[Swift-devel] hang checker fun
Allan Espinosa
aespinosa at cs.uchicago.edu
Sun Mar 27 18:29:30 CDT 2011
Here you go. (see attached)
-Allan
2011/3/27 Mihael Hategan <hategan at mcs.anl.gov>:
> May I also see the log? It looks like there's something weird around
> line 186.
>
> Mihael
>
> On Sun, 2011-03-27 at 17:56 -0500, Allan Espinosa wrote:
>> oops. trimmed the first part.
>>
>> Thanks
>>
>> type SgtDim;
>> type Variation;
>> type Seismogram;
>> type PeakValue;
>>
>> type Station {
>> string name;
>> float lat;
>> float lon;
>> int erf;
>> int variation_scenario;
>> }
>>
>> type Sgt {
>> SgtDim x;
>> SgtDim y;
>> }
>>
>> type Rupture {
>> int source;
>> int index;
>> int size;
>> }
>>
>> /* some constants used by the apps*/
>> global int num_time_steps = 3000;
>> global string spectra_period1 = "all";
>> global float filter_highhz = 5.0;
>> global float simulation_timeskip = 0.1;
>>
>> app (Sgt _ext) extract(Sgt _sgt, Station _stat, Variation _var) {
>> extract @strcat("stat=", _stat.name) "extract_sgt=1"
>> @strcat("slon=", _stat.lon) @strcat("slat=", _stat.lat)
>>
>> @strcat("rupmodfile=", @filename(_var))
>> @strcat("sgt_xfile=", @filename(_sgt.x))
>> @strcat("sgt_yfile=", @filename(_sgt.y))
>> @strcat("extract_sgt_xfile=", @filename(_ext.x))
>> @strcat("extract_sgt_yfile=", @filename(_ext.y));
>> }
>>
>> app (Seismogram _seis, PeakValue _peak)
>> seispeak(Sgt _sgt, Variation _var, Station _stat) {
>> seispeak
>> /* Args of seismogram synthesis */
>> @strcat("stat=", _stat.name) "extract_sgt=0"
>> @strcat("slon=", _stat.lon) @strcat("slat=", _stat.lat)
>> "outputBinary=1" "mergeOutput=1" @strcat("ntout=", num_time_steps)
>>
>> @strcat("rupmodfile=", @filename(_var))
>> @strcat("sgt_xfile=", @filename(_sgt.x))
>> @strcat("sgt_yfile=", @filename(_sgt.y))
>> @strcat("seis_file=", @filename(_seis))
>>
>> /* Args of peak ground acceleration */
>> "simulation_out_pointsX=2" "simulation_out_pointsY=1"
>> "surfseis_rspectra_seismogram_units=cmpersec"
>> "surfseis_rspectra_output_units=cmpersec2"
>> "surfseis_rspectra_output_type=aa"
>> "surfseis_rspectra_apply_byteswap=no"
>>
>> @strcat("simulation_out_timesamples=", num_time_steps)
>> @strcat("simulation_out_timeskip=", simulation_timeskip)
>> @strcat("surfseis_rspectra_period=", spectra_period1)
>> @strcat(" surfseis_rspectra_apply_filter_highHZ=", filter_highhz)
>> @strcat("in=", @filename(_seis))
>> @strcat("out=", @filename(_peak));
>> }
>>
>> app (Seismogram _seis, PeakValue _peak)
>> seispeak_local(Sgt _sgt, Variation _var, Station _stat) {
>> seispeak_local
>> /* Args of seismogram synthesis */
>> @strcat("stat=", _stat.name) "extract_sgt=0"
>> @strcat("slon=", _stat.lon) @strcat("slat=", _stat.lat)
>> "outputBinary=1" "mergeOutput=1" @strcat("ntout=", num_time_steps)
>>
>> @strcat("rupmodfile=", @filename(_var))
>> @strcat("sgt_xfile=", @filename(_sgt.x))
>> @strcat("sgt_yfile=", @filename(_sgt.y))
>> @strcat("seis_file=", @filename(_seis))
>>
>> /* Args of peak ground acceleration */
>> "simulation_out_pointsX=2" "simulation_out_pointsY=1"
>> "surfseis_rspectra_seismogram_units=cmpersec"
>> "surfseis_rspectra_output_units=cmpersec2"
>> "surfseis_rspectra_output_type=aa"
>> "surfseis_rspectra_apply_byteswap=no"
>>
>> @strcat("simulation_out_timesamples=", num_time_steps)
>> @strcat("simulation_out_timeskip=", simulation_timeskip)
>> @strcat("surfseis_rspectra_period=", spectra_period1)
>> @strcat(" surfseis_rspectra_apply_filter_highHZ=", filter_highhz)
>> @strcat("in=", @filename(_seis))
>> @strcat("out=", @filename(_peak));
>> }
>>
>> app (Seismogram _seis[], PeakValue _peak[])
>> seispeak_agg(Sgt _sgt, Variation _var[], Station _stat, int n) {
>> seispeak_agg
>> /* System args */
>> _stat.name _stat.lon _stat.lat num_time_steps
>> num_time_steps simulation_timeskip spectra_period1 filter_highhz
>>
>> @filename(_sgt.x) @filename(_sgt.y)
>>
>> n @filenames(_var) @filenames(_seis) @filenames(_peak);
>> }
>>
>> // Auxillary functions for the mappers
>> type StationFile;
>> app (StationFile _stat) getsite_file(int _run_id) {
>> getsite _run_id stdout=@filename(_stat);
>> }
>> (Station _stat) get_site(int _run_id) {
>> StationFile file<"/var/tmp/site_tmp">;
>> /*file = getsite_file(_run_id);*/
>> _stat = readData(file);
>> }
>>
>> type RuptureFile;
>> app (RuptureFile _rup) getrupture_file(int _run_id) {
>> getrupture _run_id stdout=@filename(_rup);
>> }
>> (Rupture _rup[]) get_ruptures(int _run_id, Station _site) {
>> /*RuptureFile file<single_file_mapper; file=@strcat(_site.name,
>> "/rup_tmp")>;*/
>> RuptureFile file<"LGU/rup_tmp">;
>> /*file = getrupture_file(_run_id);*/
>> _rup = readData(file);
>> }
>>
>> type VariationFile;
>> app (VariationFile _var) getvariation_file(Station _site, Rupture _rup,
>> string _loc) {
>> variation_mapper "-e" _site.erf "-v" _site.variation_scenario
>> "-l" _loc "-s" _rup.source "-r" _rup.index stdout=@_var;
>> }
>> (string _vars[]) get_variations(Station _site, Rupture _rup, string _loc){
>> string fname = @strcat(_rup.source, "_", _rup.index);
>> VariationFile file<single_file_mapper;
>> file=@strcat(_site.name, "/varlist/", _rup.source, "/", fname, ".txt")>;
>> /*file = getvariation_file(_site, _rup, _loc);*/
>> _vars = readData(file);
>> }
>>
>> type offset {
>> int off;
>> int size;
>> }
>> type offset_file;
>> (offset _off[]) mkoffset(int _size, int _group_size) {
>> offset_file file <single_file_mapper; file=@strcat("LGU/offset-",_size)>;
>> file = mkoffset_file(_size, _group_size);
>> _off = readData(file);
>> }
>> app (offset_file _off) mkoffset_file(int _size, int _group_size) {
>> mkoffset _size _group_size;
>> }
>>
>> /* TODO: data management zip jobs */
>>
>> /* Main program */
>> int run_id = 664;
>> int agg_size = 80;
>> int loc_size = 20;
>> string datadir =
>> "gsiftp://gridftp.pads.ci.uchicago.edu//gpfs/pads/swift/aespinosa/science/cybershake/Results";
>>
>> Station site = get_site(run_id);
>>
>> Sgt sgt_var <ext; exec="getsgtvar.rb", r=run_id, s=site.name,
>> l="gsiftp://gridftp.pads.ci.uchicago.edu//gpfs/pads/swift/aespinosa/science/cybershake/SgtFiles">;
>> Rupture rups[] = get_ruptures(run_id, site);
>>
>> foreach rup in rups {
>> string loc_sub = @strcat(datadir, "/", site.name, "/", rup.source,
>> "/", rup.index);
>> Sgt sub <ext; exec="getsub.rb", l=loc_sub, n=site.name, s=rup.source,
>> r=rup.index>;
>> string var_str[] = get_variations( site, rup,
>> "gsiftp://gridftp.pads.ci.uchicago.edu//gpfs/pads/swift/aespinosa/science/cybershake/RuptureVariations"
>> );
>> Variation vars[] <array_mapper; files=var_str>;
>>
>> sub = extract(sgt_var, site, vars[rup.size-1]);
>>
>> string seis_str[];
>> string peak_str[];
>>
>> foreach var,i in vars {
>> seis_str[i] = @strcat(loc_sub, "/Seismogram_", site.name, "_", rup.source,
>> "_", rup.index, "_", i, ".grm");
>> peak_str[i] = @strcat(loc_sub, "/PeakVals_", site.name, "_", rup.source,
>> "_", rup.index, "_", i, ".bsa");
>> }
>>
>> Seismogram seis[] <array_mapper; files=seis_str>;
>> PeakValue peak[] <array_mapper; files=peak_str>;
>>
>> if(rup.size <= loc_size) {
>> /*
>> * Not worth to transfer the data. Execute on TeraGrid instead.
>> * Also execute on localhost.
>> */
>> foreach var,i in vars {
>> (seis[i], peak[i]) = seispeak_local(sub, var, site);
>> }
>> } else {if(rup.size <= agg_size) {
>> /* Execute on a single resource */
>> (seis, peak) = seispeak_agg(sub, vars, site, rup.size);
>> } else {
>> /*offset offs[] = mkoffset(rup.size, agg_size);*/
>> /*for i in offs {*/
>> /*(seis, peak) = seispeak_agg(sub, vars[i.off:i.off+off.size],*/
>> /*off.size);*/
>> /*}*/
>> }}
>> }
>>
>>
>> 2011/3/27 Mihael Hategan <hategan at mcs.anl.gov>:
>> > I don't believe you. There is no SgtDim data type in that script.
>> >
>> > Mihael
>> >
>> > On Sun, 2011-03-27 at 16:55 -0500, Allan Espinosa wrote:
>> >> Here it is. The get_app() calls are simple wrappers to readData()
>> >>
>> >> type offset {
>> >> int off;
>> >> int size;
>> >> }
>> >> type offset_file;
>> >> (offset _off[]) mkoffset(int _size, int _group_size) {
>> >> offset_file file <single_file_mapper; file=@strcat("LGU/offset-",_size)>;
>> >> file = mkoffset_file(_size, _group_size);
>> >> _off = readData(file);
>> >> }
>> >> app (offset_file _off) mkoffset_file(int _size, int _group_size) {
>> >> mkoffset _size _group_size;
>> >> }
>> >>
>> >> /* TODO: data management zip jobs */
>> >>
>> >> /* Main program */
>> >> int run_id = 664;
>> >> int agg_size = 80;
>> >> int loc_size = 20;
>> >> string datadir =
>> >> "gsiftp://gridftp.pads.ci.uchicago.edu//gpfs/pads/swift/aespinosa/science/cybershake/Results";
>> >>
>> >> Station site = get_site(run_id);
>> >>
>> >> Sgt sgt_var <ext; exec="getsgtvar.rb", r=run_id, s=site.name,
>> >> l="gsiftp://gridftp.pads.ci.uchicago.edu//gpfs/pads/swift/aespinosa/science/cybershake/SgtFiles">;
>> >> Rupture rups[] = get_ruptures(run_id, site);
>> >>
>> >> foreach rup in rups {
>> >> string loc_sub = @strcat(datadir, "/", site.name, "/", rup.source,
>> >> "/", rup.index);
>> >> Sgt sub <ext; exec="getsub.rb", l=loc_sub, n=site.name, s=rup.source,
>> >> r=rup.index>;
>> >> string var_str[] = get_variations( site, rup,
>> >> "gsiftp://gridftp.pads.ci.uchicago.edu//gpfs/pads/swift/aespinosa/science/cybershake/RuptureVariations"
>> >> );
>> >> Variation vars[] <array_mapper; files=var_str>;
>> >>
>> >> sub = extract(sgt_var, site, vars[rup.size-1]);
>> >>
>> >> string seis_str[];
>> >> string peak_str[];
>> >>
>> >> foreach var,i in vars {
>> >> seis_str[i] = @strcat(loc_sub, "/Seismogram_", site.name, "_", rup.source,
>> >> "_", rup.index, "_", i, ".grm");
>> >> peak_str[i] = @strcat(loc_sub, "/PeakVals_", site.name, "_", rup.source,
>> >> "_", rup.index, "_", i, ".bsa");
>> >> }
>> >>
>> >> Seismogram seis[] <array_mapper; files=seis_str>;
>> >> PeakValue peak[] <array_mapper; files=peak_str>;
>> >>
>> >> if(rup.size <= loc_size) {
>> >> /*
>> >> * Not worth to transfer the data. Execute on TeraGrid instead.
>> >> * Also execute on localhost.
>> >> */
>> >> foreach var,i in vars {
>> >> (seis[i], peak[i]) = seispeak_local(sub, var, site);
>> >> }
>> >> } else {if(rup.size <= agg_size) {
>> >> /* Execute on a single resource */
>> >> (seis, peak) = seispeak_agg(sub, vars, site, rup.size);
>> >> } else {
>> >> /*offset offs[] = mkoffset(rup.size, agg_size);*/
>> >> /*for i in offs {*/
>> >> /*(seis, peak) = seispeak_agg(sub, vars[i.off:i.off+off.size],*/
>> >> /*off.size);*/
>> >> /*}*/
>> >> }}
>> >> }
>> >>
>> >>
>> >> 2011/3/27 Mihael Hategan <hategan at mcs.anl.gov>:
>> >> > May I see the script?
>> >> >
>> >> > On Fri, 2011-03-25 at 19:42 -0500, Allan Espinosa wrote:
>> >> >> this has been occurring for 70 times already. What i expect is for
>> >> >> the app with SgtDim sub to run and close the future.
>> >> >>
>> >> >> 2011-03-25 19:40:12,217-0500 WARN HangChecker No events in 10s.
>> >> >> 2011-03-25 19:40:12,217-0500 WARN HangChecker
>> >> >> Registered futures:
>> >> >> Rupture[] rups Closed, 1 elements, 0 listeners
>> >> >> Variation vars - Closed, no listeners
>> >> >> SgtDim sub - Open, 1 listeners
>> >> >> string site Closed, no listeners
>> >> >> Variation[] vars Closed, 72 elements, 0 listeners
>> >> >> ----
>> >> >>
>> >> >> Waiting threads:
>> >> >> 0-13
>> >> >> 0-13-0-7
>> >> >> 0-13-0-8-1-1
>> >> >> ----
>> >> >>
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> >
>> >>
>
>
>
>
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