, argv[2]); } else if (sameWord(command, "try")) { maxPush = 10; paraPush(batch); } else if (sameWord(command, "stop")) { paraStop(batch); } else if (sameWord(command, "chill")) { paraChill(batch); } else if (sameWord(command, "hung")) { paraListState(batch, jaHung); } else if (sameWord(command, "slow")) { char temp[256]; safef(temp, sizeof(temp), "%d", warnTime); paraRunning(batch, temp); } else if (sameWord(command, "crashed")) { paraListState(batch, jaCrashed); } else if (sameWord(command, "failed")) { paraListFailed(batch); } else if (sameWord(command, "finished")) { paraListState(batch, jaFinished); } else if (sameWord(command, "status")) { paraStatus(batch); } else if (sameWord(command, "problems") || sameWord(command, "problem")) { paraProblems(batch); } else if (sameWord(command, "running") || sameWord(command, "hippos") || sameWord(command, "hippo")) { paraRunning(batch, argv[2]); } else if (sameWord(command, "time") || sameWord(command, "times")) { paraTimes(batch); } else if (sameWord(command, "priority")) { if (argc != 3) usage(); paraPriority(argv[2]); } else if (sameWord(command, "maxJob") || sameWord(command, "maxNode")) { if (argc != 3) usage(); /* backwards compatibility */ if (sameWord(command, "maxNode")) warn("maxNode deprecated, use maxJob"); paraMaxJob(argv[2]); } else if (sameWord(command, "ram")) { if (argc != 3) usage(); paraRam(batch, argv[2]); } else if (sameWord(command, "cpu")) { if (argc != 3) usage(); paraCpu(batch, argv[2]); } else if (sameWord(command, "resetCounts")) { if (argc != 2) usage(); paraResetCounts(); } else if (sameWord(command, "freeBatch")) { if (argc != 2) usage(); freeBatch(); } else if (sameWord(command, "flushResults")) { if (argc != 2) usage(); flushResults(); } else if (sameWord(command, "clearSickNodes")) { clearSickNodes(); } else if (sameWord(command, "showSickNodes")) { showSickNodes(FALSE); } else { errAbort("Unrecognized command '%s'. Run para with no arguments for usage summary", command); } verbose(2, "Total para time: %.2f seconds\n", (clock1000() - startTime) / 1000.0); return 0; }