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doku:simple [2014/05/14 06:24] – markusdoku:simple [2014/06/10 09:58] (current) – markus
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 </code> </code>
  
-compilation:+compilation (use fftw that comes with simple):
 <code> <code>
-FFTWLIB=/home/lv70172/blaas/software/simple2/fftw/lib+export FFTWLIB=/home/lv70172/blaas/software/simple2/fftw/lib
 ./simple_compile.pl prg=all_fast mac=no compiler=gfortran ./simple_compile.pl prg=all_fast mac=no compiler=gfortran
 </code> </code>
Line 29: Line 29:
 script to run the different steps (should be done via a cronjob) script to run the different steps (should be done via a cronjob)
  
-<code> +{{:doku:simple:run_simple_vsc.sh}}
-#!/bin/bash+
  
- 
-source $HOME/.bashrc 
-export SIMPLESYS=VSC2 
- 
-PRIME_RUN_DIR=${HOME}/SIMPLE-TEST 
-ITERATION_START=3 
-ITERATION_STOP=7 
-VOL1=recvol_state1.spi 
-NODES=8 
-PRIME_ARGS="stk=ALIGNED.spi box=240  smpd=1.89 dynlp=yes ring2=105 nthr=16 oritab=rndoris.txt" 
-PRIME_CMD="$HOME/SIMPLE-TEST/distr_simple_prime_vsc2.pl" 
-PRIME_ITERATION_STORAGE="$PRIME_RUN_DIR/iteration" 
- 
- 
-function get_current_iteration(){ 
-        if [ ! -f "$PRIME_ITERATION_STORAGE" ]; then 
-                echo "found file $PRIME_ITERATION_STORAGE" 
-                CURRENT_ITERATION=$ITERATION_START 
-                echo ${CURRENT_ITERATION} > ${PRIME_ITERATION_STORAGE} 
-        else 
-                #CURRENT_ITERATION=$(echo `cat ${PRIME_ITERATION_STORAGE}` + 1 |bc) 
-                CURRENT_ITERATION=`cat ${PRIME_ITERATION_STORAGE}` 
-                #update iteration 
-        fi 
-} 
- 
-function get_status(){ 
-        RUNNING_JOBS=`ls JOB_RUNNING_* 2> /dev/null |wc -l` 
-        if [ $RUNNING_JOBS == 0 ] && [ ! -f "${PRIME_RUN_DIR}/JOB_FINISHED_1" ]; then 
-                SUBMIT="submit=1" 
-                #JOB_FINISHED seems not to be needed any more .. 
-                rm -f JOB_FINISHED_* 
-                #proceed to next iteration 
-                CURRENT_ITERATION=$(echo "$CURRENT_ITERATION + 1" | bc) 
-                echo ${CURRENT_ITERATION} > ${PRIME_ITERATION_STORAGE} 
-        else 
-                SUBMIT="" 
-        fi 
-} 
- 
-cd $PRIME_RUN_DIR 
-get_current_iteration 
-get_status 
-CMD="${PRIME_CMD} ${PRIME_ARGS} vol1=${VOL1} npart=${NODES} startit=${CURRENT_ITERATION} maxits=${ITERATION_STOP} ${SUBMIT}" 
-echo $CMD 
-$CMD 
- 
-</code> 
  
  
 adjusted distr_simple_prime_vsc2.pl: adjusted distr_simple_prime_vsc2.pl:
  
-<code> +{{:doku:simple:distr_simple_prime_vsc2.pl}}
- +
-#!/usr/bin/perl +
- +
-use warnings; +
-use strict; +
-use Env; +
-use Cwd qw(getcwd); +
-use List::Util qw(max min); +
- +
-# ASSUMES SIMPLEBIN ENVIRONMENT VARIABLE SET +
-# ASSUMES SIMPLESYS ENVIRONMENT VARIABLE SET +
- +
-# global variables +
-my%name_value; +
-my$folder; +
-$name_value{'prime'}          = $ENV{SIMPLEBIN}.'/simple_prime'; +
-$name_value{'merge_algndocs'} = $ENV{SIMPLEBIN}.'/simple_merge_algndocs'; +
-$name_value{'volassemble'}    = $ENV{SIMPLEBIN}.'/simple_volassemble'; +
-$name_value{'automask'}       = $ENV{SIMPLEBIN}.'/simple_automask'; +
-$name_value{'check_conv'}     = $ENV{SIMPLEBIN}.'/simple_check_conv'; +
-$name_value{'check_nptcls'}   = $ENV{SIMPLEBIN}.'/simple_check_nptcls'; +
-$name_value{'execdir'}        = getcwd(); +
- +
-# make command line instructions +
-my$instructions = `$name_value{'prime'}`; +
-$instructions =~ s/SIMPLE_PRIME/DISTR_SIMPLE_PRIME/; +
-$instructions =~ s/\[nthr\=\<nr of OpenMP threads\{1\}\>\]/npart\=\<nr of partitions\>/; +
-my@should_not_be_there = glob("recvol_state*"); +
-# +
-#markus stoehr +
-#comment out to allow restart of the script: +
-#if( scalar(@should_not_be_there) >= 1 ){ +
-#   die "ERROR: files match the pattern recvol_state*, remove these from cwd\n"; +
-#} +
- +
-# if too few argument given, print instructions +
-if(scalar(@ARGV) < 5){ +
-  print $instructions; +
-} +
- +
-# parse the command line +
-# %name_value is the hash with input data +
-foreach my $cmd (@ARGV){ +
-    chomp($cmd); +
-    my @tmp = split('=', $cmd); +
-    $name_value{$tmp[0]} = $tmp[1]; +
-} +
- +
-# check so that a volume is inputted +
-if( !defined($name_value{'vol1'}) ){ +
-    die "Need at least one starting volume for prime exec!\n";    +
-} +
- +
-# set the number of particles +
-$name_value{'nptcls'} = exec_check_nptcls(); +
- +
-# check so that npart is set (number of partitions) +
-if( !defined $name_value{'npart'} ){ +
-    die "npart need to be set\n"; +
-} +
- +
-# check so that nspace is set (number of projection directions) +
-if( !defined $name_value{'nspace'} ){ +
-    $name_value{'nspace'} = 1000;    +
-} +
- +
-# check so that nthr is set (number of threads) +
-if( !defined $name_value{'nthr'} ){ +
-    $name_value{'nthr'} = 1;    +
-} +
- +
-# check so that fstep is set +
-if( !defined $name_value{'fstep'} ){ +
-    $name_value{'fstep'} = 1;    +
-} +
- +
-# check so that dynlp is set  +
-if( !defined($name_value{'dynlp'}) ){ +
-    $name_value{'dynlp'} = 'no'; +
-} +
- +
-# determine initial and final Fourier index +
-if( $name_value{'dynlp'} eq 'yes' ){ +
-    # determine the initial low-pass limit +
-    if( !defined($name_value{'find'}) ){ +
-        $name_value{'find'} = get_find(($name_value{'box'}*0.7*$name_value{'smpd'})/8.0); +
-        my$lp = get_lp($name_value{'find'}); +
-#        print "LPLOW :$lp\n"; +
-    } +
-    # determine the final low-pass limit +
-    if( defined($name_value{'fmax'}) ){ +
-        delete $name_value{'fmax'}; +
-    } +
-    $name_value{'fmax'} = get_find(($name_value{'box'}*0.7*$name_value{'smpd'})*0.07); +
-    my$lp = get_lp($name_value{'fmax'}); +
-#    print "LPHIGH: $lp\n"; +
-} +
- +
-# check so that trs is set (origin shift) +
-if( !defined $name_value{'trs'} ){ +
-    $name_value{'trs'} = 0;    +
-} +
- +
-# check so that maxits is set  +
-if( !defined($name_value{'maxits'}) ){ +
-    $name_value{'maxits'} = 50; +
-} +
- +
-# set number of states (by counting input volumes) +
-my @keys    = keys %name_value; +
-my $nstates = 0; +
-foreach my $key(@keys){ +
-    if($key =~ /vol\d/ ){$nstates++};    +
-} +
-$name_value{'nstates'} = max 1,$nstates; +
- +
-# set time per image +
-if( defined($name_value{'time_per_image'}) ){ +
-} else { +
-    if( defined($name_value{'trs'}) ){ +
-        $name_value{'time_per_image'} = 100*$name_value{'nstates'}*($name_value{'nspace'}/1000); +
-    }else{ +
-        $name_value{'time_per_image'} = 90*$name_value{'nstates'}*($name_value{'nspace'}/1000); +
-    } +
-} +
- +
-# do the refinement +
-my$converged = 0; +
-my$round; +
-my$round_stop; +
-if( defined($name_value{'startit'}) ){ +
-    $round = $name_value{'startit'}-1;  +
-} else { +
-    $round = 0; +
-} +
-while( $round < $name_value{'maxits'} ){ +
-     +
-    # make refinement folder +
-    $round++; +
-    $folder = 'prime_round_'.$round; +
-    mkdir $folder; +
-     +
-    # parallell execution +
-    if (defined($name_value{'submit'})){ +
-            exec_prime_para(); +
-            die; +
-    }else{ +
-     +
-            # determine when the jobs have finished +
-            #system("rm -f JOB_FINISHED_*"); +
-            #sleep(10) while( njobs_finished() < $name_value{'npart'} ); +
-            #system("rm -f JOB_FINISHED_* OUT* prime_script*"); +
-            # +
-            # +
-            #markus stoehr +
-            #for usage with cronjob, here you need an exit +
-            if ( njobs_finished() < $name_value{'npart'} ) { die "\n not all jobs finished yet\n";} +
-            # merge alignment docs +
-            if( defined($name_value{'oritab'}) ){ +
-                delete $name_value{'oritab'};   +
-            } +
-            $name_value{'oritab'} = 'merged.txt'; +
-            system("$name_value{'merge_algndocs'} fbody=algndoc_ nptcls=$name_value{'nptcls'} ndocs=$name_value{'npart'} outfile=$name_value{'oritab'}"); +
-            system("mv algndoc_* ./$folder"); +
-            system("cp merged.* ./$folder"); +
-     +
-            # assemble volumes +
-            exec_assemble_volumes(); +
-             +
-            # automask +
-            if( defined($name_value{'mw'}) ){  +
-                exec_automask(); +
-            } +
-     +
-            my $conv = exec_check_conv(); +
-            if( $round > 1 ){ +
-                if( $conv == 2 ){ +
-                    die "**** DISTR_SIMPLE_PRIME NORMAL STOP ****\n"; +
-                }elsif ( $conv == 1 ){ +
-                    if( !defined($name_value{'find'}) ){ +
-                        die "Want 2 do dynamic low-pass update, but find is not defined, weird!\n";    +
-                    } +
-                    if( defined($name_value{'deterministic'}) ){ +
-                        delete $name_value{'deterministic'}; +
-                        $name_value{'deterministic'} = 'yes'; +
-                    } +
-                    $name_value{'find'} = $name_value{'find'}+$name_value{'fstep'}; +
-                    if( $name_value{'find'} > $name_value{'fmax'} ){ +
-                        $name_value{'find'} = $name_value{'fmax'}       +
-                    } +
-                } +
-            } +
-           #markus stoehr +
-           system("rm -f JOB_FINISHED_*"); +
-        die; +
-        } +
-} +
- +
-sub exec_prime_para{ +
-    my$i; +
-    my$vol; +
-    my@submitted; +
-    my$qsubout; +
-    my@args = parse_args($name_value{'prime'}); +
-    my$prime_cmd_string = $name_value{'prime'}.' '; +
-    $i = 1; +
-    $vol = 'vol'.$i; +
-    while( defined($name_value{$vol}) ){ +
-        $prime_cmd_string = add2string($vol, $prime_cmd_string); +
-        $i++; +
-        $vol = 'vol'.$i; +
-    } +
-    foreach (@args) { +
-        $prime_cmd_string = add2string($_, $prime_cmd_string); +
-    }    +
-    $prime_cmd_string =~ s/\s+$//; # removes trailing whitespace +
-    print $prime_cmd_string, "\n"; +
-    my $stop; +
-    my $start; +
-    my $ptcls_per_part = int($name_value{'nptcls'}/$name_value{'npart'}); +
-    for(my $i=1; $i<=$name_value{'npart'}; $i++){ +
-        $stop     = min $i*$ptcls_per_part,$name_value{'nptcls'}; +
-        if($i == $name_value{'npart'}){$stop = $name_value{'nptcls'}}; +
-        $start    = max 1,$i*$ptcls_per_part-$ptcls_per_part+1; +
-        my $time  = $name_value{'time_per_image'}*($stop-$start+1); +
-        my $hours = int($time/3600); +
-        my $min   = (($time/60)%60); +
-        open(FHANDLE, ">prime_script_$i"); +
-        if ($ENV{SIMPLESYS} eq 'BIOX3' or $ENV{SIMPLESYS} eq 'LOCAL'){ +
-            print FHANDLE "#!/bin/sh +
-#PBS -N distr_simple +
-#PBS -l nodes=1:ppn=$name_value{'nthr'} +
-#PBS -l walltime=$time +
-#PBS -o outfile.\$PBS_JOBID +
-#PBS -e errfile.\$PBS_JOBID +
-#PBS -q SP     +
-cd $name_value{'execdir'}  +
-$prime_cmd_string fromp=$start top=$stop part=$i outfile=algndoc_$i.txt > OUT$i\nexit\n"; +
-        }elsif ($ENV{SIMPLESYS} eq 'DELPHI' ){ +
-            print FHANDLE "#!/bin/bash +
-#\$ \-N d_simple +
-#\$ \-cwd +
-#\$ \-pe multi $name_value{'nthr'} +
-#\$ \-V +
-#\$ \-o outfile.\$PBS_JOBID +
-#\$ \-e errfile.\$PBS_JOBID +
-cd $name_value{'execdir'}  +
-$prime_cmd_string fromp=$start top=$stop part=$i outfile=algndoc_$i.txt > OUT$i\nexit\n"; +
-        }elsif ($ENV{SIMPLESYS} eq 'VSC2' ){ +
-            print FHANDLE "#!/bin/bash +
-#\$ \-N d_simple +
-#\$ \-cwd +
-#\$ \-pe mpich $name_value{'nthr'} +
-#\$ \-V +
-#\$ \-o outfile.\$PBS_JOBID +
-#\$ \-e errfile.\$PBS_JOBID +
-cd $name_value{'execdir'}  +
-$prime_cmd_string fromp=$start top=$stop part=$i outfile=algndoc_$i.txt > OUT$i\n  +
-rm -f JOB_RUNNING_$i\n +
-exit\n"; +
-        } else { +
-            die "Unrecognized system!\n"; +
-        } +
-        close(FHANDLE); +
-        chmod 0777, 'prime_script_'.$i;   +
-        if( $ENV{SIMPLESYS} eq 'LOCAL' ){ +
-            system("nohup ./prime_script_$i &\n"); +
-        }elsif( $ENV{SIMPLESYS} eq 'BIOX3' ){ +
-            my$qsubcmd = "qsub ./prime_script_$i"; +
-            $qsubout = `$qsubcmd`; +
-            if( $qsubout =~ /\d+\.biox3\-frontend\-1\.stanford\.edu/ ){ +
-                $submitted[$i] = 1;    +
-            }else{     +
-                $submitted[$i] = 0;  +
-            } +
-        }elsif( ($ENV{SIMPLESYS} eq 'DELPHI') or ($ENV{SIMPLESYS} eq 'VSC2')  ) { +
-            print "submitting job\n"; +
-            my$qsubcmd = "qsub ./prime_script_$i"; +
-            $qsubout = `$qsubcmd`; +
-            if( $qsubout =~ /has been submitted/ ){ +
-                $submitted[$i] = 1;    +
-                print "success\n"; +
-                #markus stoehr: +
-                #mark submitted jobs for external script +
-                system ("touch JOB_RUNNING_$i"); +
-            }else{     +
-                $submitted[$i] = 0;  +
-            } +
-        }else{ +
-            die "Unrecognized system!\n"; +
-        } +
-    } +
-    print "finished submission"; +
-    if( $ENV{SIMPLESYS} eq 'BIOX3' ){ +
-        # resubmission if failed +
-        for(my $i=1; $i<=$name_value{'npart'}; $i++){ +
-            if( $submitted[$i] == 0 ){ +
-                my$qsubcmd = "qsub ./prime_script_$i"; +
-                $qsubout = `$qsubcmd`; +
-                if( $qsubout !~ /\d+\.biox3\-frontend\-1\.stanford\.edu/ ){ +
-                    chomp($qsubout);   +
-                    print "ERROR, $qsubout\n"; +
-                } +
-            } +
-        } +
-    #} elsif( ($ENV{SIMPLESYS} eq 'DELPHI') or ($ENV{SIMPLESYS} eq 'VSC2') ){ +
-    } elsif( ($ENV{SIMPLESYS} eq 'DELPHI')  ){ +
-        # resubmission if failed +
-        for(my $i=1; $i<=$name_value{'npart'}; $i++){ +
-            if( $submitted[$i] == 0 ){ +
-                my$qsubcmd = "qsub ./prime_script_$i"; +
-                $qsubout = `$qsubcmd`; +
-                if( $qsubout !~ /has been submitted/ ){ +
-                    chomp($qsubout);   +
-                    print "ERROR, $qsubout\n"; +
-                } +
-            } +
-        } +
-    } +
-    print "....done\n"; +
-} +
- +
-sub njobs_finished{ +
-    my$nfini = 0; +
-    my@jobs; +
-    @jobs = <JOB_FINISHED_*>; +
-    return scalar(@jobs);      +
-} +
- +
-sub exec_assemble_volumes{ +
-    my$i; +
-    my$vol; +
-    my@refvols; +
-    my@recvols; +
-    my@args = parse_args($name_value{'volassemble'}); +
-    my$assemble_cmd_string = $name_value{'volassemble'}.' '; +
-    foreach (@args) { +
-        $assemble_cmd_string = add2string($_, $assemble_cmd_string); +
-    } +
-    $assemble_cmd_string =~ s/\s+$//; # removes trailing whitespace +
-    print $assemble_cmd_string, "\n"; +
-    system($assemble_cmd_string);      +
-    my@kernels = <kernel_state*bin>; +
-    my@recbins = <recvol_state*bin>; +
-    if( scalar(@kernels) != scalar(@recbins) ){ +
-        die "Number of kernels not equal to number of recbins";    +
-    } +
-    foreach my$i (0 .. $#kernels){ +
-        system("rm -f $kernels[$i] $recbins[$i]"); +
-    } +
-    @recvols = <recvol_state*spi>; +
-    if( scalar(@recvols) != $name_value{'nstates'} ){ +
-        die "Number of reference volumes not equal to number of states";    +
-    } else { +
-        @refvols = @recvols; +
-    } +
-    foreach $i ( 1 .. $name_value{'nstates'} ){ +
-        $vol = 'vol'.$i; +
-        if( defined($name_value{$vol}) ){ +
-            delete $name_value{$vol}; +
-        } +
-        $name_value{$vol} = $refvols[$i-1]; +
-        system("cp $name_value{$vol} ./$folder"); +
-    } +
-} +
- +
-sub exec_automask{ +
-    my$i; +
-    my$vol; +
-    my@args = parse_args($name_value{'automask'}); +
-    my$automask_cmd_string = $name_value{'automask'}.' '; +
-    $i = 1; +
-    $vol = 'vol'.$i; +
-    while( defined($name_value{$vol}) ){ +
-        $automask_cmd_string = add2string($vol, $automask_cmd_string); +
-        $i++; +
-        $vol = 'vol'.$i; +
-    } +
-    foreach (@args) { +
-        $automask_cmd_string = add2string($_, $automask_cmd_string); +
-    } +
-    $automask_cmd_string =~ s/\s+$//; # removes trailing whitespace +
-    print $automask_cmd_string, "\n"; +
-    system($automask_cmd_string); +
-    my$fbody      = $name_value{'vol1'}; +
-    $fbody        =~ s/\d+\.spi//; +
-    my@maskedvols = <$fbody*msk.spi>; +
-    foreach $i ( 1 .. $name_value{'nstates'} ){ +
-        $vol = 'vol'.$i; +
-        system("cp $maskedvols[$i-1] ./$folder"); +
-        system("mv $maskedvols[$i-1] $name_value{$vol}"); +
-    } +
-} +
- +
-sub exec_check_conv{ +
-    my$status; +
-    my@args = parse_args($name_value{'check_conv'}); +
-    my$check_conv_cmd_string = $name_value{'check_conv'}.' '; +
-    foreach (@args) { +
-        $check_conv_cmd_string = add2string($_, $check_conv_cmd_string); +
-    } +
-    $check_conv_cmd_string =~ s/\s+$//; # removes trailing whitespace +
-    print $check_conv_cmd_string, "\n"; +
-    my$conv_info = `$check_conv_cmd_string`; +
-    my@conv_info_lines = split(/\n/,$conv_info); +
-    $status = 0; +
-    foreach my$line (@conv_info_lines){ +
-        print $line, "\n"; +
-        if( $line =~ /\>\>\> UPDATE LOW-PASS LIMIT\: \.YES\./ ){ $status = 1 }; +
-        if( $line =~ /\>\>\> CONVERGED\: \.YES\./ )            { $status = 2 }; +
-    } +
-    return $status; +
-} +
- +
-sub exec_check_nptcls{ +
-    my$nptcls; +
-    my$check_nptcls_cmd_string = $name_value{'check_nptcls'}.' '; +
-    $check_nptcls_cmd_string = add2string('stk', $check_nptcls_cmd_string); +
-    $check_nptcls_cmd_string = add2string('box', $check_nptcls_cmd_string); +
-    $check_nptcls_cmd_string =~ s/\s+$//; # removes trailing whitespace +
-    print $check_nptcls_cmd_string, "\n"; +
-    my$nptcls_info = `$check_nptcls_cmd_string`; +
-    if( $nptcls_info =~ />>>\sNPTCLS\:\s+(\d+)/ ){ +
-        $nptcls = $1;    +
-    } +
-    return $nptcls; +
-} +
- +
-sub add2string{ +
-    my$var = shift; +
-    my$str = shift; +
-    if( defined($name_value{$var}) ){ +
-        $str = $str.$var.'='.$name_value{$var}.' '; +
-    } +
-    return $str; +
-} +
- +
-sub parse_args{ +
-    my$prg = shift; # get program name with absolute path +
-    # make command line instructions +
-    my$instructions = `$prg`; +
-    # parse the instructions +
-    my@splitted = split(/\s/,$instructions); +
-    my@args; +
-    foreach (@splitted) { +
-        if( $_ =~ /(\w+\d*)\=/ ){ +
-            if( $1 !~ /vol\d+/ ){ +
-                push(@args,$1); +
-            }   +
-        } +
-    } +
-    return @args; +
-} +
- +
-sub get_find{ +
-    my$res = shift; +
-    return int((($name_value{'box'}-1)*$name_value{'smpd'})/$res) +
-} +
- +
-sub get_lp{ +
-    my$find = shift; +
-    return (($name_value{'box'}-1)*$name_value{'smpd'})/$find +
-} +
- +
- +
-</code>+
  
  • doku/simple.1400048648.txt.gz
  • Last modified: 2014/05/14 06:24
  • by markus