ó ŕ™xTc@ s´dZddlmZddlZddlZddlZddlZddlZddlZddl Z ddl m Z ddl m Z i ed6ed6ed6ed 6ed 6ed 6ed 6ed 6ed6ed6ed6ed6ed6ZdZdZdZdZdZdZd„Zd„Zd„Zd„Zddddddddddddded „Zd!ddd"d#d$„Zed%kr°ej dZ!ee!ƒZ"ee"ndS(&s, libtbx.qsub( where=path_to_where_you_want_to_run_your_jobs, source="/net/chevy/raid1/afonine/build/setpaths.csh", commands=[list of commands]) where [list of commands]) is ["python run.py model1.pdb data1.mtz", "python run.py model2.pdb data2.mtz", ..., "python run.py modelN.pdb dataN.mtz" ] i˙˙˙˙(tdivisionN(teasy_run(tSorryt phenix_sourcetwheretcommandstnumber_of_chunkstsize_of_chunkstcodetjstqsub_cmdtstarttendthost_scratch_dirt python_scripttparallel_nodess• import os, sys from libtbx import easy_run cmds = [ %s ] def run(only_i=None, chunk_n=1, chunk_size=len(cmds), ): try: only_i = int(only_i) except ValueError: only_i=None try: chunk_n = int(chunk_n) except ValueError: chunk_n=1 try: chunk_size = int(chunk_size) except ValueError: chunk_size=len(cmds) #assert chunk_size==len(cmds) or chunk_n==1 assert chunk_n>0 assert chunk_size>0 #if chunk_n!=1: # chunk_size = (len(cmds)-1)//chunk_n+1 #elif chunk_size!=1: # chunk_n = len(cmds)%%chunk_size+1 for i, cmd in enumerate(cmds): if only_i is None: print i, cmd continue else: if chunk_n!=1 or chunk_size!=len(cmds): if only_i!=i//chunk_size+1: continue else: if only_i!=i+1: continue print 'Running', i+1 print 'Command', cmd easy_run.call(cmd) if __name__=="__main__": run(*tuple(sys.argv[1:])) s“ set work_dir=$PWD set host_scratch_dir=/net/$host/scratch1/$user if (! -d $host_scratch_dir) then echo "================================" echo " Creating host scratch directory $host_scratch_dir" echo "================================" mkdir $host_scratch_dir endif set host_scratch_dir=/net/$host/scratch1/$user/%s if (! -d $host_scratch_dir) then echo "================================" echo " Creating host scratch directory $host_scratch_dir" echo "================================" mkdir $host_scratch_dir endif set host_scratch_dir=/net/$host/scratch1/$user/%s/$SGE_TASK_ID if (! -d $host_scratch_dir) then echo "================================" echo " Creating host scratch directory $host_scratch_dir" echo "================================" mkdir $host_scratch_dir endif echo "==============" echo " Changing into $host_scratch_dir" echo "==============" cd $host_scratch_dir sk echo "===================" echo " Move files back to $work_dir" echo "===================" mv * $work_dir sĽ#! /bin/csh -q #$ -cwd #$ -o %s_queue.output -j y -N %s limit datasize 2000000 source %s %s libtbx.python %s $SGE_TASK_ID %s %s >& %s.$SGE_TASK_ID.out %s exit sÍ import os, sys def run(only_i=None): print "%s " % only_i f=file("test_%s.output" % only_i, "wb") f.write("Testing %s\n" % only_i) f.close() if __name__=="__main__": run(*tuple(sys.argv[1:])) s2#! /bin/csh -q #$ -j y while (1) sleep 3600 end c C sBd„}d„}d„}d„}ddGHdGHddGHd}|}xăd d d d gd d d d gd d d d gd ddd gd ddd gd dddgd dddgddddgdddd gg D]T\}}}} ||}|ƒ||ƒtj|ƒ|ƒ|d|d| ƒqŐW|ƒtjƒdS(NcS sLxEtjtjƒƒD].}|jdƒrdG|GHtj|ƒqqWdS(NRtremove(tostlistdirtgetcwdt startswithR(tfilename((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pyt_clean¤s cS sgdGHd}x&t|ƒD]}|d|d7}qW|GHtddƒ}|j|d ƒ|jƒdS(Ns test list of commandstsecho %d ies commands.txttwbi˙˙˙˙(trangetfiletwritetclose(tnumber_of_cmdstoutltitf((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pyt _write_cmdsŠscS sxddl}|jdƒt}xR|rst}x?tjdƒD].}|jdƒdkr>dG|GHt}Pq>q>Wq"WdS(Ni˙˙˙˙itqstatRtrunning(ttimetsleeptTruetFalseRtpopentfind(R$R#tline((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pyt_wait˛s    cS súg}xÓtjtjƒƒD]ź}|jdƒr|jdƒr|d8}t|dƒ}|jƒ}|jƒxf|D][}|jdƒdkrv|d8}|j ƒ}|d|ks˝t ‚|j |dƒqvqvWqqW| sét ‚| söt ‚dS(NRs.outitrbtRunningi˙˙˙˙( RRRRtendswithRt readlinesRR)tsplittAssertionErrortappend(tnumber_of_output_filestnumber_of_runstrunsRR tlinesR*ttmp((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pyt_check˝s       t#iPs# testing easy_qsubsTlibtbx.easy_qsub phenix_source="/net/cci/xp/phenix/phenix_env" commands=commands.txti Rs number_of_chunks=2ii s size_of_chunks=2iis start=6s end=5is start=5 size_of_chunks=2i s end=5 size_of_chunks=2R3R4(Rtsystemtsystexit( RR!R+R8tcmdtold_cmdtcmdstnew_cmdR3R4((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pyttest_easy_qsubŁs8    %     cC sęi}xÝ|D]Ő}|d kr1dGHtjƒn0|dkrHtƒiS|dkrat|dNsž Submits a job to run commands on the queueing system using qsub. One master job is sent, which then deploys multiple sub jobs (Of the same job ID) to run each separate command. phenix_source: A path to the script used to initial the phenix environment where: A path to the directory in which to run the commands commands: A list of commands to run on the queue size_of_chunks: Number of commands to run within each queue job code: The task name used during submissions js: queue priority (default 0) qsub_cmd: The command to submit a job from a shell start: The start number for the task range end: The end number for the task range host_scratch_dir: If not None, will run the job within a local scratch directory on each queue machine, then copy back all output files to the directory set by where Returns the job id of the submission. Example of python script: run( where = path_to_where_you_want_to_run_your_jobs, phenix_source = "/net/chevy/raid1/nigel/build/setpaths.csh", commands = ["phenix.fetch_pdb 101m", "phenix.fetch_pdb 1s72"]) For more help type: libtbx.easy_qsub --help t-iPtPHENIXRsE Automatically setting phenix_source to current $PHENIX/phenix_env s %s/phenix_envs5 Generating a test run script and queuing 10 times seasy_qsub_test_script.pyRi slibtbx.python %s %sids Inputss phenix_sourcet phenix_envi˙˙˙˙tsetpaths0 Need to supply file to source. e.g. phenix_envs1source file for PHENIX environment not found "%s"s wheret easy_qsubs commandsissimilar to > %s is../RLs size_of_chunkss number_of_chunkss$ Need to choose number_of_chunks>1R,s(Need to supply "end=n" for python_scripts%s %s %ds" Number of lines in command files Number of queue jobss% Number of command in each queue jobc s<ˆ|dˆ|dˆ|dˆ|dkr8dSdS(Niii˙˙˙˙((tk1tk2(tdetails(sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pyt_cmp_gapĽs4s#Only one job can be run in parallels qblock.cshs -q %ss%s -t 1-%d qblock.cshs Blocking %d slots on %ss Need to remove them manuallys s.No queue machine found with %d available slotss0 Setting up scratch directories on queue hostsseasy_qsub_python_script.pyseasy_qsub_qsub_script.shs s '''%s ''', s% Writing queue python script: %ss& Writing queue command script: %ss%s -t %d-%d -js %d %ss Queue command s> %s s Skipping run...RJRKs6Your job-array (\d+)\..* \(\".*\"\) has been submittedsUnable to determine job ID(3RtenvirontgetRRttest_run_scriptRRR2tpathtjoinRR)R'texistsRttypetNonetlentreplaceR1R/R\tmintmaxRUtkeystsorttqblocktchmodtstattS_IREADtS_IWRITEtS_IXUSRRtcalltchdirthost_scratch_dir_prethost_scratch_dir_postt script_filetrun_fileRMRNROtretcompileRPR0tsearchRRtgroup($RRRRRRR R R R R RRRBthelpR Rt old_whereR6tphenix_python_bintnumber_of_jobsRfRst queue_nameR=tpretposttpython_run_filenametqsub_run_filenameRR*RSRKtpatterntmatchtjob_id((ResK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pytrunsF+        *                 !                  !                  RbR"i c C s‡|rUt|dƒr=g|D]}t|ƒjƒ^q}qUt|ƒjƒg}n|rŞt|dƒr’g|D]}t|ƒjƒ^qq}qŞt|ƒjƒg}nxÖtr‚tj|gdtjƒ}|jƒd}x‘|jdƒdD]{}|sqňn|r$|d jƒ|kr$Pn|dd!jƒ|krň|d k ri|d d !jƒ|krjPqjqmPqňqňWPt j |ƒq­Wd S( sƒ Repeatedly checks the queue and waits until all jobs for a user have completed. The caller may specify further information, such as the job name, id, and user if jobs of another user are to be monitored. This function returns when there are no more jobs matching any of the parameters. i.e. No jobs matching , no jobs matching , and no jobs matching . Parameters ---------- task_name : int or str or list of int or list of str or None, optional job_id : int or str or list of int or list of str or None, optional user : str, optional qstat_cmd : str, optional sleep_time : int, optional t__iter__tstdoutis iiii'iiN( thasattrtstrtstripR&t subprocesstPopentPIPEt communicateR0RnR$R%( t task_nameRtusert qstat_cmdt sleep_timeRtpR“R*((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pytwaits.((  t__main__(#t__doc__t __future__RRRR—RNR;R$RwR[Rt libtbx.utilsRR•RRRDRR}R~R€RiRuRARIRUR\RnR'R‘R t__name__targvRERF(((sK/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/command_line/easy_qsub.pyt sr        .!  J    ç <