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Hi Rob & Ed, I think that the machine i am using is not that bad. It was commissioned in '12. Some basic info: Performance 360 TFLOPS Peak & 304 TFLOPS sustained on LINPACK Hardware HP blade system C7000 with BL460c Gen8 blades 1088 nodes with 300 GB disk/node (319 TB) 2,176 Intel Xeon E5 2670 processors@ 2.6 GHz 17,408 processor cores, 68 TB main memory FDR Infiniband based fully non-blocking fat-tree topology 2 PB high performance storage with lustre parallel file system ---- Using netCDF configured for parallel applications, i did manage to write data on a single netCDF file using 512 procs --- but this was when i reduced the grid nodes per proc to about 20-30. When i made the grid nodes to about 100 i got this error too: NetCDF: HDF error ---- There is another issue i need to share --- while compiling netCDF4 for parallel usage, i had encountered errors during 'make check' in these files: run_par_test.sh, run_f77_par_test.sh and run_f90_par_test.sh These were related to mpiexec commands --- mpd.hosts issue. These errors did not occur when i compiled netcdf for parallel on my desktop. ---- Dumping outputs from each processor gave me these errors --- it is not that all such errors appear together - they are a bit random. proxy:0:13@cn0083] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:73): one of the processes terminated badly; aborting [proxy:0:13@cn0083] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for completion [proxy:0:13@cn0083] HYD_pmci_wait_for_childs_completion (./pm/pmiserv/pmip_utils.c:1476): bootstrap server returned error waiting for completion [proxy:0:13@cn0083] main (./pm/pmiserv/pmip.c:392): error waiting for event children completion [mpiexec@cn0002] control_cb (./pm/pmiserv/pmiserv_cb.c:674): assert (!closed) failed [mpiexec@cn0002] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status [mpiexec@cn0002] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:388): error waiting for event [mpiexec@cn0002] main (./ui/mpich/mpiexec.c:718): process manager error waiting for completion cn0137:b279:beba2700: 132021042 us(132021042 us!!!): ACCEPT_RTU: rcv ERR, rcnt=0 op=1 <- 10.1.1.136 cn1068:48c5:4b280700: 132013538 us(132013538 us!!!): ACCEPT_RTU: rcv ERR, rcnt=-1 op=1 <- 10.1.5.47 cn1075:dba3:f8d7700: 132099675 us(132099675 us!!!): CONN_REQUEST: SOCKOPT ERR Connection refused -> 10.1.1.51 16193 - RETRYING... 5 cn1075:dba3:f8d7700: 132099826 us(151 us): CONN_REQUEST: SOCKOPT ERR Connection refused -> 10.1.1.51 16193 - RETRYING...4 cn1075:dba3:f8d7700: 132099942 us(116 us): CONN_REQUEST: SOCKOPT ERR Connection refused -> 10.1.1.51 16193 - RETRYING...3 cn1075:dba3:f8d7700: 132100049 us(107 us): CONN_REQUEST: SOCKOPT ERR Connection refused -> 10.1.1.51 16193 - RETRYING...2 cn1075:dba3:f8d7700: 132100155 us(106 us): CONN_REQUEST: SOCKOPT ERR Connection refused -> 10.1.1.51 16193 - RETRYING...1 cn1075:dba3:f8d7700: 132100172 us(17 us): dapl_evd_conn_cb() unknown event 0x0 ---- Rob, I guess i will need to look into the io methods you listed. Thanks for your time, Samrat. On Fri, Oct 17, 2014 at 10:00 PM, Rob Latham <robl@xxxxxxxxxxx> wrote: > > > On 10/17/2014 11:25 AM, Ed Hartnett wrote: > >> Unless things have changed since my day, it is possible to read pnetcdf >> files with the netCDF library. It must be built with --enable-pnetcdf >> and with-pnetcdf=/some/location, IIRC. >> > > Ed! > > In this case, Samrat Rao was using pnetcdf to create CDF-5 (giant > variable) formatted files. To refresh your memory, Argonne and > Northwestern developed this file format with UCARS's signoff, with the > understanding that we (ANL and NWU) would never expect UCAR to add support > for it unless we did the work. I took a stab at it a few years back and > Wei-keng is taking a second crack at it right now. > > the classic file formats CDF-1 and CDF-2 are fully inter-operable between > pnetcdf and netcdf. > ==rob > > > >> On Fri, Oct 17, 2014 at 6:33 AM, Samrat Rao <samrat.rao@xxxxxxxxx >> <mailto:samrat.rao@xxxxxxxxx>> wrote: >> >> Hi, >> >> I'm sorry for the late reply. >> >> I have no classic/netcdf-3 datasets --- datasets are to be >> generated. All my codes are also new. >> >> Initially i tried with pnetcdf, wrote a few variables, but found >> that the format was CDF-5 which 'normal' netcdf would not read. >> >> I also need to read some bits of netcdf data in Matlab, so i thought >> of sticking to the usual netcdf-4 compiled for parallel io. It is >> also likely that i will have to share my workload with others in my >> group and/or leave the code for future people to work on. >> >> Does matlab read cdf-5 files? >> >> So i preferred the usual netcdf. Rob, i hope you are not annoyed. >> >> But most of the above is for another day. Currently i am stuck >> elsewhere. >> >> With a less no of processors, 216, the single netcdf file gets >> created (i create i single netcdf file for each variable), but for >> anything above that i get these errors: >> NetCDF: Bad chunk sizes. >> Not sure where these errors come from. >> >> Then i shifted to dumping outputs from each processor in simple >> binary --- this works till about 1500 processors. Above this number >> the code gets stuck and eventually aborts. >> >> This issue is not new. My colleague too had problems with running >> his code on 1500+ procs. >> >> Today i came to know that opening a large number of files (each proc >> writes 1 file) can overwhelm the system --- solving this requires >> more than rudimentary techniques of writing --- or understanding the >> system's inherent parameters/bottlenecks. >> >> So netcdf is probably out of bounds for now --- will try again if >> the simple binary write from each processor gets sorted out. >> >> Does anyone have any suggestion? >> >> Thanks, >> Samrat. >> >> >> On Thu, Oct 2, 2014 at 7:52 PM, Rob Latham <robl@xxxxxxxxxxx >> <mailto:robl@xxxxxxxxxxx>> wrote: >> >> >> >> On 10/02/2014 01:24 AM, Samrat Rao wrote: >> >> Thanks for your replies. >> >> I estimate that i will be requiring approx 4000 processors >> and a total >> grid resolution of 2.5 billion for my F90 code. So i need to >> think/understand which is better - parallel netCDF or the >> 'normal' one. >> >> >> There are a few specific nifty features in pnetcdf that can let >> you get really good performance, but 'normal' netCDF is a fine >> choice, too. >> >> Right now I do not know how to use parallel-netCDF. >> >> >> It's almost as simple as replacing every 'nf' call with 'nfmpi' >> but you will be just fine if you stick with UCAR netCDF-4 >> >> Secondly, i hope that the netCDF-4 files created by either >> parallel >> netCDF or the 'normal' one are mutually compatible. For >> analysis I will >> be extracting data using the usual netCDF library, so in >> case i use >> parallel-netCDF then there should be no inter-compatibility >> issues. >> >> >> For truly large variables, parallel-netcdf introduced, with some >> consultation from the UCAR folks, a 'CDF-5' file format. You >> have to request it explicitly, and then in that one case you >> would have a pnetcdf file that netcdf tools would not understand. >> >> In all other cases, we work hard to keep pnetcdf and "classic" >> netcdf compatible. UCAR NetCDF has the option for an HDF5-based >> backend -- and in fact it's not an option if you want parallel >> I/O with NetCDF-4 -- is not compatible with parallel-netcdf. By >> now, your analysis tools surely are updated to understand the >> new HDF5-based backend? >> >> I suppose it's possible you've got some 6 year old analysis tool >> that does not understand NetCDF-4's HDF5-based file format. >> Parallel-netcdf would allow you to simulate with parallel i/o >> and produce a classic netCDF file. But I would be shocked and a >> little bit angry if that was actually a good reason to use >> parallel-netcdf in 2014. >> >> >> ==rob >> >> >> -- >> Rob Latham >> Mathematics and Computer Science Division >> Argonne National Lab, IL USA >> >> >> >> >> -- >> >> Samrat Rao >> Research Associate >> Engineering Mechanics Unit >> Jawaharlal Centre for Advanced Scientific Research >> Bangalore - 560064, India >> >> _______________________________________________ >> netcdfgroup mailing list >> netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@xxxxxxxxxxxxxxxx> >> For list information or to unsubscribe, visit: >> http://www.unidata.ucar.edu/mailing_lists/ >> >> >> > -- > Rob Latham > Mathematics and Computer Science Division > Argonne National Lab, IL USA > -- Samrat Rao Research Associate Engineering Mechanics Unit Jawaharlal Centre for Advanced Scientific Research Bangalore - 560064, India
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